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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
gpuccio: The claim is that semiotic systems include a necessary discontinuity, and that they are always the result of conscious design. Do you mean semiotic systems are always the result of conscious design? Or you mean 'systems include a necessary discontinuity' are always the result of conscious design? If the former, there's no reason to mention necessary discontinuity. If the latter, there's no reason to mention semiotic system. Or do you mean only those semiotic systems that include a necessary discontinuity, excluding semiotic systems that do not include a necessary discontinuity? gpuccio: Completely implausible at all empirical levels and with all that we know and observe. What is implausible about Wolf & Koonin? gpuccio: In empirical science , we infer from observed facts and good methodology. We don’t simply say: “no one knows at this point”. When the observed facts don't lead to supportable conclusions, then, of course, we say we don't know. Vy: (i) RNA is too complex a molecule to have arisen prebiotically; A number of pathways in plausible abiotic conditions have been found. Vy: (iii) catalysis is a relatively rare property of long RNA sequences only; and RNA catalysis can be initiated with sequences as short as eighteen in length. Vy: (iv) the catalytic repertoire of RNA is too limited. RNA is at least capable of self-replication.Zachriel
November 5, 2015
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200+ comments thanks to the delusional ramblings of a mentally unstable individual? Wow! Zach, let go of those RNA strands you're clutching at. Even your Darwine buddies know the RNA World is fiction:
(i) RNA is too complex a molecule to have arisen prebiotically; (ii) RNA is inherently unstable; (iii) catalysis is a relatively rare property of long RNA sequences only; and (iv) the catalytic repertoire of RNA is too limited.
The RNA world hypothesis has been criticized because of the belief that long RNA sequences are needed for catalytic activity, and for the enormous numbers of andomized sequences required to isolate catalytic and binding functions using in vitro selection. For example, the best ribozyme replicase created so far -- able to replicate an impressive 95-nucleotide stretch of RNA -- is ~190 nucleotides in length, far too long a sequence to have arisen through any conceivable process of random assembly. And typically 10,000,000,000,000-1,000,000,000,000,000 randomized RNA molecules are required as a starting point for the isolation of ribozymic and/or binding activity in in vitro selection experiments, completely divorced from the probable prebiotic situation. As Charles Carter, in a published review of our recent paper in Biology Direct, puts it:
"I, for one, have never subscribed to this view of the origin of life, and I am by no means alone. The RNA world hypothesis is driven almost entirely by the flow of data from very high technology combinatorial libraries, whose relationship to the prebiotic world is anything but worthy of "unanimous support". There are several serious problems associated with it, and I view it as little more than a popular fantasy"
10^14 - 10^16 is an awful lot of RNA molecules.
I basically agree with Bernhardt. The RNA World scenario is bad as a scientific hypothesis: it is hardly falsifiable and is extremely difficult to verify due to a great number of holes in the most important parts. To wit, no one has achieved bona fide self-replication of RNA which is the cornerstone of the RNA World.
As if that wasn't bad enough for you Darwinists, the OOL wizards have got four insanity-stopping paradoxes (amongst others) to deal with when making their potions:
We have failed in any continuous way to provide a recipe that gets from the simple molecules that we know were present on early Earth to RNA. There is a discontinuous model which has many pieces, many of which have experimental support, but we’re up against these three or four paradoxes, which you and I have talked about in the past. The first paradox is the tendency of organic matter to devolve and to give tar. If you can avoid that, you can start to try to assemble things that are not tarry, but then you encounter the water problem, which is related to the fact that every interesting bond that you want to make is unstable, thermodynamically, with respect to water. If you can solve that problem, you have the problem of entropy, that any of the building blocks are going to be present in a low concentration; therefore, to assemble a large number of those building blocks, you get a gene-like RNA — 100 nucleotides long — that fights entropy. And the fourth problem is that even if you can solve the entropy problem, you have a paradox that RNA enzymes, which are maybe catalytically active, are more likely to be active in the sense that destroys RNA rather than creates RNA.
Like I've said before, abiogenesis (spontaneous generation aka chemical evolution) NEVER happened, it can NOT be demonstrated and will never be demonstrated. The only evidence for it exists in the min ... er ... 3 pound meats of the indoctrinated. Abiogenesis is worse than fiction, it's a refuted hunch that has been resurrected by reality denialists. It, like evolution and secular science in general, is nothing but Norse mythology in a cheap tux.Vy
November 5, 2015
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The hypercredulity is absolutely staggering.Phinehas
November 5, 2015
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UB: "Like I said, Zach, no one can take away your faith. And no one can falsify any conception you wish to propose from that faith" Sad but true.gpuccio
November 5, 2015
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Zachriel: "The claim is that translation could not evolve because of a “necessary discontinuity”." No. The claim is that semiotic systems include a necessary discontinuity, and that they are always the result of conscious design. Which is empirically verified. "Starting with a simple RNA replicator, and the synthesis of simple peptides, a translation system could plausibly evolve." Plausibly for you and for your vivid imagination. Completely implausible at all empirical levels and with all that we know and observe. "Whether this happened or not, no one knows at this point," In empirical science , we infer from observed facts and good methodology. We don't simply say: "no one knows at this point". "but it is sufficient to show how such a system could evolve." Maybe a simple generic statement about logical (not empirical) possibility is sufficient for you (and your vivid imagination). It is certainly not sufficient for people who want to make good scientific inferences, and to understand reality from observed facts and correct methodology.gpuccio
November 5, 2015
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And if you can't remove parts Zachriel what does that mean?Andre
November 5, 2015
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Andre: And do you know what that means Zachriel? Sure. Irreducible means that you can't remove a part without the system failing, like an arch.Zachriel
November 5, 2015
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And do you know what that means Zachriel?Andre
November 5, 2015
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Andre: what is an encoder without a decoder? We've already agreed that the current translation system is irreducible.Zachriel
November 5, 2015
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Upright BiPed: The ribozyme is now the genome. In RNA World, RNA acted both to store genetic information and to catalyze chemical reactions. An entailment of this theory is that RNA could catalyze its own replication, which has now been demonstrated.Zachriel
November 5, 2015
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Let me try Zachriel what is an encoder without a decoder?Andre
November 5, 2015
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The ribozyme is now the genome. Like I said, Zach, no one can take away your faith. And no one can falsify any conception you wish to propose from that faith.Upright BiPed
November 5, 2015
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EugeneS: How can rate-dependent processes (i.e. physics/chemistry of the particles of matter) result in the formation of rate-independent representations/symbols/encodings? Evolution can only precede by selectable steps, so intermediates couldn't have evolved with the goal of creating a translation system, but only for current function. Here is one plausible model of how it might have happened:
Wolf & Koonin, On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization, Biology Direct 2007: The proposed scenario for the evolution of translation consists of the following steps: binding of amino acids to a ribozyme resulting in an enhancement of its catalytic activity; evolution of the amino-acid-stimulated ribozyme into a peptide ligase (predecessor of the large ribosomal subunit) yielding, initially, a unique peptide activating the original ribozyme and, possibly, other ribozymes in the ensemble; evolution of self-charging proto-tRNAs that were selected, initially, for accumulation of amino acids, and subsequently, for delivery of amino acids to the peptide ligase; joining of the peptide ligase with a distinct RNA molecule (predecessor of the small ribosomal subunit) carrying a built-in template for more efficient, complementary binding of charged proto-tRNAs; evolution of the ability of the peptide ligase to assemble peptides using exogenous RNAs as template for complementary binding of charged proteo-tRNAs, yielding peptides with the potential to activate different ribozymes; evolution of the translocation function of the protoribosome leading to the production of increasingly longer peptides (the first proteins), i.e., the origin of translation.
Zachriel
November 5, 2015
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Why does Zachriel continue to site someone that does not support the claim that drift and natural selection can produce IC as if it does? Hermann Joseph Muller was ignorant of the IC molecular machinery. He was ignorant of the structure of DNA and he was ignorant of the genetic code. Only Zachriel would think that ignorance is an argument.Virgil Cain
November 5, 2015
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EugeneS: How can rate-dependent processes (i.e. physics/chemistry of the particles of matter) result in the formation of rate-independent representations/symbols/encodings?
Hermann Joseph Muller (1918): "... thus a complicated machine was gradually built up whose effective working was dependent upon the interlocking action of very numerous different elementary parts or factors, and many of the characters and factors which, when new, were originally merely an asset finally became necessary because other necessary characters and factors had subsequently become changed so as to be dependent on the former."
Zachriel
November 5, 2015
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Zachriel, "a translation system could plausibly evolve." How can rate-dependent processes (i.e. physics/chemistry of the particles of matter) result in the formation of rate-independent representations/symbols/encodings? The hypothetical chemical evolution could not have caused the rise of representations because the discontinuity is degeneracy with respect to the chemical laws of nature. The chemistry is therefore completely irrelevant to the formation of this discontinuity. So chemistry cannot be the driver behind the formation of symbolic representations. It is the other way around. The discontinuity is the necessary condition of information processing that utilizes chemistry.EugeneS
November 5, 2015
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Zachriel gets it wrong again:
The claim is that translation could not evolve because of a “necessary discontinuity”
The claim is that translation could not evolve via physicochemical processes because of a “necessary discontinuity”. And because no one knows how to model such a thing nor what it predicts.
Starting with a simple RNA replicator
You need to produce one via physicochemical processes. One that is capable of function adding and changing evolution.
and the synthesis of simple peptides, a translation system could plausibly evolve.
That isn't evidence and it isn't an argument.Virgil Cain
November 5, 2015
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gpuccio: The credibility of it, and how much it is supported by facts, are under the eyes of everyone, and everyone will judge for himself. The claim is that translation could not evolve because of a "necessary discontinuity". Starting with a simple RNA replicator, and the synthesis of simple peptides, a translation system could plausibly evolve. Whether this happened or not, no one knows at this point, but it is sufficient to show how such a system could evolve.Zachriel
November 5, 2015
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Zachriel: OK, you have recited your catechism. The credibility of it, and how much it is supported by facts, are under the eyes of everyone, and everyone will judge for himself. However, thank you for your compliance. :)gpuccio
November 5, 2015
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Darwinian evolution requires a replicator subject to variation and competing for limited resources, such as in Robertson & Joyce, Highly Efficient Self-Replicating RNA Enzymes, Chemistry & Biology 2014: “The enzyme also can cross-replicate with a partner enzyme, resulting in their mutual exponential growth and enabling self-sustained Darwinian evolution.”
But no new functions evolved and Spiegelman's monster applies.Virgil Cain
November 5, 2015
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gpuccio: Do you mean that your RNA world is an RNA-protein world? RNA World would obviously have evolved over time. RNAs catalyze. RNAs synthesize proteins. Proteins catalyze. gpuccio: Where everything is done by proteins, except protein synthesis? No. RNAs catalyze, including their own replication. But this process would be aided by increasingly complex protein networks. gpuccio: your FUCA is just the same as our prokaryotes, only with RNA instead of DNA? No. RNA within a protein complex is derived. Prokaryotes are highly derived. The first universal common ancestor may have been a simple replicator in a primitive membrane of some sort. gpuccio: And the genetic code and the translation apparatus already there, well functioning? The genetic code would have evolved from simpler associations. Mung: Where is the evidence for double-stranded helices of RNA? https://en.wikipedia.org/wiki/Double-stranded_RNA_viruses Zachriel: If a single molecule can replicate, then it is subject to darwinian evolution. Andre: where information comes from? It comes from mutation and selection. Upright BiPed: No one has demonstrated any evidence that an RNA “template-replicator” results in translation. While no one knows how translation evolved, there is evidence of a historical process, including the evidence from the ribosome, as already noted. Upright BiPed: We agree that a physicochemical discontinuity is required for translation, Yes. Upright BiPed: for the genome to exist, No. Upright BiPed: and for the organization of the heterogeneous cell. A replicator within a lipid membrane is heterogeneous, but the formation doesn't entail any discontinuity. Upright BiPed: OoL researchers have already engineered “template replicators” that weren’t capable of Darwinian evolution – and they’ve clearly said so. Darwinian evolution requires a replicator subject to variation and competing for limited resources, such as in Robertson & Joyce, Highly Efficient Self-Replicating RNA Enzymes, Chemistry & Biology 2014: "The enzyme also can cross-replicate with a partner enzyme, resulting in their mutual exponential growth and enabling self-sustained Darwinian evolution." Upright BiPed: 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”. RNAs are catalysts. When RNA catalyzes peptides and those peptides aid the primordial cell, then those cells are subject to selection and tend to predominate the population. Upright BiPed: 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? Presumably, short peptides were formed first. gpuccio: Structural and catalytic molecule. Therefore, the point seems to be that, in the RNA world hypothesis, RNA molecules did the things that after became the task of proteins. Sure, but in their own way, originally as aids, then eventually replacing many of the old structures. gpuccio: So, what took care of metabolism, ATP and GTP generation for example, in your RNA world? Early metabolism may have been fueled by natural proton gradients. No one knows at this point, of course. But there doesn't seem to be any intrinsic barrier.Zachriel
November 5, 2015
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Prokaryotes do not have a nucleus and still engage in transcription and translation. The symbols are the mRNA codons which represent amino acids, they do not become them via some physicochemical process. Source code in (mRNA codons) and object code out (polypeptide that folds/ gets folded into a functioning protein). It's almost as if we got our idea for a computer program compiler from ribosomes.Virgil Cain
November 5, 2015
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Upright Biped: I hope you will find the meeting of our two views in the writing I have presented.
In my philosophy the material world symbolizes the mental world. In other words, when we look at the material world we see mental phenomena symbolized by matter.
Well that’s very interesting Box, so do tell us, which mental phenomena are symbolized by semiotics and specifically protein production?
I will attempt to answer that question in a moment. First some preliminary thoughts: (1) Translation is information transfer through contexts. The essence of translation is the transfer of information (meaning) from one context to another context. We can see the two separate contexts in UB's example of a music box. Here the information resides in the spatial context of the cylinder and is transferred to another context of sounds. If I understand things correctly we can also see two separate contexts, neatly separated by (double) membranes, in the case of protein production. Here information is transferred from the context of the cell nucleus to the context of cytoplasm — DNA resides in the nucleus and ribosomes reside in the cytoplasm. - Note, with respect to symbolism, that the nucleus resides inside the cytoplasm; therefore we can envision the nucleus symbolizing the “inner world” and the cytoplasm the “outer world”. (2) Information relevant to one context only. There are two separate contexts, however the information that is being transferred is only functional in one context. In other words, the information is about one context only. In the case of the music box, the information that resides in the rotating cylinder has no function in the separate context of the rotating cylinder. Obviously it is only functional in the context of sound.
Upright Biped: This third material condition is the preservation of the natural discontinuity that exists between the arrangement of a representation and its post-translation effect. Representations and their effects are physicochemically discontinuous; meaning that the effects of translation are not determined by the dynamic properties of the representation being translated. This is to say, the representation evokes the effect to happen, but does not determine what the effect will be.
The discontinuity UB mentions is guaranteed by the discontinuity between the two contexts.
Okay, how about answering our question?
I’ll give you the short version: The nucleus symbolizes the “inner world” and DNA symbolizes thoughts about the “outer world” (cytoplasm) — non-functional thoughts in the context of the inner world by definition. Nucleotides are “letters”, codons are “words” and combinations of codons are “sentences/ideas about the outer world”. These “ideas” are then transferred to the outer world (cytoplasm) and transformed (translated) into functional objects/ideas.Box
November 5, 2015
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Z, that knocking at your door is a delegation of ghosts inquiring about the status of the vera causa principle. Newton and Lyell were looking particularly sad and Darwin, a bit sheepish. KFkairosfocus
November 5, 2015
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Yes, whenever an evo says "posit" they are actually dePOSITing another promissory note. ;)Virgil Cain
November 5, 2015
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What does posit mean?
posit ?p?z?t/ verb verb: posit; 3rd person present: posits; past tense: posited; past participle: posited; gerund or present participle: positing 1. put forward as fact or as a basis for argument. "the Confucian view posits a perfectible human nature" synonyms: postulate, put forward, advance, propound, submit, predicate, hypothesize, take as a hypothesis, set forth, propose, pose, assert; More presuppose, assume, presume "there are those who posit a purely biological basis for this phenomenon" base something on the truth of (a particular assumption). "these plots are posited on a false premise about women's nature as inferior" 2. put in position; place. "the Professor posits Cohen in his second category of poets" nounPhilosophy noun: posit; plural noun: posits 1. a statement which is made on the assumption that it will prove to be true.
Ahhhh so Zachriel has absolutely nothing. No evidence, just hoping his assumptions will be proven one day.Andre
November 5, 2015
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Zachriel: Just a personal note. When I credited you with "verbal creativity" about "posit", I did not mean to imply that you had made it up. I was simply praising your ability in choosing rare words in a specific context, for a purpose. Indeed, "posits" sounds a lot better than "assumes", or "imagines", or "fantasizes". I appreciate your choice.gpuccio
November 5, 2015
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Carpathian #169, "What I do is discard some cards and get new ones. That's evolution at its simplest." Emphasis mine. Note again, it is you who chooses new cards. Evolution has no means to choose for a future function. You have a strategy in mind. Evolution does not. You have a heuristic for winning based on your experience, if you're a good player. Evolution does not. Evolution chooses only from among existing functions, it never chooses for a future function. This is where the great divide is between you, an intelligent player, and evolution, a dumb 'player'. A blind unintelligent watchmaker is no watchmaker. This is where all evolutionists make a leap of faith without any empirical warrant. Evolution is no substitute for intelligence, planning or forethought. Evolution accounts for noise around existing functions and can at best drive a system back to an existing attractor. It has no means for creating genuine novelty.EugeneS
November 5, 2015
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Zachriel: And let's not forget the energy requirements, which are the reason why "metabolism first" theories, bizarre as they are, have gained importance over "RNA first" theories. Again from Wikipedia: "Energy Used for Protein Synthesis: One GTP is hydrolysed to GDP as each successive amino acid-tRNA complex attaches to the A site of the ribosome. A second GTP is broken down to GDP as the ribosome moves to each new codon in the mRNA. One ATP is hydrolysed to AMP during amino acid activation. Thus, the formation of each peptide bond uses 3 high-energy molecules, one ATP and two GTP." So, what took care of metabolism, ATP and GTP generation for example, in your RNA world? RNA? Proteins?gpuccio
November 5, 2015
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Zachriel: From Wikipedia (emphasis mine): "RNA can also act as a hereditary molecule, which encouraged Walter Gilbert to propose that in the distant past, the cell used RNA as both the genetic material and the structural and catalytic molecule rather than dividing these functions between DNA and protein as they are today; this hypothesis is known as the "RNA world hypothesis" of the origin of life." Structural and catalytic molecule. Therefore, the point seems to be that, in the RNA world hypothesis, RNA molecules did the things that after became the task of proteins. That was exactly my point.gpuccio
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