Regardless of one’s views on the origin of life, isn’t this objectively true?
appsandorgs:
Next you’ll be telling me that at the origin of life, “RNA can carry information just like DNA and be a catalyst at the same time!!
misterme987:
Regardless of one’s views on the origin of life, isn’t this objectively true?
No, it’s objectively false.
Any particular codon of DNA specifies just one of twenty alternative amino acids to be appended to a growing polypeptide during protein synthesis (with stop codons as well). Which one of the twenty alternative amino acids to be presented (for binding) is physically established by the genetic descriptions of a set of twenty molecular constraints. This means that the information that the system acquires from a codon of DNA (i.e. which amino acid it specifies in the genetic code) requires the simultaneous coordination of twenty sequences of genetic memory. This necessary state of coordination (variously described as closure or self-reference) was predicted to exist in 1948 and its molecular implementation was predicted in 1955, which was then confirmed via experiment in 1956-58.
It is the presence of this coordination that physically enables a sequence of DNA to specify a protein, or any variation of that protein. This informational capacity is completely absent in an RNA sequence that perhaps folds itself into a ribozyme, let’s say, at the origin of life. The latter requires only an environment of (rate-dependent) natural law, while the former requires both natural law as well as the (rate-independent) coordination of its constraints.
Well I guess it depends on what you meant by “information” which is a notoriously ambiguous term. But as far as I know, you’re right that an RNA can’t be a catalyst and encode an amino acid sequence. Is there anyone in the field of OOL research that claims this?
Why not? And whatever does this have to do with the proper distinction between science and theology?
“As far as I know” is very little, I should’ve just refrained from saying anything about this topic. And you’re right this is way off topic for the thread.
Correct.
A self-replicating RNA, often envisioned at the origin of life, does not establish the set of contraints required to specify genetic information like DNA — which was my comment.
Actually seems an interesting question which (if I’m understanding it) is: can a particular RNA molecule serve both as a genetic message (by encoding a protein) and as a catalyst? I can’t think of any reason why the answer has to be no. At any given moment, a catalytic RNA sequence probably can’t also undergo translation (just thinking of basic biophysics and folding etc). But that’s not an interesting limitation, since the molecule could either contain both (a catalytic domain and a “coding” domain) or it could serve a “coding” function when not folded.
I’m not sure, in any case, whether the other commenter meant to address that question in their vacuous claims about “informational capacity”…
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Can’t see any reason why not. All an RNA needs to be coding is start with AUG and not have a stop codon too soon. I see no reason why there couldn’t be a ribozyme with those characteristics.
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Last time I checked, DNA was much more than codons in protein-encoding sequences. Are you aware of this?
Yes, it’s all just physical. We use “code” and its derivatives metaphorically.
I have no idea what you’re trying to say here, but I suspect that you are trying to sneak in creationism.
Utterly, objectively false.
Many proteins are modified posttranslationally so that they lose their termini (making all proteins start with methionine residues is pretty dumb), or even more devastating to your claim, they require modification by a massive enzymatic system (ignored by IDcreationists, of course) that change some of those 20 amino-acid residues to different ones before they are functional. This massive system is a major reason why the basics of molecular biology don’t even appear to have been designed, particularly in conjunction with the use of 61 codons to specify 20 amino acids.
Are you aware that the central enzyme in protein synthesis is a ribozyme?
Having stop codons that allow proteins to end with any residue seems like an intelligent design choice, but it also provides a control. Why not have a similar design at the other end, meaning a start codon that doesn’t insert a methionine that later needs to be removed/modified in so many functional proteins?
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Group II introns are catalytic RNAs that contain coding regions as part of the RNA structure which, when folded, are actual ribozymes.
Red arrow here points to the part of group II introns that encode a protein sequence.
Curiously, the part of the intron that encodes the protein (Intron Encoded Protein, IEP) also contains a binding site where that very same protein will bind to when expressed (depicted in the box above the red arrow.
So yes, catalytic RNAs can also simultaneously function as messenger RNA, and even contain protein-RNA binding spots, at the same time.
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Also, ribosomal RNA can contain coding regions, and some authors have proposed on the basis of multiple lines of evidence that originally the ribosomal RNA encoded many core ribosomal proteins:
Some of the evidence they go through here is rather mindboggling.
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Whoa! There sure appears to be a lot of bluster in here.
I did little more than describe a couple of the fundamental control pathways in the gene translation system … and three or four regulars go directly to insults.
This should probably send a little signal to each of you, but given the terrain, it is not entirely obvious that any of you are prepared for such an event as that.
Perhaps you should tear up the extant gene system and start over with your own ideas. Each of the objects in your system must follow inexorable law with zero degrees of freedom, and from that, you are to implement open-ended control and self-reference. When you have to coordinate your constraints, then you can come back and insult me about my vacuous statements.
All I can suggest here is that you re-read my comments for context.
Your first move is to position and insult.
Use whatever words you wish. Your terms don’t change the physical properties of the system, and neither do your assumptions.
More positioning.
See Crick’s “Adapter Hypothesis” of 1955 and its subsequent confirmation by Hoagland and Zamecnik.
If you are unaware that the sequence GARS or KARS or LARS have to be coordinated with the genetic code they establish, then I just don’t know what to tell you.
Really gentlemen, you should probably take a moment. Give the bluster a rest.
A self-replicating RNA, often envisioned at the origin of life, does not establish the set of contraints required to specify genetic information like DNA — which was my comment.
So what you meant to say was merely that no single RNA molecule can function as an entire translation system by itself, that it? Not that a ribozyme can’t contain a coding region that can be translated, just that a ribozyme alone isn’t an entire translation system.
If so, are you aware that nobody has proposed otherwise? It isn’t at all clear what point you are trying to make here overall.
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This is just false. The translation system makes errors. They are deleterious to be sure, but they happen to all organisms. There are even some organisms where one of the codons is ambiguous and the proteins produced by translation from mRNA using that codon, one of two amino acids are used and the “choice” is random. It is said it has a “statistical proteome”.
This is really something of a misnomer since all organisms in fact, though at a very low rate, make errors during translation and as such all would have a “statistical proteome” in that sense. All that differs is really the rate at which this occurs, with some organisms having particular codons associated with tRNAs being aminoacylated by promiscuous tRNA-synthetases.
Broadly speaking, in contemporary hypotheses, the idea with translation originating in the RNA world is that at some point in the past there either were no proteins at all, or at least there were only some short peptides of limited functionality (for example stabilizers that weren’t strictly critical to function) that tolerated a high degree of error, and that translation essentially began with a very high degree of randomness, possibly even producing statistical peptides as a byproduct of some other reaction. As this system evolved greater specificity, the produced peptides took on more critical functions and at some point the genetic code basically was locked in place since any additional changes would have become strongly deleterious since more and more critical functions were carried out by peptides and proteins with much less tolerance for errors.
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Have you considered the possibility that what you said was unclear? I certainly don’t know what you were trying to say.
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I don’t see an insult. I do see that you didn’t answer the question.
No assumptions involved.
I’m familiar with it. Are you familiar with anything that’s been learned in the last >65 years?
I am aware that the term “genetic code” refers only to the correspondence between codons and amino acids. Your use of it here is unintelligible. I do notice that you removed context. Why?
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Adding another data point to @Rumraket’s interesting examples - RNA viruses most certainly carry the “informational capacity” @appsandorgs seems to be speaking of, and they also possess other biochemical functionality borne of RNA-based structures. And their “information” is never manifest as DNA.
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That sounds fun! But I’ll need to negotiate a few of the parameters of the project. One minor one is time and resources. The first time this system arose, the designer (whether a “mind” or not) took at least 400 million years and worked in a chemical environment different from today’s, without living competitors. I think I’m a lot smarter than that designer and would first seek a diverse team of experts to help with the project. But it seems only fair to grant us a hundred million years or so and material resources to match. I actually think it would take us a tiny fraction of that time – maybe, say, one million years – with adequate resources but let’s plan for the long haul, eh?
More importantly, though, is that in order to design something like the “extant gene system,” we’ll be designing something with significant flexibility – with far more than zero “degrees of freedom.” As all moderately informed people know, “zero degrees of freedom” is not an accurate description of the extant systems of molecular biology. It is, in fact, the opposite. This is true all throughout biology, and is so plainly obvious and widely known that… well, not to sound like I’m “blustering”…
I mean no particular offense when I say that your challenge reveals that you know next to nothing about molecular biology.
I do not find any bluster here, and one statement that your claim (not you) was vacuous. You are discussing with working professionals who know what they are talking about, not some averages Joes found on Facebook. Please be more careful in your own characterizations.
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I would think it embarrassing to know that one of the pioneers of information science understood and lectured on this issue over 70 years ago — before objects like codons, tRNA synthetase, or ribosomes were even known to exist. Physicists of a half century ago knew and wrote of it in the literature as well.
Again (again) I have done nothing more than state what is known directly from the literature. The observations aren’t even in question, yet half dozen regulars here have lost their shorts. It is quite a sight to see.