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Writing Biosemiosis.org

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In September of 2009 I started a new document on my computer entitled “A System of Symbols”, where I was going to write about the part of design theory that interested me the most – that is, the representations that are required for self-replication (von Neumann, Pattee). My goal was to inventory all the physical conditions necessary for one thing to represent another thing in a material universe. I wrote and rewrote that essay for more than four years — reading, learning, and sharing along the way. As it turns out, writing that essay was my way of coming to understand the issues, and I spent a great deal of that time trying to articulate things I had come to understand conceptually, but could not yet put into words. Eventually I came into contact with the types of scientists and researchers who had substantial experience with these issues, up to and including those who had spent their entire careers on the subject. It was a humbling experience to share my thoughts with people of that caliber, and have them respond by sending me papers of their own that reflected the same concepts.

Then In 2014, I retired that essay and began writing Biosemiosis.org in its place. Since that work is available to any reader, I won’t recapitulate it here, but there are a couple of concepts I’d like to highlight – particularly the discontinuity found in the translation of recorded information. Read More

[I’d like to thank Barry and Uncommon Descent for allowing me to publish this introduction to my two projects]

Comments
Zachriel,
Upright BiPed: Even though you agree that one process provides no evidence of the other, it’s consistent. Zach: No. Not having an “engineered RNA ‘template-replicator’ resulting in translation” doesn’t mean there isn’t any evidence.
No one has demonstrated any evidence that an RNA “template-replicator” results in translation. Like i said, “one process provides no evidence of the other”, and you agreed.
Upright BiPed: Then the diagram at the top of this page, illustrating that a physicochemical discontinuity is required for translation; required for the genome to exist; required to organize the heterogeneous cell, is accurate. Zach: Glad we agree. However, there is nothing that prevents a priori such a system from evolving from a simpler system.
Good to know. We agree that a physicochemical discontinuity is required for translation, for the genome to exist, and for the organization of the heterogeneous cell.
Upright BiPed: The irreducible structure in question is the singular physical condition that allows nucleotides to be translated into amino acids. It is the physical prerequisite of Darwinian evolution. It is indeed intrinsic. No. Darwinian evolution only requires reproduction. If a single molecule can replicate, then it is subject to darwinian evolution.
It’s silly to suggest that all Darwinian evolution requires is reproduction. OoL researchers have already engineered “template replicators” that weren’t capable of Darwinian evolution – and they’ve clearly said so. I have a question for you: You’ve moved RNA-specified production of protein into your RNA world, yet when asked where the information resides to specify the ordering of those amino acids, you gave an unclear answer, suggesting in “sequences of RNA that directly catalyzed the formation of peptides”. Are you actually suggesting that to form a peptide of say 200 monomers (which is less half the length of any extant aaRS the system would need to produce in order to make the transition to a DNA-Protein world) the structure of the RNA catalyst itself establishes the order of those amino acids? And if you are not saying that (as outlandish as it is) then you’ve gained absolutely nothing in regards to perceived “simplicity”, and everything in the observations made here remains in full effect.Upright BiPed
November 4, 2015
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Zachriel
No. Darwinian evolution only requires reproduction. If a single molecule can replicate, then it is subject to darwinian evolution.
So tell us sugar plum, where information comes from? The input machinery comes from? The encoding machinery comes from? The networking systems? Protocols? The decoding machinery. The output machinery? The error correction machinery? The integrity check systems? You can't have one or the other, you can't have incremental steps you can't have step by step.... you have to have everything in place at absolutely the same time! Without it there is no replication!Andre
November 4, 2015
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You have a life apart from Biosemiosis dot org? That's not a good sign.Mung
November 4, 2015
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I'm just now returning. Give me a chance to read and catch up.Upright BiPed
November 4, 2015
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gpuccio: is it really a problem to add DNA, at this point? It is. Don't let him skate on that point either. Where is the evidence for double-stranded helices of RNA? Does any exist? And yet that is vital for copying DNA.Mung
November 4, 2015
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Zachriel: "Rather you have ribozyme A which catalyzes the production of a peptide, then in some future you have a ribozyme which still catalyzes the production of the peptide. The balance of your comment reflects this misunderstanding." Do you mean that your RNA world is an RNA-protein world? Where everything is done by proteins, except protein synthesis? IOWs, the only functions of rybozimes would be protein synthesis? So, in your first beings, there is only the ribosome, and maybe an RNA substitute of the 20 aa-tRNA synthetases (let's say 20 aa-tRNA rybozimes), and all the rest of your RNA is just a symbolic template for proteins, and proteins do everything? IOWs, your FUCA is just the same as our prokaryotes, only with RNA instead of DNA? And the genetic code and the translation apparatus already there, well functioning? Do you realize what you are suggesting? You are suggesting an RNA world which is completely useless to explain anything, because its functional complexity is exactly the same as the functional complexity in a DNA-RNA-protein world (is it really a problem to add DNA, at this point?). So, maybe that sooner or later you will agree with me: that LUCA was FUCA, and was essentially a DNA-RNA-protein being (IOWs, the only type of autonomous living being ever observed)? Maybe be that sooner or later science can go back to being empirical, and based on observed facts?gpuccio
November 4, 2015
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Steve: This is a clear barrier to neo-darwinian evolutionary concepts. Steve: design deniers never talk about excess reproduction
Darwin, Origin of Species 1859: Every being, which during its natural lifetime produces several eggs or seeds, must suffer destruction during some period of its life, and during some season or occasional year, otherwise, on the principle of geometrical increase, its numbers would quickly become so inordinately great that no country could support the product. Hence, as more individuals are produced than can possibly survive, there must in every case be a struggle for existence, either one individual with another of the same species, or with the individuals of distinct species, or with the physical conditions of life.
Zachriel
November 4, 2015
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Zachriel, Your comment below reflects your misunderstanding of evolution. It is not reproduction per se that evolution only requires. Random variation and selection require excess reproduction. It is excess reproduction which drives variation and selection. So by your very admission, variation and selection are sub-components in a system which is driven by excess reproduction, said excess reproduction not definable by neo-darwinian evolutionary concepts. Excess reproduction is costlier that one to one replication. Further, excess reproduction infers foresight- that to survive in the long term, one-off reproduction won't cut it. By neo-darwinian accounts, the first multi-cellular organisms most certainly started off with one-to-one reproduction. But one-to-one reproduction would never give these multi-cellular organisms the opportunity to transform from one-off reproduction to excess reproduction. This is a clear barrier to neo-darwinian evolutionary concepts.
No. Darwinian evolution only requires reproduction. If a single molecule can replicate, then it is subject to darwinian evolution. RNA World could have evolved the use of peptides to extend their capabilities, while later on DNA may have coopted the replication mechanism, perhaps virally. For an overview, see Takeuchi et al., On the Origin of DNA Genomes: Evolution of the Division of Labor between Template and Catalyst in Model Replicator Systems, PLOS 2011.
Steve
November 4, 2015
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Zachriel:
Darwinian evolution only requires reproduction.
And Spiegelman's monster says tat Darwinian evolution would produce more simple replicators starting with complex replicators.
If a single molecule can replicate, then it is subject to darwinian evolution.
Nothing new ever evolves, though.Virgil Cain
November 4, 2015
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Mung: Yes it does. Else there’s no self to replicate. Template reproduction is a counterexample to your claim. gpuccio: Posited. I like your verbal creativity. posit, transitive verb, assume as a fact; put forward as a basis of argument. gpuccio: If you have a rybozime A which catalyzes reaction a, and then in some future you have protein B which catalyzes reaction a Rather you have ribozyme A which catalyzes the production of a peptide, then in some future you have a ribozyme which still catalyzes the production of the peptide. The balance of your comment reflects this misunderstanding. Mung: Darwinian evolution requires two separate and distinct entities, the genotype and the phenotype. No. Darwinian evolution only requires reproduction. If a single molecule can replicate, then it is subject to darwinian evolution. Upright BiPed: Even though you agree that one process provides no evidence of the other, it’s consistent. No. Not having an "engineered RNA 'template-replicator' resulting in translation" doesn't mean there isn't any evidence. One line of evidence is that RNA can act to both store genetic information and to catalyze chemical reactions. Another line of evidence is that ribosomes are ribozymes. Upright BiPed: Then the diagram at the top of this page, illustrating that a physicochemical discontinuity is required for translation; required for the genome to exist; required to organize the heterogeneous cell, is accurate. Glad we agree. However, there is nothing that prevents a priori such a system from evolving from a simpler system. Upright BiPed: The irreducible structure in question is the singular physical condition that allows nucleotides to be translated into amino acids. It is the physical prerequisite of Darwinian evolution. It is indeed intrinsic. No. Darwinian evolution only requires reproduction. If a single molecule can replicate, then it is subject to darwinian evolution. RNA World could have evolved the use of peptides to extend their capabilities, while later on DNA may have coopted the replication mechanism, perhaps virally. For an overview, see Takeuchi et al., On the Origin of DNA Genomes: Evolution of the Division of Labor between Template and Catalyst in Model Replicator Systems, PLOS 2011.Zachriel
November 4, 2015
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There is no intrinsic barrier to the evolution of irreducible systems, so pointing out that the system is irreducible doesn’t mean it didn’t evolve.
The irreducible structure in question is the singular physical condition that allows nucleotides to be translated into amino acids. It is the physical prerequisite of Darwinian evolution. It is indeed intrinsic.Upright BiPed
November 4, 2015
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Upright BiPed: Are you yet able to unambiguously acknowledge that to translate D/RNA into proteins requires the discontinuity? Zach: Yes, we have already granted there is a “necessary discontinuity”
. Then the diagram at the top of this page, illustrating that a physicochemical discontinuity is required for translation; required for the genome to exist; required to organize the heterogeneous cell, is accurate.Upright BiPed
November 4, 2015
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Zachriel: Our objection is to the argument that genetic translation is an intrinsic barrier to evolution. Well, that's not the argument. So you can stop objecting. :) Genetic translation is not a barrier to biological (Darwinian) evolution, but a prerequisite for it.Mung
November 4, 2015
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Notice to all UD contributors: As long as Caprathian can come up with inane metaphors for evolution, he will be impervious to evidence and logic. And his supply of inane metaphors is apparently inexhaustible.Barry Arrington
November 4, 2015
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Zachriel: The extant genetic code is posited to have evolved from a simpler relationships code Fixed it for you. How does that help your position? It certainly doesn't rebut gpuccio's argument in the slightest.Mung
November 4, 2015
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Upright BiPed: Then, knowing that the physical processes involved in RNA templating do nothing whatsoever to resolve the singular issues associated with the translation of a dimensional semiotic code, what is the real impetus to keep repeating it? Zach: It’s a valid hypothesis consistent with the evidence.
Even though you agree that one process provides no evidence of the other, it’s consistent. Good to know.Upright BiPed
November 4, 2015
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Carpathian:
What I do is discard some cards and get new ones. That’s evolution at its simplest.
LoL! Evolution is playing the hand you're dealt. Why on earth would you want to discard cards and get new ones? Whatever reason you can come up with, it's not evolution. Please stop insulting our intelligence. It just incites people to insult you back. But if that's what you're looking for ...Mung
November 4, 2015
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Let's start out with some basic biological facts, since Zachriel likes facts. Darwinian evolution requires two separate and distinct entities, the genotype and the phenotype. Reproduction involves not just the copying of the genotype, but also the construction of the phenotype. Enter von Neumann.Mung
November 4, 2015
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Zachriel: Great master of elusion! "The extant genetic code is posited to have evolved from a simpler relationships, in particular, sequences of RNA that directly catalyzed the formation of peptides." Posited. I like your verbal creativity. :) "Not sure what this means. RNA produced proteins. They still do." Not sure what I mean? I will explain it again: I wrote: And the information which produced rybozymes has to be found again, if the function has to be assumed by proteins, for the reasons I have already stated. That means: If you have a rybozime A which catalyzes reaction a, and then in some future you have protein B which catalyzes reaction a (which is more or less what must have happened according to your view, because in the RNA world RNA was the effector molecule, but in today's world, with very rare exceptions, like the ribosome, almost all reactions are catalyzed by proteins), then: The information for the sequence of nucleotides for rybozime A and The symbolic information in the sequence of nucleotides which guides the synthesis of protein B (either in DNA or RNA) have no relationship one with the other. Therefore, from an informational point of view, they must be "discovered" independently. IOWs, all the information in your RNA being, which codes for rybozimes, is completely useless to define the proteins that, in the new protein based being, will take the place of the "old" rybozimes. Is it clear now? And please, don't go on repeating this new trivial gospel: "RNA produced proteins." It's simply not true. Proteins, as far as we know, are "produced", and always were, using symbolic stored information in the protein coding genes in DNA, transcribed by messenger RNA, and translated by a very complex apparatus which includes, at least, the ribosome (with its RNA and proteins), the tRNAs, and above all the 20 aa-tRNA synthetases, which are the real part of the system were the genetic code is written. You say: "No one knows exactly how it happened, but the hypothesis is that RNA used DNA to store information in a more stable form. Eventually, DNA became the main storage of information." But that is not any answer to what I wrote, which was: The point remains, the information (in nucleotide sequence) to effect a function by RNA has nothing to do with the information (in nucleotide sequence) to effect the same function by a protein, coded by the genetic code. IOWs, the same point I have re-explained here. IOWs, I have never discussed the problem of how the genetic information was transferred from RNA to DNA (that is a problem too, but certainly not the biggest one). My point, instead, is that the genetic information in RNA for rybozimes is completely different, and unrelated, to the symbolic genetic information in RNA or DNA to produce a protein, even if the function of the rybozime and of the protein be the same. That's why your theory "posits" an OOL where the information for rybozimes is magically found, and a re-OOL where the information for proteins is, again, magically found. Is that clear now? I confide in your intelligence, which has always been as great as your ability at elegant elusion.gpuccio
November 4, 2015
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We should at least give Zachriel credit for showing up for the party. :) A toast to Zachriel.Mung
November 4, 2015
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Zachs: There is no intrinsic barrier to the evolution of irreducible systems, so pointing out that the system is irreducible doesn’t mean it didn’t evolve. To determine that we have to look at the specifics.
Let's do that. Can you describe a step-by-step evolution of genetic translation? Allow me to set up the first line for you: 1. RNA in a membrane. 2. ...Box
November 4, 2015
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Zachriel: Self-replication does not require von Neumann architecture. Yes it does. Else there's no self to replicate.Mung
November 4, 2015
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Carpathian:
Our side provides the questions and your side provides the insults.
I agree with you that we could all do without the insults. You could do your part by not insulting our intelligence. Deal?Mung
November 4, 2015
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gpuccio: For RNA to produce proteins you need the genetic code and the translation apparatus. The extant genetic code is posited to have evolved from a simpler relationships, in particular, sequences of RNA that directly catalyzed the formation of peptides. gpuccio: And the information which produced rybozymes has to be found again, if the functions has to be assumed by proteins, for the reasons I have already stated. Not sure what this means. RNA produced proteins. They still do. gpuccio: The point remains, the information (in nucleotide sequence) to effect a function by RNA has nothing to do with the information (in nucleotide sequence) to effect the same function by a protein, coded by the genetic code. No one knows exactly how it happened, but the hypothesis is that RNA used DNA to store information in a more stable form. Eventually, DNA became the main storage of information. gpuccio: The simple truth is that cell functions, for all we know, are effected by proteins, from LUCA on. Right. And it's RNA that produces proteins, not DNA. gpuccio: I am not aware of any evidence that “the primitive ribosome was made entirely of RNA”. The active site of the ribosome is a ribozyme. It's also highly conserved. This is exactly what is expected from the hypothesis of RNA World. gpuccio: It has always been known that the ribosome is mainly an RNA structure, with many proteins playing some role. Ut Philosophus dixit, but it was Cech and Altman who won the Nobel Prize in 1989 for its discovery. Upright BiPed: A process has been posited as the precursor of another process that it bears no physical relationship to, containing singular features that are entirely absent in the proposed precursor. The posited precursor acts to store genetic information and also to catalyze chemical reactions, including the formation of peptides. Upright BiPed: Then, knowing that the physical processes involved in RNA templating do nothing whatsoever to resolve the singular issues associated with the translation of a dimensional semiotic code, what is the real impetus to keep repeating it? It's a valid hypothesis consistent with the evidence. Upright BiPed: Are you yet able to unambiguously acknowledge that to translate D/RNA into proteins requires the discontinuity? Yes, we have already granted there is a "necessary discontinuity", which is just a specific instance of irreducible complexity. There is no intrinsic barrier to the evolution of irreducible systems, so pointing out that the system is irreducible doesn't mean it didn't evolve. To determine that we have to look at the specifics. The fact that ribosomes are ribozymes is empirical support for RNA World. EugeneS: You appear to believe that repeating some sciency word combinations will help you resolve the gigantic challenge naturalism is facing at the origin of life. Not at all. The origin of life is still a great mystery. Our objection is to the argument that genetic translation is an intrinsic barrier to evolution.Zachriel
November 4, 2015
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gpuccio:
If I understand well (you seem very reticent to say things clearly) you believe: That darwinian principles can explain all evolution of life after OOL. That “No one has any idea how life started.” Except you, apparently. Because you say that: “There is no evidence to suggest that life was “obviously designed” by any hands-on method.”
I don't think I can be clearer. I said that no one has any idea how life started. I didn't say, "Except me". I don't know how life started and neither do you. Here's something to think about concerning how it evolved. Life evolved in the same way man-made products evolve and that is due to "market" pressures, not primarily "design" issues. If the "market" (i.e the environment), accepted a biological organism, (i.e. a product), that product would continue to be "developed" until the "market" no longer accepted it.Carpathian
November 4, 2015
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Mapou:
To do what you are suggesting, a designer would have to have all possible body plans (from single cell organisms to dung beetles, caribous and whales) incorporated in the first self-replicating cell a billion years ago. This is nonsense, of course .
Of course it is nonsense. Neither the "designer" nor "Darwinism" suggests such a thing. If I'm dealt five cards in poker, I don't have every possible hand that could be made. What I do is discard some cards and get new ones. That's evolution at its simplest.Carpathian
November 4, 2015
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Before typing responses, you need to understand the challenge.
#53Upright BiPed
November 4, 2015
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Zachriel #161, You appear to believe that repeating some sciency word combinations will help you resolve the gigantic challenge naturalism is facing at the origin of life. Before typing responses, you need to understand the challenge.EugeneS
November 4, 2015
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Upright BiPed: “More complex relationships” isn’t the physical requirement, translation is. Zachriel: Translation is posited to have evolved from simpler associations.
Yes, we've already been here. A process has been posited as the precursor of another process that it bears no physical relationship to, containing singular features that are entirely absent in the proposed precursor. It is also understood that this proposed precursor is widely used as an intellectual placemat to avoid the universal observation that those singular features result from a singular source. Are you able to acknowledge that source as unambiguously as our universal experience suggests? [Edit: This isn't to suggest that you have changed your position, but are you even able to acknowledge the universal observation?]
Upright BiPed: And as we have come to agree, no one has demonstrated an engineered RNA “template-replicator” resulting in translation. Zachriel: That is correct.
Then, knowing that the physical processes involved in RNA templating do nothing whatsoever to resolve the singular issues associated with the translation of a dimensional semiotic code, what is the real impetus to keep repeating it? Why make a veritable career of going out on the web to repeat the claim at every opportunity, as if you didn’t already know the claim is seriously flawed (if not downright deceptive) from an empirical point of view? Of course, there is no need to answer that question here, after all you are not alone. There are knowledgeable people on the web that (with a completely straight face) will tell you that a “one amino acid system” can result into a “two amino acid system”. And if you bring it to their attention that a “one amino system” (what system!?) doesn’t have the informational capacity to encode itself into a translation system at all (and doesn’t resolved any of the unique physical conditions required of a semiotic code), you only incite them to increase their mockery. Do you think that is a rational scientific response to empirical facts?
Upright BiPed: The diagram at the top of this page (which you have referred to) does not make any claims about “what could not plausible occur”. Instead, it shows what *does occur* during the translation of functional effects from an informational medium. Zachriel: That’s fine. Translation, including the “necessary discontinuity”, is posited to have evolved from simpler associations.
Yes Zach, we’ve already covered this. Are you yet able to unambiguously acknowledge that to translate D/RNA into proteins requires the discontinuity?
Upright BiPed: An RNA “template-replicator” encapsulated inside a dissociated lipid membrane still does not achieve translation, and thus, is not capable of organizing the heterogeneous living cell. Zachriel: Not sure what you are claiming. Posited RNA replicators within a lipid membrane are an organized heterogeneous cell capable of making other organized heterogeneous cells.
An RNA “template replicator” that does not translate information cannot organize the heterogeneous cell. Two RNA “template replicators” that do not translate information cannot organize the heterogeneous cell any more than one can. Give it a rest already.Upright BiPed
November 4, 2015
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Zachriel:
Translation is posited to have evolved from simpler associations.
Of course it is. However that alone doesn't solve the problem.
DNA is a template replicator.
DNA gets replicated with the help of many proteins.
RNA World is posited to have preceded DNA World,
The alleged RNA world lacks evidentiary support.
As such, the ribosome is a primordial structure predicted by RNA World.
Except the primordial world is not capable of producing a ribosome. Natural selection and drift are incapable of producing a ribosome. So you lose, again.Virgil Cain
November 4, 2015
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