ATTN JVL, this is the new post dialogue box

_{kairosfocus

May 13, 2022

Intelligent Design}

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From screen shot:

No, authors cannot target a specific commenter.

U/D, May 15: How to contact UD and how to see weak argument corrections:

One trusts this is enough. END

F/N, May 14: It being now an obvious tactic to sidetrack non technical UD threads into ID debates (even where there is a thread that is live on the topic with relevant information, graphics and video) I will augment basic correction below by adding here a chart showing tRNA as a Drexler style molecular nanotech position-arm device:

We may expand our view of the Ribosome’s action:

The Ribosome, assembling a protein step by step based on the instructions in the mRNA “control tape”

As a comparison, here is punched paper tape used formerly to store digital information:

In Yockey’s communication system framework, we now can see the loading [blue dotted box] and how tRNA is involved in translation, as the AA chain towards protein formation is created, step by step — algorithm — under control of the mRNA chain of three base codons that match successive tRNA anticodons, the matching, of course is by key-lock fitting of G-C or C-G and A-T or T-A, a 4-state, prong height digital code:

Yockey’s analysis of protein synthesis as a code-based communication process

Further to this, DNA has been extended with other similar monomers, and DNA has been used as a general purpose information storage medium for digital codes, apparently even including for movie files.

The point of this is, for record, to expose and correct how hyperskeptical objectors have inappropriately tried to deny that D/RNA acts as a string based digital information storage unit, that it holds algorithmic code used in protein synthesis, and latterly that tRNA acts in this process in the role of a position-arm nanotech robot device with a CCA tool tip, CCA being a universal joint that attaches to the COOH end of an AA.

Speaking of which, AA structure, with side branches [R] and chaining links, i.e. NH2-alpha Carbon + R – COOH:

Comments

RNA World, KF. Evidence suggests RNA was acting as both template and catalyst prior to DNA adopting the template role and prior to proteins as catalysts. Indeed, RNA still plays a pivotal role as both template and catalyst in cellular metabolism.Fred Hickson_{May 14, 2022
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Kairosfocus: wordfence is a security service similar to disqus. Yes, I know what WordFence is; in the past I gave a link to its homepage and published some quotes. Disqus is not the same thing at all: https://disqus.com Since you didn't answer my questions I'll ask versions of them again: what WordFence settings or protocols am I violating when I get banned from commenting on a thread? If I know what triggers I'm triggering I can possibly avoid them. If you don't know then just say so. If you don't know then can you tell me who could answer those questions for this site please?JVL_{May 14, 2022
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JVL and FH, wordfence is a security service similar to disqus. None of these services is wholly satisfactory but they are better than the alternative given the amount of antisocial and outright criminal behaviour on the Internet. See https://wordpress.org/plugins/wordfence/ KFkairosfocus_{May 14, 2022
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FH, chicken-egg loops are common issues on origin of life studies; here, which comes first, the tRNA that helps to assemble proteins (including enzymes) or the enzyme that loads it with the correct AA. Second, a position-arm device with a tool tip is reasonably describable in such terms. Third, you may find it advisable to reconsider given here on: https://uncommondescent.com/intelligent-design/casey-luskin-asks-can-claims-about-punctuated-equilibrium-accommodate-the-scientific-data/#comment-754466 KF PS, Just for information for those willing to think outside the box, https://www.writingsbyraykurzweil.com/the-drexler-smalley-debate-on-molecular-assembly
. . . It was left to Eric Drexler to found the modern field of nanotechnology, with a draft of his seminal Ph.D. thesis in the mid 1980s .. . Drexler described a Von Neumann Kinematic Constructor, which for its “sea of parts” used atoms and molecular fragments, as suggested in Feynman’s speech. Drexler’s vision cut across many disciplinary boundaries, and was so far reaching, that no one was daring enough to be his thesis advisor, except for my own mentor, Marvin Minsky. Drexler’s doctoral thesis (premiered in his book, Engines of Creation in 1986 and articulated technically in his 1992 book Nanosystems) laid out the foundation of nanotechnology and provided the road map still being pursued today. Von Neumann’s Universal Constructor, as applied to atoms and molecular fragments, was now called a “universal assembler.” Drexler’s assembler was universal because it could essentially make almost anything in the world. A caveat is in order here. The products of a universal assembler necessarily have to follow the laws of physics and chemistry, so only atomically stable structures would be viable. Furthermore, any specific assembler would be restricted to building products from its sea of parts, although the feasibility of using individual atoms has been repeatedly demonstrated. Although Drexler did not provide a detailed design of an assembler, and such a design has still not been fully specified, his thesis did provide extensive existence proofs for each of the principal components of a universal assembler, which include the following subsystems: - The computer: to provide the intelligence to control the assembly process. As with all of the subsystems, the computer needs to be small and simple. Drexler described an intriguing mechanical computer with molecular “locks” instead of transistor gates. Each lock required only 5 cubic nanometers of space and could switch 20 billion times a second. This proposal remains more competitive than any known electronic technology, although electronic computers built from three-dimensional arrays of carbon nanotubes may be a suitable alternative. - The instruction architecture: Drexler and his colleague Ralph Merkle have proposed a “SIMD” (Single Instruction Multiple Data”) architecture in which a single data store would record the instructions and transmit them to trillions of molecular-sized assemblers (each with their own simple computer) simultaneously. Thus each assembler would not have to store the entire program for creating the desired product. This “broadcast” architecture also addresses a key safety concern by shutting down the self-replication process if it got out of control by terminating the centralized source of the replication instructions. However, as Drexler points out[1], a nanoscale assembler does not necessarily have to be self-replicating. Given the inherent dangers in self-replication, the ethical standards proposed by the Foresight Institute contain prohibitions against unrestricted self-replication, especially in a natural environment. - Instruction transmission: transmission of the instructions from the centralized data store to each of the many assemblers would be accomplished electronically if the computer is electronic or through mechanical vibrations if Drexler’s concept of a mechanical computer were used. - The construction robot: the constructor would be a simple molecular robot with a single arm, similar to Von Neumann’s kinematic constructor, but on a tiny scale. The feasibility of building molecular-based robot arms, gears, rotors, and motors has been demonstrated in the years since Drexler’s thesis . . . - The robot arm tip: Drexler’s follow-up book in 1992, Nanosystems: molecular machinery, manufacturing, and computation, provided a number of feasible chemistries for the tip of the robot arm that would be capable of grasping (using appropriate atomic force fields) a molecular fragment, or even a single atom, and then depositing it in a desired location. We know from the chemical vapor deposition process used to construct artificial diamonds that it is feasible to remove individual carbon atoms, as well as molecular fragments that include carbon, and then place them in another location through precisely controlled chemical reactions at the tip. The process to build artificial diamond is a chaotic process involving trillions of atoms, but the underlying process has been harnessed to design a robot arm tip that can remove hydrogen atoms from a source material and deposit it at desired location in a molecular machine being constructed. In this proposal, the tiny machines are built out of a diamond-like (called “diamondoid”) material. In addition to having great strength, the material can be doped with impurities in a precise fashion to create electronic components such as transistors. Simulations have shown that gears, levers, motors, and other mechanical systems can also be constructed from these carbon arrays. Additional proposals have been made in the years since, including several innovative designs by Ralph Merkle [2]. In recent years, there has been a great deal of attention on carbon nanotubes, comprised of hexagonal arrays of carbon atoms assembled in three dimensions, which are also capable of providing both mechanical and electronic functions at the molecular level. - The assembler’s internal environment needs to prevent environmental impurities from interfering with the delicate assembly process. Drexler’s proposal is to maintain a near vacuum and build the assembler walls out of the same diamondoid material that the assembler itself is capable of making. - The energy required for the assembly process can be provided either through electricity or through chemical energy. Drexler proposed a chemical process with the fuel interlaced with the raw building material. More recent proposals utilize nanoengineered fuel cells incorporating hydrogen and oxygen or glucose and oxygen. Although many configurations have been proposed, the typical assembler has been described as a tabletop unit that can manufacture any physically possible product for which we have a software description. Products can range from computers, clothes, and works of art to cooked meals. Larger products, such as furniture, cars, or even houses, can be built in a modular fashion, or using larger assemblers. Of particular importance, an assembler can create copies of itself. The incremental cost of creating any physical product, including the assemblers themselves, would be pennies per pound, basically the cost of the raw materials. The real cost, of course, would be the value of the information describing each type of product, that is the software that controls the assembly process. Thus everything of value in the world, including physical objects, would be comprised essentially of information. We are not that far from this situation today, since the “information content” of products is rapidly asymptoting to 100 percent of their value. In operation, the centralized data store sends out commands simultaneously to all of the assembly robots. There would be trillions of robots in an assembler, each executing the same instruction at the same time. The assembler creates these molecular robots by starting with a small number and then using these robots to create additional ones in an iterative fashion, until the requisite number of robots has been created. Each local robot has a local data storage that specifies the type of mechanism it is building . . .
In short, there was a molecular nanotech background context for my terms, apart from the rather obvious one of simple recognition of tRNA's function. But then, one can also see the neck-head beak structures of a bird as a similar position arm robot with a built in sensor turret. Ponder, birds building nests and feeding their young with worms.kairosfocus_{May 14, 2022
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KF
Notice, the tRNA is in effect a molecular nanotech position-arm robot with a CCA universal joint tool tip at one end and an anticodon key-lock fit element at the other. Chemically, any AA can attach to any TRNA but there is enzyme control of which goes to which, hence, loading. Enzymes are of course proteins synthesised by the protein synthesis process, there is a chicken-egg first reflexive causal loop. And so forth.
I mean... Nope, words fail me. Robot arms? Chicken-egg?. First understand, KF, then criticize.Fred Hickson_{May 13, 2022
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Re Wordfence. What is it designed to achieve? Is there something useful it is doing to offset the false positives. An ID experiment is called for. Disable the plugin and observe the result.Fred Hickson_{May 13, 2022
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And there are people who insist that Stonehenge is a natural formation.
Are there? Depends what the antonym of "natural" is, I guess. Unnatural? Well, I don't think the structure is unnatural and not heard anyone promoting the idea. Supernatural? Did von Däniken claim this for his space aliens? Didn't catch on. Artificial? The etymology (from the Latin "made by artisans") seems spot on. Stonehenge was envisaged, designed and built by people with purpose and for a purpose, even we do not know the names of individuals nor the precise details of their reasons.Fred Hickson_{May 13, 2022
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Kairosfocus: you have been triggering WF spam, hacking etc protocols What are they? If I know what they are I can attempt to avoid them.JVL_{May 13, 2022
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Plus glacial deposits, like drop stones. And drop stones from prehistoric floods. Earthquakes flaking off huge stones.ET_{May 13, 2022
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Lieutenant Commander Data @13,
“Evolved almost inevitably”
Wow, "inevitably" is a way-cooler way to say MUSTA or MIGHTA, but it means the same thing. ET @18, The term that geologists use is "differential erosion." -QQuerius_{May 13, 2022
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JVL:
But my point was that people were taking the idea seriously and doing research about it. And that clearly is true.
And there are people who insist that Stonehenge is a natural formation.ET_{May 13, 2022
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JVL, as for speculations on D/RNA codons and protein codes, you are looking at guesswork. Worse, it compounds it by imagining there were prior metabolic process flow networks and linked cell replication etc that were unobserved. Rube Goldberg would have been proud. The highly speculative nature is clear from your clips. As it is, I can again refer you to L&FP 55, OP, the communication system chart from Yockey, as annotated. See https://uncommondescent.com/intelligent-design/lfp-55-defining-clarifying-intelligent-design-as-inference-as-theory-as-a-movement/ Note there, the blue curved dotted box. When tRNA folds, its anticodon is at one end and a tip for attaching AAs is at the other, out of range of chemical determination. In effect, CODON =A-C ----CCA tip, with AA load point. The tip carries the common code CCA, and can load to any AA at the COOH end. The loading enzyme detects the configuration of the tRNA and loads the required AA, this is where the encoding happens. And, it happens at a universal joint. This has been used to generate novel AA chains. KF PS, again, Wikipedia's admissions:
While the specific nucleotide sequence of an mRNA specifies which amino acids are incorporated into the protein product of the gene from which the mRNA is transcribed, the role of tRNA is to specify which sequence from the genetic code corresponds to which amino acid.[3] The mRNA encodes a protein as a series of contiguous codons, each of which is recognized by a particular tRNA. One end of the tRNA matches the genetic code in a three-nucleotide sequence called the anticodon. The anticodon forms three complementary base pairs with a codon in mRNA during protein biosynthesis. On the other end of the tRNA is a covalent attachment to the amino acid that corresponds to the anticodon sequence. Each type of tRNA molecule can be attached to only one type of amino acid, so each organism has many types of tRNA. Because the genetic code contains multiple codons that specify the same amino acid, there are several tRNA molecules bearing different anticodons which carry the same amino acid. The covalent attachment to the tRNA 3’ end is catalyzed by enzymes called aminoacyl tRNA synthetases. During protein synthesis, tRNAs with attached amino acids are delivered to the ribosome by proteins called elongation factors, which aid in association of the tRNA with the ribosome, synthesis of the new polypeptide, and translocation (movement) of the ribosome along the mRNA. If the tRNA's anticodon matches the mRNA, another tRNA already bound to the ribosome transfers the growing polypeptide chain from its 3’ end to the amino acid attached to the 3’ end of the newly delivered tRNA, a reaction catalyzed by the ribosome . . . . The acceptor stem is a 7- to 9-base pair (bp) stem made by the base pairing of the 5?-terminal nucleotide with the 3?-terminal nucleotide (which contains the CCA 3?-terminal group used to attach the amino acid) . . . The CCA tail is a cytosine-cytosine-adenine sequence at the 3? end of the tRNA molecule. The amino acid loaded onto the tRNA by aminoacyl tRNA synthetases, to form aminoacyl-tRNA, is covalently bonded to the 3?-hydroxyl group on the CCA tail.[9] This sequence is important for the recognition of tRNA by enzymes and critical in translation.[10][11] . . . The anticodon arm is a 5-bp stem whose loop contains the anticodon.[6] The tRNA 5?-to-3? primary structure contains the anticodon but in reverse order, since 3?-to-5? directionality is required to read the mRNA from 5?-to-3?.
Notice, the tRNA is in effect a molecular nanotech position-arm robot with a CCA universal joint tool tip at one end and an anticodon key-lock fit element at the other. Chemically, any AA can attach to any TRNA but there is enzyme control of which goes to which, hence, loading. Enzymes are of course proteins synthesised by the protein synthesis process, there is a chicken-egg first reflexive causal loop. And so forth.kairosfocus_{May 13, 2022
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JVL, you have been triggering WF spam, hacking etc protocols. KFkairosfocus_{May 13, 2022
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Right here is the error message I just got when trying to post at: https://uncommondescent.com/intelligent-design/casey-luskin-asks-can-claims-about-punctuated-equilibrium-accommodate-the-scientific-data/#comment-754615
A potentially unsafe operation has been detected in your request to this site Your access to this service has been limited. (HTTP response code 403) If you think you have been blocked in error, contact the owner of this site for assistance. Block Technical Data Block Reason: A potentially unsafe operation has been detected in your request to this site Time: Fri, 13 May 2022 20:43:28 GMT About Wordfence Wordfence is a security plugin installed on over 4 million WordPress sites. The owner of this site is using Wordfence to manage access to their site. You can also read the documentation to learn about Wordfence's blocking tools, or visit wordfence.com to learn more about Wordfence.
This happens to me all the time.JVL_{May 13, 2022
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ET: On the whole, it appears that the aptamer experiments, although suggestive, fail to clinch the case for the stereochemical theory of the code. As noticed earlier, the affinities are rather weak, so that even the conclusions on their reality hinge on the adopted statistical models. But my point was that people were taking the idea seriously and doing research about it. And that clearly is true.JVL_{May 13, 2022
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JVL Genetic code evolved almost inevitably, study finds The idea that the genetic code may have originated via chemical affinities
:lol: JVL , this is not science . "Evolved almost inevitably" is allowed to Shakespeare or Milton not to scientific "researchers". PS: Search for "Cellular signal processing", "signal transduction" to get a taste about the complexity of a cell.Figure that : There are like in human society : NEWS TV "public signalling processes "(endocrine system ) and FBI "private signalling processes" ( the nervous system) :)Lieutenant Commander Data_{May 13, 2022
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Origin and evolution of the genetic code: The universal enigma:
On the whole, it appears that the aptamer experiments, although suggestive, fail to clinch the case for the stereochemical theory of the code. As noticed earlier, the affinities are rather weak, so that even the conclusions on their reality hinge on the adopted statistical models. Even more disturbing, for different amino acids, the aptamers show enrichment for either codon or anticodon sequence or even for both (76), a lack of coherence that is hard to reconcile with these interactions being the physical basis of the code.
ET_{May 13, 2022
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OK, thank you. So, there aren't any chemical affinities between mRNA and amino acids in the current system.ET_{May 13, 2022
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ET: Sigh. The Genetic Code and RNA-Amino Acid Affinities
A significant part of the genetic code likely originated via a chemical interaction, which should be experimentally verifiable. One possible verification relates bound amino acids (or perhaps their activated congeners) and ribonucleotide sequences within cognate RNA binding sites. To introduce this interaction, I first summarize how amino acids function as targets for RNA binding. Then the experimental method for selecting relevant RNA binding sites is characterized. The selection method's characteristics are related to the investigation of the RNA binding site model treated at the outset. Finally, real binding sites from selection and also from extant natural RNAs (for example, the Sulfobacillus guanidinium riboswitch) are connected to the genetic code, and by extension, to the evolutionary progression that produced the code. During this process, peptides may have been produced directly on an instructive amino acid binding RNA (a DRT; Direct RNA Template). Combination of observed stereochemical selectivity with adaptation and co-evolutionary refinement is logically required, and also potentially sufficient, to create the striking order conserved throughout the present coding table.
https://pubmed.ncbi.nlm.nih.gov/28333103/ published in 2017. The chemical basis for the origin of the genetic code and the process of protein synthesis
The major thrust is to understand just how the process of protein synthesis, including that very important aspect, genetic coding, came to be. Two aspects of the problem: the chemistry of active aminoacyl species; and affinities between amino acids and nucleotides, and specifically, how these affinities might affect the chemistry between the two are stressed.
https://ntrs.nasa.gov/citations/19830017073 published in 1982. So, not a new idea. Evolution of the Genetic Code: The Ribosome-Oriented Model
There are currently three major theories on the origin and evolution of the genetic code: the stereochemical theory, the coevolution theory, and the error-minimization theory. The first two assume that the genetic code originated respectively from chemical affinities and from metabolic relationships between codons and amino acids. The error-minimization theory maintains that in primitive systems the apparatus of protein synthesis was extremely prone to errors, and postulates that the genetic code evolved in order to minimize the deleterious effects of the translation errors. This article describes a fourth theory which starts from the hypothesis that the ancestral genetic code was ambiguous and proposes that its evolution took place with a mechanism that systematically reduced its ambiguity and eventually removed it altogether. This proposal is distinct from the stereochemical and the coevolution theories because they do not contemplate any ambiguity in the genetic code, and it is distinct from the error-minimization theory because ambiguity-reduction is fundamentally different from error-minimization. The concept of ambiguity-reduction has been repeatedly mentioned in the scientific literature, but so far it has remained only an abstract possibility because no model has been proposed for its mechanism. Such a model is described in the present article and may be the first step in a new approach to the study of the evolution of the genetic code
https://philpapers.org/rec/BAREOT-9 published in 2015. Genetic code evolved almost inevitably, study finds
Researchers studying the beginnings of human life on Earth say that the development of the genetic code was an inevitable consequence of naturally-occurring chemical relationships between nucleotides and amino acids. By piecing together how 'Ida' and 'Luca' - what scientists call the initial Darwinian ancestor and the last universal common ancestor - assembled themselves from the chemicals thought to be present on the primordial Earth, international research teams are closer to understanding how organisms developed the ability to, not only self-replicate, but store genetic information.
https://www.bionews.org.uk/page_92305 published in 2010. The idea that the genetic code may have originated via chemical affinities is not new and has been examined for quite a while. So, can we dispense with the idea that no one is taking this idea seriously or that it's not a real possibility? Not saying you agree with it but can you at least admit it's a viable option? If you think it's not a viable option then can you at least have the respect to give specific and clear biological and chemical reasons why it isn't? If you have a real, clear and scientific objection then please give it.JVL_{May 13, 2022
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JVL:
You could do a literature search and read some research.
I have. It's a given that I have done so more than you have. So, you can huff and bluff all you want.ET_{May 13, 2022
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ET: I would love to hear about the alleged chemical affinities between mRNA codons and amino acids. You could do a literature search and read some research. I know you'd rather I did a lot of work tracking down references for you but I've been down that road before and I can't recall a time when that ever generated a different response from what you had already given. From your point of view that's because the work I cite doesn't contradict your statements but it's pretty clear that some of it does and you don't really want to engage with the actual work and research. IF you're really interested you'll search out things that might question your beliefs; I do that for myself all the time because I want to know if I'm wrong. If you're sure you're right to the point that you don't actually have a falsification criteria that you can not only specify but stick with . . . then you won't bother. I'll leave it up to you.JVL_{May 13, 2022
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Kairosfocus: I fully believe that you, personally, would not limit access to the site without first giving fair warning and explaining why. I also believe you are being completely honest regarding your understanding of the phenomena. What I also know is that I frequently get banned from threads after publishing a few replies. I know not to make my replies too long; I know not to use profanity; I try not to cast aspersions on other people's view s or opinion (but I suspect I tread the line sometimes). Recently all the bans have been generated by WordFence with a particular error saying I was trying to do something 'illegal' or not allowed. This makes no sense whatsoever as I do not think I am clearly violating any site rule. Disagreeing with some views is NOT verboten I hope. If I need to slow down the frequency of my replies I can do that. If I need to limit the number of my replies . . . I can work on that. What I don't know and, it seems, no one knows is why I am frequently falling foul of the site security as that is what WordFence is about. There must be some setting that I am tripping. I wish someone could tell me what was causing the fouls. It must tripped for individual threads since being banned from one does not (immediately anyway) mean being banned from others. Sometimes thread bans last days and days, sometimes not. If my transgression is based on some objective measure then it potentially could affect any commenter. I would think the site admins would want to be sure that the observed site behaviour is what they want.JVL_{May 13, 2022
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Thank you, Kairosfocus! This problem has also happened to me randomly but infrequently. Usually, I also see my comments appear instantly as Martin_r noted, but sometimes not. You've posted that there have been these kinds of problems several times before, but I noticed that some people here jumped to the conclusion that they were being "locked out" of a thread and then others ungenerously piled on about UD. I think they owe you an apology. -QQuerius_{May 13, 2022
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i can understand JVL's paranoia .... I also run a WORD PRESS blog (http://www.stuffhappens.info) and as far as i know, there is an optional settings, that comments have to be approved by moderator before published. So in theory, JVL's comments can be 'banned' by not approving it. But i doubt this is the case with UD, because all comments (not only JVL's) have to be approved one by one before published, and i can't imagine that UD administrator spends so much time with approving comments, moreover, my comments appear instantly ... so obviously, there is no moderator approving the comments one by one...martin_r_{May 13, 2022
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Oh. I thought it was a thread for JVL to post comments to and answer questions so he didn't muck up other threadsET_{May 13, 2022
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ET, you cross threaded. This is to show JVL that authors cannot target particular commenters here at UD. KFkairosfocus_{May 13, 2022
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I would love to hear about the alleged chemical affinities between mRNA codons and amino acids. Especially given the fact that the two molecules never touch. Is it some new phenomena called chemical affinities at a distance?ET_{May 13, 2022
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ATTN JVL, this is the new post dialogue boxkairosfocus_{May 13, 2022
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