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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
Alicia I'm dissapointed you huffed and you puffed but you did not blow the house down.Andre
November 7, 2015
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Upright BiPed: As the author of the OP, I am not aware that the words “conscious design” appear anywhere in that description. That was gpuccio's description. You probably haven't made your point clear. Can you state provide a brief statement of your claim? We've asked a few times? What is a heterogeneous cell? Does a posited RNA World cell qualify? Upright BiPed: To organize the first living cell, a set of physical representations and a set of physical protocols must arise together. One set must encode the information and the other set must establish (specify) what the result of that encoding will be. RNA World posits that the same molecule encoded the information and determined what the result of that encoding would be.Zachriel
November 7, 2015
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The argument in the original post is that semiotic systems include a necessary discontinuity, and that they are always the result of conscious design. To contradict this assertion…
The OP provides a short description of the material conditions required to translate a spatially-oriented representation, such as a nucleic codon. This is the physical basis of the open-ended (evolvable) information system required to organize the heterogeneous living cell. As the author of the OP, I am not aware that the words “conscious design” appear anywhere in that description. In any case, these are observations gleaned from scientific investigation; proposed in theory, confirmed by experiment, and documented in peer-review. You’ve contradicted nothing because you haven’t provided any details that would provide the basis of a contradiction. And your notion that in order to contradict these observations you only need to contrive a physics-free idea that seems plausible to the person making the proposal is patently ridiculous. To contradict the observations you’ll need to address the issue of energy degeneracy – how a rate-dependent process formalizes a necessary set of rate-independent representations in linear sequence memory. Additionally, to contradict the issue of spatial-orientation, you’ll need to address the issue of how the necessary systematic rules of interpretation become simultaneously formalized in that memory. You’ve done neither. Alternatively, having provided no details, there is nothing anyone can say to falsify your beliefs. All that can be done is to continue to point out the flaws. And with each round, you can fall back on the lack of detail. This is exceptionally true of subject matter that has interdependent objects, like translation. It does grow tiresome though. It is also notable that you refuse to acknowledge our universal experience regarding the systems being discussed. In the end, you will walk away from this conversation with the firm commitment that you’ve contradicted the observations, and this will be the outcome regardless of anything that is said here. For that, nothing can be done, so it is of little consequence. - - - - - - - - - - - - Biosemiosis.org -- BibliographyUpright BiPed
November 7, 2015
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Barry Arrington:
You’ve been participating on this blog for years. Yet, your comment at 368 illustrates that you do not have the first clue about what ID posits. Since you’ve been exposed to the truth countless times, I can only surmise that you are either blindingly stupid or willfully ignorant, or perhaps both. Please try to do better. I won’t be holding my breath.
Did Mapou get it wrong too? Mapou, an IDist, says ID is Creationism and I agree with him as do many others here. He has provided a very open and realistic comment on ID. Instead of making personal statements about me, why don't you just answer a few simple questions and follow the evidence. ID states there was a designer of life. Did I get that wrong? kairosfocus claims that there was a lab of some sort which created life. Did I get that wrong? If this lab is where life was created, it must have been run by entities which themselves were not alive. Am I wrong to think that?Carpathian
November 7, 2015
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Thank you for the basic biology lesson gpuccio. And now let me get this straight, to support the claim that “a lot of amino acid sequences are so conserved,” you specifically take the subunits with the most highly conserved sequences in one of the most important biomolecules across all domains of life. In the same breath you admit that the other subunits are not nearly as well conserved, but hey, let’s just ignore those! Have you ever heard the phrase “confirmation bias?” Also, your conservation percentages ignore the amino acids that are present in one species and not the other, while this is necessary to align the sequences, those can all be considered differences in amino acid sequence, which is the topic at hand. So from the comparison between subunits in human and A. halopraeferens, the resulting ~80% range will be significantly reduced when you take into account the 50 amino acids that are not present in this bacterial species. “The commentary at evolutionnews eloquently explains.” Please, Box. That’s a good one. The points evolutionnews tries to make amount to stabs in the dark. First they play word games with “selection” vs. “sorting” and “piles of amino acids” The question is how is a genetic code produced? And the researchers propose that an early code emerged which recognized amino acids based on hydrophobicity and size via early tRNA molecules. Again this system is not as precise as the one we see today, but the ability to consistently add hydrophobic or hydrophilic amino acids or large or small amino acids or some combination of these properties would be plenty to produce proteins. This certainly is a “code” or “specification” although it is not as simple as the codon-amino acid code that we see today. Instead it is some 3D shape and the underlying sequence of the early tRNA which binds a type of amino acid. Pretty much everything on evolutionnews either begins with something taken out of context or is flat-out wrong. Mung, the only thing that “detaches the amino acid from the tRNA so that it can be added to the peptide chain” is the ribosome.Alicia Cartelli
November 7, 2015
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Carpathian, You've been participating on this blog for years. Yet, your comment at 368 illustrates that you do not have the first clue about what ID posits. Since you've been exposed to the truth countless times, I can only surmise that you are either blindingly stupid or willfully ignorant, or perhaps both. Please try to do better. I won't be holding my breath.Barry Arrington
November 7, 2015
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kairosfocus, Show me how a non-living, non-god entity, that cannot control the physics of the universe, is able to design and then distribute life. Since the ID designer pre-dates life, he cannot be alive and also cannot be God if ID is to be taken as science.Carpathian
November 7, 2015
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kairosfocus:
BTW, on life, I’d suggest that several generations of Moore’s law scaling point to pretty awesome computing power so I remain at the point, molecular nanotech lab is all that is required.
Since this lab had to exist before life did, who would be running it? It couldn't have been God since God doesn't need computers. Since it wasn't God and it was not a living being, I'm going to say with some confidence that the lab never existed. Other than the God of Genesis then, there is no plausible designer.Carpathian
November 7, 2015
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Thanks gpuccio, I understand what you are saying and respect it. You've provided a good example. But you can always keep me honest if I say anything dumb. :)Mung
November 7, 2015
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Mung: There’s also an enzyme that detaches the amino acid from the tRNA so that it can be added to the peptide chain. Alicia Cartelli: What enzyme is that?
Peptidyl transferases are also a type of aminoacyltransferase that catalyze the formation of peptide bonds, as well as the hydrolytic step that leads to the release of newly synthesized proteins off the tRNA. wikipedia
The tRNA needs to be detached. It doesn't just detach by magic. (Well, perhaps we are seeing real magic in action.)Mung
November 7, 2015
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gpuccio: The claim is that semiotic systems include a necessary discontinuity, and that they are always the result of conscious design. Which is the claim? 1. Semiotic systems are always the result of conscious design because they include a necessary discontinuity. 2. The subset of semiotic systems which include a necessary discontinuity are always the result of conscious design. If #1, then it's an argument from irreducibility applied to a specific case. If so, we can rewrite the claim as 'systems with a necessary discontinuity, e.g. semiotic systems, are always the result of conscious design.' We presume #2 is not the case, as the post seems to suggest that a necessary discontinuity is inherent in semiotic systems.Zachriel
November 7, 2015
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Alicia Cartelli:
Do I need to find a pop-up book?
Probably not for gpuccio, but I'd sure love to have one! My cartoon guide to genetics has nice pictures but they don't pop up and my complete idiot's guide, well, that's for idiots.Mung
November 7, 2015
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Box: The commentary at evolutionnews.org eloquently explains why Sorting implies an historical sifting process.Zachriel
November 7, 2015
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Upright BiPed: So, an RNA template replicator exists. A complex network of RNA and peptides. Upright BiPed: Then a DNA molecule – with a purpose – takes over. Perhaps virally. There's no "purpose" in the sense of having a conscious choice, but something that provides a stepwise selective advantage. Upright BiPed: nor can anyone falsify anything you wish to propose from that faith. The argument in the original post is that semiotic systems include a necessary discontinuity, and that they are always the result of conscious design. To contradict this assertion, it is only necessary to provide a plausible pathway, not necessarily the historical transition. However, we would point out there is evidence that DNA synthesis appears to be a relic of RNA metabolism, and some families of DNA polymerases are likely homologous with RNA polymerases.Zachriel
November 7, 2015
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Alicia Cartelli,
Earlier work also uncovered the existence of a pronounced bias in the relationship between amino acid hydrophobicity and the genetic code. Thus, a pyrimidine at the second codon position signals amino acids whose average hydrophobicity is much greater than those coded by a purine at the same position (2, 3). The values reported here allow a more detailed analysis, described in a companion paper (16), which reveals that two separate codes for amino acid size and hydrophobicity appear to be embedded in different parts of their tRNA sequences, with size (represented by vapor-to-cyclohexane equilibria) encoded in the acceptor stem, and hydrophobicity (represented by water-to-cyclohexane equilibria) embedded in the anticodon.
Here (and elsewhere in their paper) Carter and Wolfenden seem to suggest that the genetic code and the protein code may be linked to “hydrophobicity” and “size” respectively. Clearly, this is an absurd attempt to explain the codes and the bridge between them. The commentary at evolutionnews.org eloquently explains why:
At best, he gets piles of amino acids with similar properties and folds. That's not selection; that's just sorting. You can find that in riverbeds where rocks of various sizes sort themselves out in layers. Those "patterns" are even "preserved", but that constitutes neither a code nor a specification.
Box
November 7, 2015
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Mung: "I love having gpuccio around as well to help keep them honest about the biochemical details." Thank you. I am in a delicate position. I don't want to discuss with Alicia Cartelli, because I don't like her attitude, absolutely offensive and unrespectful of others, and her inability to understand what a discussion is. However, I have a few things to say, so I will say them to you and to all who are interested. ATP synthase is a complex molecule, and a very conserved one. It is essentially formed by 2 parts, FO and F1. The most conserved sequences are those in subunits alpha and beta of the F1 structure. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex. Gamma, delta and epsilon sequences also contribute to F1. Subunits A, B and C are the main components of FO. The sequences which I have always debated here at UD as an example of extremely conserved functional sequences are the alpha and beta subunits of F1. That can easily be verified, in all my posts on the subject, for example here: https://uncommondescent.com/intelligent-design/four-fallacies-evolutionists-make-when-arguing-about-biological-function-part-1/ The paper linked by Alicia Cartelli is a very good paper about the structural and functional properties of ATP synthase, in particular the interactions between its different parts. It does show that many residues are critically conserved and have important functions in those interactions, while other parts are less conserved, or not conserved. And so? What it does not show is the desgree of conservation of the alpha and beta subunits of F1. I quote:
The sequence alignment of the gamma subunit shows that the overall sequence is not that conserved in comparison to the alpha and beta subunits, although subunit gamma is one of the essential subunits for the function of the F1 motor
The paper then analyzes subunit gamma, and the subunits of FO. Just as a reminder, I have blasted again the human beta subunit of F1 against bacteria. The first hit (Azospirillum halopraeferens) shows an alignment of 479 AAs (out of 529): Identities:392/479(82%) Positives: 425/479(88%) Expect (obviously!): 0.0 The 106th hit (the last in my first page of results, Kiloniella sp.) shows an alignment of 457 AAs (out of 529): Identities:366/457(80%) Positives: 403/457(88%) Expect (obviously!): 0.0 Does anyone want to argue that these are not extremely conserved sequences? Just for the record.gpuccio
November 7, 2015
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Then show us your reverse engineered system!Andre
November 6, 2015
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Andre, you're grasping at straws and barely making sense. I've explained my system multiple times now and you seem to lack any coherent response. You've reached the end of your usefulness. Take care now!Alicia Cartelli
November 6, 2015
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Alicia And the fact that you are doing some reverse engineering work also seem to have escaped you. What is a trade off and how does it apply to engineering? http://link.springer.com/article/10.1007%2FBF01581342 And what on earth is reverse engineering? http://searchsoftwarequality.techtarget.com/definition/reverse-engineeringAndre
November 6, 2015
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Alicia A Trade off is of course and engineering term. Don't let it go lost on you. Seriously though if you have a hypothetical then please can you share your findings so you can shut us up once and for all. Have you ever considered that all we want is to be proven wrong?Andre
November 6, 2015
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Kairos, I never said this work was a breakthrough, only that my hypothetical “first translational system” was based on some of the findings in these papers. Don’t get your panties in a bunch. Box, evolutionnews “debunked” that paper? Get real. The majority of what evolutionnews talks about in that link is the UNC press release. And pretty much everything they say is either wrong or demonstrates a fundamental misunderstanding. Mungy, for the third time now, my system translates using the same template that would be used for replication, but amino acids are also present in the active site now. Amino acid sequence is controlled by chemical interactions with the nucleotides of the template and the code would be something like this: purine base - polar amino acid, pyrimidine base - hydrophobic amino acid. Joining these amino acids together by the active site creates an amino acid sequence based on the nucleic acid template sequence: translation. My system does not use tRNA, it is a much simpler system, but also a much less efficient system than that which we see today. There are always trade-offs in biology, but the ability to create the first proteins would be well worth it for life. “There’s also an enzyme that detaches the amino acid from the tRNA so that it can be added to the peptide chain.” What enzyme is that? You think Gpuccio is keeping anyone “honest about the biochemical details?” That’s a good one. He doesn’t even understand basic biology. He’s still trying to figure out how little of the peptide sequences in ATP synthase subunits are actually conserved across species. This is after I gave him a paper that shows him how wrong he is in picture form. Do I need to find a pop-up book?Alicia Cartelli
November 6, 2015
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The key to the translation system would appear to be the transfer RNA (tRNA). Have either Zachriel or Alicia addressed that? Or it could be the assignment enzyme, which attaches the appropriate amino acid to the tRNA. Perhaps both are needed. There's also an enzyme that detaches the amino acid from the tRNA so that it can be added to the peptide chain. And, of course, there is the ribosome. I love having gpuccio around as well to help keep them honest about the biochemical details. Even a dumbed down system is still quite complex. Again from John Maynard Smith and Eors Szathmary: We have, therefore, no intermediate between a complete system [of translation] and no system at all to guide us in guessing at it's evolution. It's like the missing link from hell.Mung
November 6, 2015
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According to John Maynard Smith and Eors Szathmary, "RNA is therefore suitable as the genetic material only in organisms with very small genomes." Now in addition to that problem, RNA, not being double-stranded like DNA, can fold on itself to take on a 3D shape. Of course, that would also hinder the utility of RNA as genetic material.Mung
November 6, 2015
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Alicia Cartelli:
You asked for the papers that I based my hypothetical system on, I provided them.
Your hypothetical system went from no translation to translation as if by magic. Any plans to fill in the missing pieces in your hypothetical system?Mung
November 6, 2015
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kf, Fear of the divine foot.Mung
November 6, 2015
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Alicia Cartelli: Carter & Wolfenden (2015) PNAS
For those interested, that paper has been debunked at good ol' evolutionnews.org.Box
November 6, 2015
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Mung, please explain. KFkairosfocus
November 6, 2015
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Alicia, hints and suggestions that on reasonable grounds, exaggerate the significance. How do I know that? Had there been a genuine breakthrough, it would have been trumpeted from the roofs and we would hear that announced with fanfares and drum rolls year by year, day by day over these past 30 years since. We are not seeing that, so immediately you are going beyond what is reasonably warranted, making unwarranted extrapolations that do not squarely answer to the origin of relevant information and organisation. The want of substantial details sends much the same message. KFkairosfocus
November 6, 2015
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Alicia A good day to you too and when you actually have anything be so kind to inform us. RegardsAndre
November 6, 2015
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F/N2: Wicken, 1979:
‘Organized’ systems are to be carefully distinguished from ‘ordered’ systems. Neither kind of system is ‘random,’ but whereas ordered systems are generated according to simple algorithms [[i.e. “simple” force laws acting on objects starting from arbitrary and common- place initial conditions] and therefore lack complexity, organized systems must be assembled element by element according to an [[originally . . . ] external ‘wiring diagram’ with a high information content . . . Organization, then, is functional complexity and carries information. It is non-random by design or by selection, rather than by the a priori necessity of crystallographic ‘order.’ [[“The Generation of Complexity in Evolution: A Thermodynamic and Information-Theoretical Discussion,” Journal of Theoretical Biology, 77 (April 1979): p. 353, of pp. 349-65.]
FSCO/I is real, it is commonplace, it is informational, that information requires adequate causal explanation and the empirical evidence strongly points to design. That is what is on the table, and that is what is being ducked. KFkairosfocus
November 6, 2015
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