Are you referring to “Upright Biped”? What evidence do you have that they’re the same person? At any rate, we have sufficient evidence from the current thread that @appsandorgs is uninterested in actual interaction.
seems like confirmation to me.
Perhaps, but only you would know, apparently. The post wasn’t noted as a reply to anything, so it’s unclear to anyone else just what he was agreeing to.
Thank you, Alan.
My explanatory comment at the top of this page had not even a hint of abrasiveness (see below):
appsandorgs: 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.
Then, in an effort to keep the conversation on the topic, I repeated my original statement from the prior thread, again, without an ounce of abrasiveness (see below).
appsandorgs: A self-replicating RNA, often envisioned at the origin of life, does not establish the set of constraints required to specify genetic information like DNA — which was my comment.
Immediately thereafter, Matheson pulls out the “vacuous” cudgel, Harshman quickly passes over everything I say and tells me “All an RNA needs” to code is a start codon, Mercer holds up a post-translational apparatus at the OoL, and Rumraket carpet bombs me with irrelevant papers about RNA. Someone is now pounding the metaphorically desk, demanding to know how many papers I’ve published.
After 64 responses in this thread, two things haven’t happened – and they are not going to happen. 1) No one has produced anything in my original explanation that is false. 2) No one is going to acknowledge that I am indeed correct. However, the flimsy defense that no one can understand what I am saying is just preposterous at this point – as two or three of them attempt to shuffle and reword it to suit themselves (as if no one would have ever seen that coming).
appsandorgs: The concept of the gene as a symbolic representation of the organism is a fundamental feature of the living world. Arguably the best examples of Turing’s and von Neumann’s machines are to be found in biology.
Alan Fox: Well, you already know I disagree about the symbolism.
Yes, I know, – but to your credit, I am not entirely sure we disagree about the physics or the history.
appsandorgs: I mentioned that these issues I was discussing were predicted in 1948 (by John Von Neumann, using the logical organization of Alan Turing’s Machine of 1936), and again in 1955 (put into biological context by Francis Crick in the Adapter Hypothesis), and then confirmed via experimental result in 1956-58 (Hoagland and Zamecnik).
Alan Fox: Well, what is known about biochemistry and genetics has expanded hugely since the 1950s.
Sure it has, but the physical requirements haven’t changed one iota. And if someone had any idea of how to get from dynamics to descriptions (rate-independent control) – let’s be real – everyone here would already know it. I certainly would.
And about that “symbolism”, those words just above:
“The concept of the gene as a symbolic representation of the organism is a fundamental feature of the living world. Arguably the best examples of Turing’s and von Neumann’s machines are to be found in biology”.
Those are not my words. Those words appeared in the journal Nature in 2012, and were written by Sydney Brenner, the man who helped confirm the codon at three bases in length and gave Crick’s “Adapter Hypothesis” its famous name. [Mod edit to add: Life's code script | Nature] It was perhaps his last public attempt (before his death in 2019) to get biologists to shake off their bias and fully understand the true nature of the systems they work with. Brenner was no fool, and he knew that when something is a separate encoded description, you can’t treat it like a dynamic template. He also knew Von Neumann’s “threshold of complication” (which is the general subject of this thread).
This is why I can sit here calmly and take the slings and arrows of the experts. The physics and the history of science is on my side.
You and I have had many many contentious arguments over a good period of time. I think it would be false (and sad) to say that my addressing you, and your addressing me, has not changed over the years. I believe that to be a good thing.
I think the fact that I wasn’t thrown off should be self-evident to anyone. Allow me to offer a perspective: “I was lucky to get my diploma before being thrown off campus for whistling at Mrs. Rivera and spending too much time at the pubs on the drag”.
Cheers P.S.
- Your original explanation of what? What is it you think you have explained?
- What is it you think you are correct about?
You have not even answered a single question about this.
You were quoted in the opening post as saying:
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!!”
This immediately and naturally translates to a person doubting the possibility that RNA can contain a coding region (carry the information necessary to specify a protein sequence like DNA does) while also being a catalyst (a ribozyme).
Given your later clarification, I asked whether you instead had meant by the OP quote that a ribozyme can’t simultaneously function as an entire translation system, and if so, what point you were trying to make with that question?
I directly asked you to confirm(or disconfirm) one of my attempts to re-write your statement using more standard terminology, to make sure I was understanding you correctly. You didn’t answer that, and you still haven’t. Why don’t you simply answer it?
Consider the possibility that your chosen terminology and style of communication is at fault, not anyone’s reading comprehension. After all, six people took your OP statement to mean that you disputed the possibility that a ribozyme could also simultaneously contain a protein coding-region.
Strangely, rather than simply make an effort to correct this misapprehension and explain your self better, you elected to accuse the interlocutors of feigning confusion.
Now, amazingly, you repeat the very same behavior. Expending literally no effort explaining yourself and ignoring every simple request for clarification. We are none the wiser.
So I ask again, are you merely saying that you don’t think a ribozyme also function as an entire translation system? Are you endowed with the capacity to answer this simple question?
2 Likes
Allow me to offer my own perspective:
You came with a purposefully vacuous question, and after observing that knowledgeable professionals can answer this under a range of possible interpretations, you choose to declare victory and retreat. There are of course any number of equally vacuous questions that are difficult to answer without first setting some constraint on the meaning of the question. That you have discovered one more such question is a very small accomplishment.
5 Likes
There certainly is.
This is a major failure at communication:
-
You didn’t indicate in any way that you were quoting some-one else.
-
That is not what Brenner wrote. You switched the order of the two sentences and omitted parts of one of them and the text between them:
Arguably the best examples of Turing’s and von Neumann’s machines are to be found in biology. … 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.
There’s no point in putting effort into responding to your posts if they might be just mangled plagiarism, and even less point of you’re going to ignore criticism because you’re stealth misquoting.
Perhaps you should include a disclaimer in your posts to the effect that you might be parroting text you rearranged, won’t defend and might not understand. Then people will know not to waste time responding to you.
2 Likes
Is there any more reason for this thread to go on?
2 Likes
Well, I’m still curious about just what it is he’s trying to say. But I suppose the chances him ever actually saying it are slight.
1 Like
Roy, I don’t know if its occurred to you, but I am the one who told you where the words came from. You quoted me as doing so. More importantly, I have explained why they are important. The living cell manufacturers a set of rate-independent constraints to establish the genetic code, which are then taken up in the causal pathway of protein synthesis. This is how rate-independent control of a rate-dependent process is implemented, and it is what enables open-ended control from a fully deterministic process, just as Von Neumann predicted. It’s a system of symbolic tokens and constraints, as Brenner implored his fellow biologist to realize, against their biases otherwise (i.e. the ones on display here).
John, a triplet codon (such as AUG) is not a universal object in physics – it is a particular part of a system, which is established by a set of rate-independent constraints. That set of constraints does not exist in the self-replicating RNA envisioned at the origin of life.
I’m aware of that. I’m also aware that you didn’t say where they came from when you originally ‘wrote’ them. So anything you post could potentially be words you got from elsewhere.
I’m also aware that what you posted didn’t actually match your source - as issue you haven’t addressed.
Unattributed misquotes are never important, except that they show that the person using them can be disregarded until and unless they cease concealing and misrepresenting their sources.
2 Likes
Well, as I said, you have a good argument against the idea that the observed system of gene storage and replication, and the process of protein synthesis, evolved “out of the blue”. When I first encountered your argument (2011 I think), I was sceptical of RNA world but have since accepted that RNA world is eminently plausible. I don’t think your argument, and I might as well be blunt, works at all when considering RNA world as a precursor to its subversion (though incomplete in critical ways) by DNA and proteins.
Of course, it is your prerogative to continue to be committed to your argument, in which case you might like to present a précis of your semiotic argument so that people here who are unaware of the history may criticize it, or you could remain convinced that you are correct in which further discussion would be rather pointless.
As I also said, there are experts in the field who are far more qualified than I to discuss how much more evidence has accrued in favour of RNA world and the subsequent evolution of the genetic code since you began to promote your semiotic argument. I think you should have a look at it.
2 Likes
If you would rephrase in English, that would help. What is a “universal object in physics”? What is the “set of rate-independent constraints” you are talking about?
1 Like
Many things did not exist at the origin of life that nevertheless evolved later.
1 Like
It has sparked some really good replies, so I am inclined to let it run for now. We’ve seen worse go on longer. 
2 Likes
Brenner makes the point that Schrodinger’s ideas of a fully dynamic source of genetic information (“architect’s plan and builder’s craft in one”) was shown to be false; replaced with the coordinated set of tokens and constraints of Von Neumann (with Turing and Peirce firmly in tow). Thus, there is the organizational “threshold of complication” that has to be specified by any precursor – regardless of what atoms it is made of.
As far as I am aware, you are not for the silencing those facts.
John, is it true that all an RNA at the origin of life needs to code is a start with AUG?
No. Who ever made such a claim? And while we’re at it, since I answer your questions, why won’t you ever answer mine?
3 Likes
That is correct.
People who study symbol systems will tell you that the information specified by a token is established by the constraint. In the living cell, neither DNA nor RNA specify the amino acids in a protein without that set of constraints.
.
Who?
It is people (sometimes even experts) who talk about something like a self-replicating ribozyme in the context of the origin of life and mistakenly suggest (often to the public and press) that it can carry the information to encode a protein just like DNA.
People who (in a forum about “RNA Catalyst and the Origin of Life”) say things like this:
I believe it comes from people not fully acquainting themselves with the distinction between a dynamic system and a description. That was the point Brenner had promoted over many years.
All due respect, but what in the heck are you talking about?
What I said doesn’t mean what you are claiming it does. And again, I have no idea what you think you’re saying. Try using different words.
6 Likes