Intelligent Design

Stunning Levels of Ignorance Regarding the Genetic Code

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ID critic Ed George was asked the following question: “Are you suggesting that the genetic code works through a series of chemical reactions?”

His response: “Duh!”

When asked to elucidate, he wrote the following comment:

DNA is a chemical (deoxyribonucleic acid). It interacts with other chemicals (e.g., transcriptase) to form yet other chemicals (e.g., RNA) that reacts with other chemicals (e.g., amino acids) to form other chemicals (e.g., proteins). This is admittedly overly simplified, but there is nowhere in this process that does not involve chemical reactions.

It is astonishing that someone who purports to be able to describe how DNA works (even on a simplified basis) would display such ignorance. Every educated person — theist, atheist, materialist, monist, dualist, etc. — knows that at a fundamental level DNA is about information. It is called the genetic code for a reason. Consider the very first line of the Wiki entry:

The genetic code is the set of rules used by living  cells to translate information encoded within genetic material (DNA or mRNA sequences of nucleotide triplets, or codons) into proteins.

This is not the least bit controversial, as evidenced by the fact that Wiki did not censor it as it censors anything with the slightest whiff of pro-ID slant. Yet here is EG coming into these pages and pronouncing it is all accomplished through “chemical reactions.” Graphite is a chemical. Carbon is a chemical. Ed seems to believe that a sentence written in pencil on a piece of paper can be accounted for completely by the interaction of the graphite and carbon.

Stunning. Only a person blinded by materialist dogma would express these views.

89 Replies to “Stunning Levels of Ignorance Regarding the Genetic Code

  1. 1
    orthomyxo says:

    I mean… transcription and translation are a series of chemical reactions…

    Do you have a different meaning of genetic code than is typical? In genetics, the genetic code is specifically the way in which DNA codons are translated into amino acids.

  2. 2
    awstar says:

    DNA is a chemical (deoxyribonucleic acid). It interacts with other chemicals (e.g., transcriptase) to form yet other chemicals (e.g., RNA) that reacts with other chemicals (e.g., amino acids) to form other chemicals (e.g., proteins). This is admittedly overly simplified, but there is nowhere in this process that does not involve chemical reactions.

    Well described; like someone who can draw a flowchart without any skill or knowledge of how to write the code for the functionality that the boxes in the chart represent.
    Ed George must be a salesman, a consultant, a professor or a politician.

  3. 3
    Barry Arrington says:

    Orthomyxo,
    You seem to be suggesting that the transcription and translation process can be reduced to the properties of the chemicals involved. Stunning. You seem to have no conception of what the word “translation” means. From your comment, I assume you think that “translation” is a chemical reaction. I am gobsmacked.

  4. 4
    orthomyxo says:

    Again, I think you might be missing the meaning of translation in molecular biology. Translation is tRNAs binding to complementary nucleotides so rRNA can catalyse the formation of peptide bonds.

  5. 5
    Barry Arrington says:

    And you seem to be missing the meaning of the word “translation” period full stop. The Wiki articles goes on:

    Translation is accomplished by the ribosome, which links amino acids in an order specified by messenger RNA (mRNA), using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. . . .The code defines how codons specify which amino acid will be added next during protein synthesis. With some exceptions, a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid. The vast majority of genes are encoded with a single scheme (see the RNA codon table). That scheme is often referred to as the canonical or standard genetic code, or simply the genetic code, though variant codes (such as in human mitochondria) exist.

    I assume you do not have an idiosyncratic understanding of the genetic code and thus agree with this general description. No one (except perhaps you and Ed George) believes that the information embedded in DNA, or the system by which that information is accessed and used to specify the amino acid that will be added next during protein synthesis can be reduced to the properties of the chemicals involved. It is astonishing that you would pretend otherwise. Though, given the way you like to play fast and loose with the facts, I suppose I shouldn’t be surprised.

  6. 6
    Ed George says:

    I must say, Barry never disappoints. 🙂

  7. 7
    orthomyxo says:

    It’s up to you to decide if the information in DNA is from selection or authorship. But it’s absolutely the case that the next amino acid in a developing protein is determined by chemistry. That’s how the genetic code works.

  8. 8

    .

    it’s absolutely the case that the next amino acid in a developing protein is determined by chemistry. That’s how the genetic code works.

    Neither the physical properties of the DNA or RNA triplet establish which amino acid is presented for binding in the ribosome. That is established independently (spatially and temporally) by the physical properties of the aaRS.

    This means the system is not reducible to dynamics, but to a specific type of organization, and further, to simultaneous coordination within that organization.

  9. 9
    Barry Arrington says:

    Ortho

    It’s up to you to decide if the information in DNA is from selection or authorship.

    Not even remotely the point. That the information exists is the point. I am glad you are willing to make that tiny concession (and thus align yourself with every living biologist). How the information came to be is a different matter.

    But it’s absolutely the case that the next amino acid in a developing protein is determined by chemistry.

    You still have not answered the question about whether you agree with Wiki’s description that I quoted above. I doubt you will. Because if you ever do you will be forced to admit that he next amino acid in a developing protein is determined by the information specified in the genetic code.

    That’s how the genetic code works.

    Said the man who seems to think that “chemistry” is a synonym for “information.”
    This is all the more astonishing given that you have already admitted that the information exists.
    Let me ask you this Ortho: Can the information in a book be reduced to the chemical properties of the paper and ink?
    Can the information in the genetic code by reduced to the chemical properties of the phosphates, sugars, and nitrogen of which the DNA molecule is made?

  10. 10
    Barry Arrington says:

    Ed George

    I must say, Barry never disappoints.

    A sneer is not the same as a defense of your augment Ed. You should write that down and refer to it from time to time, because you don’t seem to understand it.

  11. 11
    Barry Arrington says:

    Uh oh Orthomyxo, Upright Biped is on the case. You might as was well come out with your hands up now. It will be less humiliating for you that way.

  12. 12
    Ed George says:

    BA

    A sneer is not the same as a defense of your augment Ed.

    Since my defence needs no argument, I don’t know what else to give you. Pity? A referral to a mental health expert?

  13. 13

    .
    Ortho,

    Barry is obviously having a bit of fun with you in #11.

    I am no expert, but I do read a bit.

  14. 14
    Barry Arrington says:

    Ed George

    Since my defence needs no argument . . .

    Are you saying the truth of the statement is self-evident, that like the sentence “one plus one equals two” acceptance of the truth of your statement is compelled merely by understanding the meaning of the words employed? Wow. You have said some really stupid things over the years, but that takes it to a whole new level.

    Oh and before I part I notice that you have added a couple of ad hominems to the mix. Nice going!

  15. 15
    Barry Arrington says:

    UB at 13. I hope I didn’t scare him off. I just went for popcorn to munch while I watch you two cross swords.

  16. 16
    Barry Arrington says:

    Ed, I know you say your statement needs no defense. But for the sake of us dimwitted ID folks, why don’t you explain how the information in DNA can be accounted for by reference to chemical reactions among the phosphates, sugars, and nitrogen atoms of which the DNA molecule is made. I am sincerely curious about how you would support that position (other than by suggesting it is self-evidently true of course).

  17. 17
    orthomyxo says:

    Barry,

    Can I remind you that this thread started from you being incredulous thusly

    “Are you suggesting that the genetic code works through a series of chemical reactions?”

    The genetic code is, as your wiki link (which seems like a reasonable high-level explanation) describes, the means by which DNA bases are translated in proteins (via an mRNA intermediate). That process works through a series of chemical reactions. the production of mRNA is catalysed by RNA polymerase, the codons in the mRNA are translated into proteins via tRNAs that are complementary to the mRNA and the protein of a peptide is cayalued by RNAs. That’s how the genetic code works, and it’s a series of chemical reactions.

    Then you ask a question like this

    Can the information in the genetic code by reduced to the chemical properties of the phosphates, sugars, and nitrogen of which the DNA molecule is made?

    DNA is not the genetic code, so that’s a very odd question. You seem to be mixing technical and lay definitions of words like translate, code and information in a way that is very hard to extract any (ahem) information from.

  18. 18
    Barry Arrington says:

    Ortho

    That process works through a series of chemical reactions.

    You keep asserting that. Here’s a tip: An assertion is not a description or an explanation.
    Now I assume you are prepared to demonstrate how the “process works through a series of chemical reactions.” So by all means do so. Explain how the process can be accounted for solely by reference to chemical reactions. I’m ready, eager even, for what you are going to say next.
    Prediction: Literature bluff.

  19. 19
    Barry Arrington says:

    BTW Ortho, everyone noticed that you ignored Upright Biped’s comment at 8. Smart move on your point. You are totally outclassed. Smart, but kinda cowardly too. Life is full of tradeoffs.

  20. 20
  21. 21
    Barry Arrington says:

    Thanks KF.
    Ortho, please follow KF’s link and come back and tell us how all of that is a process that “works through a series of chemical reactions.” Or you can explain it to KF on his thread. Doesn’t matter. Still have lots of popcorn to go through.

  22. 22
    kairosfocus says:

    F/N The AA attachment to a tRNA is on a standard CCA tool tip, i.e. it is not determined by the anticodon on the other end. The AA is loaded based on a protocol carried out through loading processes. Indeed, the natural genetic code has been artificially extended by different loading protocols. KF

  23. 23

    .
    I think that Barry and Ed and Ortho are talking past each other, as sometime happens. When Barry uses the word “works” in his question (I believe) he is talking about the system result. When Ed sees the word “works” he takes the shortest route to the door. The truth is that it does not matter how the question is posed, the materialists on this blog will avoid the issue at every turn. Ed has certainly proven that, so has Sev, so has JVL, and the list goes on and on. Judging by the complete pass on my comment above in #8, we can likely add Ortho to that list. Who knows….

  24. 24
    orthomyxo says:

    Well, I’m not actualyl here to teach you highschool biology. But binding of codons to anti codons and the action of RNApol is all well-documented in many places.

    Upright BiPed’s comment gets us one layer deeper into the chemical reactions. The tRNA-ligases (also called aminoacyl-tRNA synthetase or aaRS) are the enzymes that link amino acids to a specific tRNA, but that’s chemistry too. There is one ligase for each tRNA (in vertebrates at least) and each bonds to a specific amino acid and specific loops in the appropriate tRNA. In a way, the tRNA-ligases are teh genetic code (the thing that associates codons to amnio acides via tRNAs and codons), and they do that work through chemistry.

  25. 25
    orthomyxo says:

    I will need a new code to decypher anything of meaning from KF’s post, I’m afraid!

  26. 26

    .
    Ortho, is the codon-to-anticodon association spatially and temporally independent of the anticodon-to-amino acid association?

  27. 27
    kairosfocus says:

    UB, that is the pivotal point, underscored by how AA attachment is to a STANDARD CCA tip. KF

  28. 28
    orthomyxo says:

    I don’t realyl know what you are getting at Upright, do you want to spell it out instead?

  29. 29
    Barry Arrington says:

    I will do color commentary:
    Ortho shows me he’s no coward and takes up the gauntlet. The essence of his argument:

    the tRNA-ligases are teh genetic code (the thing that associates codons to amnio acides via tRNAs and codons), and they do that work through chemistry.

    UB’s riposte:

    Ortho, is the codon-to-anticodon association spatially and temporally independent of the anticodon-to-amino acid association?

  30. 30
    ET says:

    Ortho:

    I mean… transcription and translation are a series of chemical reactions…

    There isn’t any chemical reaction that takes a mRNA codon and produces the proper amino acid. The codons are not used to make amino acids. The association between mRNA codons and amino acids is arbitrary, meaning it isn’t determined by physical laws.

    Just because there are chemical reactions throughout the process in no way means the genetic code is reducible to them.

  31. 31
    ET says:

    The ribosome is a genetic compiler. It takes the source code of mRNA codons and produces the object code of a functional protein. And it can even reject what it is translating if it finds a fault.

    The entire transcription and translation requires knowledge. It doesn’t just happen. There is knowledge of when to transcribe, what to transcribe and how to transcribe. Then there is editing and splicing. Again these don’t just happen. There has to be knowledge of what to edit and what to splice. Knowledge of how to process the mRNA before it goes to the ribosome.

    Again, if it was just chemical reactions then your scientists must be a bunch of dolts.

  32. 32

    .
    Ortho, I am having a hard time grasping how much more clear I can be. What do you not understand?

  33. 33
    ET says:

    tRNA? Did nature go shopping? They can’t even get one of the macromolecules (DNA, RNAs, proteins) involved in the process to form spontaneously.

  34. 34

    .
    Ortho,

    To specify a particular amino acid for binding during synthesis there must be (as you clearly suggest and seem to understand) two associations made.

    One of those associations is the codon-to-anticodon association, and the other is the anticodon-to-amino acid association.

    I am simply asking if those two chemical events are spatially and temporally independent of one another?

  35. 35
    orthomyxo says:

    I mean they are happening in a cell with lots of fluxes across time and heterogeneity in space. If you are trying to make some specific point that takes us beyond chemistry, please go ahead.

  36. 36

    .
    Good grief, Ortho.

    There is a point in time and space where an association is made between a codon and an anticodon. There is also a point in time and space when there is an association made between an anticodon and an amino acid.

    Are those two chemical events spatially and temporally independent of each other, or not?

    – – – – – – – – – – – – – – – – –

    EDIT: I am really finding it hard to believe that you cannot answer this question. Its been understood for well over half a century. Just follow the process that you yourself describe in comment #24 (following “Well, I’m not actually here to teach you highschool biology”). It is just a “yes” or “no”, actually, they are either spatially and temporally independent, or they are not.

  37. 37
    orthomyxo says:

    If you have a point, can you just make it? The question game is a waste of time.

    (edit: or if I just say “no” can we move on to you making a point?)

  38. 38

    .
    Actually, it is much better to have agreement on core observations if any understanding is to occur. Often ID critics visiting this blog steadfastly resist such efforts at core observations, simply because they do not want any understanding to occur.

    They are independent, Ortho. The establishment of the code is physicochemically independent of the reading of the codons, right?

  39. 39
    orthomyxo says:

    I ahve work to do today, so I’m not very interested in this trickle of questions. If you have an argument as to why the genetic code does not work through a series of chemical reactions please lay it out.

  40. 40
    Barry Arrington says:

    Color.
    Sparks fly as blades cross!

    UB tries to pin Ortho down on whether he agrees that the two key chemical events in the translation process are spatially and temporally independent of each other.

    Ortho resists, saying he does not understand what UB is getting at.

    Finally, UB comes right out and presents the key question: The establishment of the code is physicochemically independent of the reading of the codons, right?

    We wait breathlessly as Ortho prepares his response.

  41. 41
    Barry Arrington says:

    Wow!
    In a non-stunning move that surprises no one, Ortho responds with a classic burden-shifting-preliminary-to-summary-dismissal strategy.

    I ahve work to do today. If you have an argument as to why the genetic code does not work through a series of chemical reactions please lay it out.

    Ortho is the one who said it is chemical reactions all the way down. He sees exactly where UB is going with his “physicochemically independent” question. If he says yes, Ortho’s assertion comes tumbling to the ground. If he says no, he will look like an idiot as he is called on to demonstrate how that can possibly be given the overwhelming evidence that it is physicochemically independent. So what is a good materialist to do? “I’m too busy to answer your question. Make your point, so I can scoff at it and move on!”

    How will UB respond?

  42. 42
    Barry Arrington says:

    Ortho:

    I’m not very interested in this trickle of questions

    Well, it is not a trickle of questions. It is one question that you have so far (1) pretended not to understand; and (2) refused to answer when it was explained.

  43. 43

    .
    Ortho, by all means go on and do your work

    When you’ve freed up your mind from your work, you’ll find that the association between the codon and the amino acid is a discontinuous association. It is not established by dynamics, but by a) a specific type of organization, and b) simultaneous coordination between two independent sets of multiple sequences.

    That’s the way the system “works”.

  44. 44
    ET says:

    ortho:

    If you have an argument as to why the genetic code does not work through a series of chemical reactions please lay it out.

    The argument is that the genetic code didn’t arise via a series of chemical reactions. There isn’t any chemical reaction(s) that take a mRNA codon and produces an amino acid using it. As Upright Biped said there is a discontinuous association.

  45. 45
    orthomyxo says:

    When you’ve freed up your mind from your work, you’ll find that the association between the codon and the amino acid is a discontinuous association. It is not established by dynamics, but by a) a specific type of organization, and b) simultaneous coordination between two independent sets of multiple sequences.

    That’s the way the system “works”.

    I really can’t say I find this to be a very good argument.

    The question is does teh genetic code work through a series of chemical reactions.

    You say the chemical reaction that links amino acid to tRNA and the one that links loaded tRNAs to a codon are “discontinuous” because they happen at different times. (I presume by this you a refereing to the fact loaded tRNAs used in translation are drawn from a pool of already made “translation-ready” tRNAs?). But I don’t see how that changes the fact that the genetic code works via a series of chemical reactions.

    If I am misunderstanding your point then please feel free to spell it out more thoroughly.

  46. 46
    ET says:

    The question is does teh genetic code work through a series of chemical reactions.

    And if it did then scientists should be able to create life in a lab.

  47. 47
    ET says:

    I would think that the “discontinuous association” refers to the fact that there isn’t any direct link from mRNA codon to amino acid. That there has to be an existing system to link the proper amino acid to the correct tRNA. And that the relationship between mRNA codon and amino acid is indirect, not determined by chemical reactions.

  48. 48
    MatSpirit says:

    kairosfocus @ 20:

    My comment https://uncommondescent.com/design-inference/a-note-on-layer-cake-communication-systems-and-protocols/

    Thank you for posting that OP and its first diagram, the Generalized Layer-Cake Model. At the bottom of that diagram, you have the Physical Layer, which is also shown as a rightward pointing arrow labeled “CHANNEL”.

    This Physical Layer is what Ed and Ortho are talking about. ALL of the actual function of the machinery in the cells is done through chemistry. There is no known magic involved. The molecules which do the actual translation of DNA to protein and everything else in a cell operate through this physical layer which consists mainly of the electrostatic forces that bind atoms together and attract one group of atoms to another. If those chemical forces stopped, the machinery would not only stop, the molecules would fall apart.

    Some of the people on this blog believe that the actual formation of the various atoms and molecules was originally accomplished through non-material means and we can’t directly contradict them because the basic molecular biology happened billions of years ago and left no fossils.

    However, when it comes to the actual day to day construction and operation of the molecular machinery that is happening in your body at this instant, the verdict has been clear for decades and gets clearer daily. We now know how the most important molecules work. We also know how they’re made, the sections of DNA that specify their shape, how they’re actually assembled and what they actually do when they’re working. So far as we can tell, there is nothing supernatural about life. It’s all physical atoms and molecules and at the most basic, they ALL operate through chemistry.

  49. 49
    JVL says:

    ET: The argument is that the genetic code didn’t arise via a series of chemical reactions.

    Please don’t shoot the messenger! I’m just going to pass on some information!

    From https://en.wikipedia.org/wiki/Genetic_code

    A hypothetical randomly evolved genetic code further motivates a biochemical or evolutionary model for its origin. If amino acids were randomly assigned to triplet codons, there would be 1.5 × 1084 possible genetic codes. This number is found by calculating the number of ways that 21 items (20 amino acids plus one stop) can be placed in 64 bins, wherein each item is used at least once. However, the distribution of codon assignments in the genetic code is nonrandom. In particular, the genetic code clusters certain amino acid assignments.

    Amino acids that share the same biosynthetic pathway tend to have the same first base in their codons. This could be an evolutionary relic of an early, simpler genetic code with fewer amino acids that later evolved to code a larger set of amino acids. It could also reflect steric and chemical properties that had another effect on the codon during its evolution. Amino acids with similar physical properties also tend to have similar codons, reducing the problems caused by point mutations and mistranslations.

    Given the non-random genetic triplet coding scheme, a tenable hypothesis for the origin of genetic code could address multiple aspects of the codon table, such as absence of codons for D-amino acids, secondary codon patterns for some amino acids, confinement of synonymous positions to third position, the small set of only 20 amino acids (instead of a number approaching 64), and the relation of stop codon patterns to amino acid coding patterns.

    Three main hypotheses address the origin of the genetic code. Many models belong to one of them or to a hybrid:

    Random freeze: the genetic code was randomly created. For example, early tRNA-like ribozymes may have had different affinities for amino acids, with codons emerging from another part of the ribozyme that exhibited random variability. Once enough peptides were coded for, any major random change in the genetic code would have been lethal; hence it became “frozen”.

    Stereochemical affinity: the genetic code is a result of a high affinity between each amino acid and its codon or anti-codon; the latter option implies that pre-tRNA molecules matched their corresponding amino acids by this affinity. Later during evolution, this matching was gradually replaced with matching by aminoacyl-tRNA synthetases.

    Optimality: the genetic code continued to evolve after its initial creation, so that the current code maximizes some fitness function, usually some kind of error minimization.

    Hypotheses have addressed a variety of scenarios:

    Chemical principles govern specific RNA interaction with amino acids. Experiments with aptamers showed that some amino acids have a selective chemical affinity for their codons. Experiments showed that of 8 amino acids tested, 6 show some RNA triplet-amino acid association.

    Biosynthetic expansion. The genetic code grew from a simpler earlier code through a process of “biosynthetic expansion”. Primordial life “discovered” new amino acids (for example, as by-products of metabolism) and later incorporated some of these into the machinery of genetic coding. Although much circumstantial evidence has been found to suggest that fewer amino acid types were used in the past, precise and detailed hypotheses about which amino acids entered the code in what order are controversial.

    Natural selection has led to codon assignments of the genetic code that minimize the effects of mutations. A recent hypothesis suggests that the triplet code was derived from codes that used longer than triplet codons (such as quadruplet codons). Longer than triplet decoding would increase codon redundancy and would be more error resistant. This feature could allow accurate decoding absent complex translational machinery such as the ribosome, such as before cells began making ribosomes.

    Information channels: Information-theoretic approaches model the process of translating the genetic code into corresponding amino acids as an error-prone information channel. The inherent noise (that is, the error) in the channel poses the organism with a fundamental question: how can a genetic code be constructed to withstand noise while accurately and efficiently translating information? These “rate-distortion” models suggest that the genetic code originated as a result of the interplay of the three conflicting evolutionary forces: the needs for diverse amino acids, for error-tolerance and for minimal resource cost. The code emerges at a transition when the mapping of codons to amino acids becomes nonrandom. The code’s emergence is governed by the topology defined by the probable errors and is related to the map coloring problem.

    Game theory: Models based on signaling games combine elements of game theory, natural selection and information channels. Such models have been used to suggest that the first polypeptides were likely short and had non-enzymatic function. Game theoretic models suggested that the organization of RNA strings into cells may have been necessary to prevent “deceptive” use of the genetic code, i.e. preventing the ancient equivalent of viruses from overwhelming the RNA world.

    Stop codons: Codons for translational stops are also an interesting aspect to the problem of the origin of the genetic code. As an example for addressing stop codon evolution, it has been suggested that the stop codons are such that they are most likely to terminate translation early in the case of a frame shift error] In contrast, some stereochemical molecular models explain the origin of stop codons as “unassignable”.

    (I removed the reference numbers to improve readability here but you can easily go and check them.)

    Anyway, from my reading, it seems like there is some evidence/thinking that it’s possible that the genetic ‘code’ arose through chemical affinities.

    Again, please don’t vilify me for just passing this on. If you disagree with the the above excerpt then your disagreement lies with the papers behind the statements which can be found at the website given.

  50. 50
    kairosfocus says:

    MS, the physical layer is one layer in the design of a telecom system, and that is what is being missed; protocols are very real, as are linked codes. The information rich coherent functional organisation is already a sign of design. The use of string data structures with alphanumeric code and algorithms expressed in protein synthesis then points to language antecedent to cell based life. Further to this, the sequences of bases in D/RNA and AAs in proteins is arbitrary, not forced by Chemistry, that’s why it is a string data structure, closely comparable to the prong pattern in a Yale type key, fitting the matching pattern in the lock’s mechanism. The notion that such arose from molecular noise, is utterly unwarranted to the point of exposing a critical flaw in any materialistic ool account. But, I am sure there will be ever so many who will deny this all the way down to the foot of the cliff. KF

  51. 51

    .
    Orthos at #45,

    The question is does teh genetic code work through a series of chemical reactions.

    I already stated my thoughts on that in comment #23, which I will repeat it here again:

    UB: #23
    I think that Barry and Ed and Ortho are talking past each other, as sometime happens. When Barry uses the word “works” in his question (I believe) he is talking about the system result. When Ed sees the word “works” he takes the shortest route to the door. The truth is that it does not matter how the question is posed, the materialists on this blog will avoid the issue at every turn.

    I am not sure why I should be expected to address that topic beyond what I have already said. You can push the “A” key on your computer and the letter “A” will appear on your screen. You can then ignore everything else and steadfastly argue that this entire process “works” by dynamics. This is the cop out that Ed chooses because he is intellectually unwilling to face the necessary coordination of symbol vehicles and constraints (i.e. the discontinuous association) required for the system to actually function as it does. If this is your cop out as well, then you are certainly free to take it. Is this your cop out?

    Regardless of your answer to that question, when you say that it is ”absolutely the case that the next amino acid in a developing protein is determined by chemistry” you are wrong. That chain of events from DNA to binding is undeniably discontinuous, just as it is from the “A” key on your computer to the letter “A” appearing on your screen.

  52. 52
    kairosfocus says:

    JVL,

    Citing Wikipedia . . . a clue itself:

    A hypothetical randomly evolved genetic code . . . However, the distribution of codon assignments in the genetic code is nonrandom. In particular, the genetic code clusters certain amino acid assignments.

    Hypothetical is the first giveaway. Guess, then somewhat distanced from by talking about a logical structure reflecting a pattern tabulated in the OP I put up.

    Have you ever seen how a Machine Language in a microprocessor is organised? The pattern is non-random, reflecting the organising intent of its designers. Wikipedia is trying to suggest that a strong feature of designs, intelligible, coherent structure, implies blind mechanism dependent on built in natural forces.

    Engineering uses existing forces and materials to design and build coherently organised structures, with the organisation the key element that reflects design.

    In the case of D/RNA, notice, the bonding along the chain allows ANY sequence of GCAT/U elements, directly comparable to the character strings in the Wiki article. That the chaining patterns used are structured in a coherent, intelligible pattern of bases that correlates to AAs tells us much. And BTW there are THREE stop codons and the standard start/load methionine AUG . . . there are variants . . . which are markers of how we are dealing with algorithms. Where, multiple stops means that errors are much more likely to hit a stop, i.e. it is a safety feature.

    Next, the key point is the cloverleaf secondary structure of tRNA, which sets up the folded mobile tooltip arm with an anticodon at the opposite end. There is no chemical determination of the relationship between any anticodon and the STANDARD CCA tool tip. The association is set by a loading process that uses enzymes that are separate molecules. As I already noted, the loadings can be reprogrammed, indeed there are a couple of dozen variant codes, i.e. dialects . . . a direct sign of the linguistic character of the system.

    Complex, information rich functional organisation beyond blind search on observable cosmos scale, string data structures with alphanumeric codes, algorithms with forced halting, dialects within a general language. All, strong signs of design.

    All of which will predictably be brushed aside similar to how we are seeing evidence dismissed in the face of pandemic. Bad signs.

    KF

  53. 53
    JVL says:

    Kairosfocus: Citing Wikipedia . . . a clue itself:

    Not everything in Wikipedia is wrong! Anyway, there are references behind the statements.

    Hypothetical is the first giveaway. Guess, then somewhat distanced from by talking about a logical structure reflecting a pattern tabulated in the OP I put up.

    It’s an idea that some people are looking at; isn’t that how lots of scientific ideas start? You make a hypothesis and then test it?

    Have you ever seen how a Machine Language in a microprocessor is organised? The pattern is non-random, reflecting the organising intent of its designers.

    Yes, I have. Done some assembly level programming in fact.

    Wikipedia is trying to suggest that a strong feature of designs, intelligible, coherent structure, implies blind mechanism dependent on built in natural forces.

    Not in a general sense, just in this case. And it’s not ‘Wikipedia’, it’s the researchers who wrote the papers supporting the statements.

    All of which will predictably be brushed aside similar to how we are seeing evidence dismissed in the face of pandemic.

    I’m not brushing anything aside. I just brought some information to the conversation. We should consider all the data and if some researchers think they have seen indications that the genetic ‘code’ may have arisen because of chemical affinities then it makes sense that that should be explored and checked out. No one is just buying into it automatically; I’m sure all the work will be examined and cross-checked and there will be attempts to repeat it. It’s a big, important question so I’m sure the work will be scrutinised closely.

    Scientists want to know how things work, they get ideas, the better ideas get fleshed out a bit and then checked out more rigorously. That’s the way it should be. ALL scientific ‘truths’ are provisional based on the best data available at the time. As our techniques improve we get new data we didn’t have before and that means some ideas may have to change or get discarded.

  54. 54
    kairosfocus says:

    JVL, as expected. You fail to see that an organised coherent structure that makes advantageous use of the materials and forces of nature is a common FEATURE of designs, so its presence cannot point to likely absence of design. Similarly, you may have done Assembly Language programming (which converts to verbal abbreviations) but the issue was the structure of instructions at bit or hex code level, where the bit patterns tend to be very structural. I particularly recall this for the old 6800 and 6809 family. The structural features of D/RNA within the triplet-base codon framework reflect this pattern. The presence of dialects and artificial extensions that add further AAs to the system show linguistic structure. Finally, that Wiki failed to balance one side of the story with the other is a characteristic sign of how an unbalanced narrative gains currency. KF

  55. 55
    JVL says:

    Kairosfocus: JVL, as expected. You fail to see that an organised coherent structure that makes advantageous use of the materials and forces of nature is a common FEATURE of designs, so its presence cannot point to likely absence of design.

    I didn’t say it wasn’t a feature of design; all I did was pass along some references to some work done by scientists which might suggest that the genetic ‘code’ has roots in some chemical affinities.

    Finally, that Wiki failed to balance one side of the story with the other is a characteristic sign of how an unbalanced narrative gains currency

    If you have a beef with Wikipedia then take it up with them. I went there because I had seen the material I quoted before and thought it should be part of the conversation. I don’t know how far along such explorations have got but clearly there are some people taking it seriously enough to do some work on it.

    I am not attacking you or your position; I’m merely pointing out some research being done. I suspect more work along those lines will be done IF the hypotheses look promising. Or they might all fall apart. But you’ve got to check things out to see if they work or not.

  56. 56
    kairosfocus says:

    JVL, the fact that organised structures that reflect underlying materials, their properties and associated forces of nature are common features of intelligently configured structures and systems implies that presence of such aspects does not count against design or suggest not designed. It is thus a red herring to point to such features in ways that enable that fallacious conclusion. We look for signs of design elsewhere, in functionally specific, information rich complex coherent organisation. In the relevant case, this includes string data structures carrying alphanumerical, prong height key-lock fit codes used in algorithms and reflecting language. Where, such FSCO/I and language are strong signs of design as material cause. All of this in the heart of the cell, showing strong reason to infer that the cell is designed by language using intelligence. KF

    PS: There is a reason why Wikipedia is a humble source with a reputation for ideologically driven bias and bullying anyone who dares to try to correct even glaring errors and slanders.

  57. 57
    JVL says:

    Kairosfocus: It is thus a red herring to point to such features in ways that enable that fallacious conclusion.

    No one is pointing to such features in some weird way. They are just doing some basic scientific research to see if it’s possible that the genetic ‘code’ partially arose via some basic chemical affinities. I’m not doing the research, I’m not telling you they’re right and your wrong. I’m just pointing out that some research into an area of common interest is being carried out. Some scientists have some hypotheses they are checking out. If it checks out then we can consider the ramifications.

    PS: There is a reason why Wikipedia is a humble source with a reputation for ideologically driven bias and bullying anyone who dares to try to correct even glaring errors and slanders.

    Like I said, if you have a beef with Wikipedia take it up with them. The material I quoted was fully referenced and hopefully you can get ahold of some or most of the references if you so desire.

    We all support science and scientific methods. So let’s see how the research pans out! Like I said, it might all crumble to dust but sometimes you have to check things out to see if they work or not. Let them run their experiments and see what they get.

  58. 58
    ET says:

    MatSpirit:

    ALL of the actual function of the machinery in the cells is done through chemistry.

    Please explain the chemistry behind proof-reading and error-correction. Please explain the chemistry behind mRNA processing- as in how the chemicals knew what and how to process it.

    If it is all just chemistry then scientists are stupid because they cannot produce a living organism in a lab.

  59. 59
    ET says:

    JVL, In a design scenario I would expect non-randomness in the genetic code. There isn’t anything in your Wikipedia link that says blind and mindless chemical processes can produce a code of any sort. Of course there will be chemical affinities. No one says that it works via magic.

    There is still a 10 million dollar prize that remains unclaimed. The prize will go to anyone who can demonstrate that chemical processes are up to the task.

  60. 60
    ET says:

    JVL:

    We all support science and scientific methods.

    All evidence to the contrary, of course.

  61. 61
    JVL says:

    ET: JVL, In a design scenario I would expect non-randomness in the genetic code. There isn’t anything in your Wikipedia link that says blind and mindless chemical processes can produce a code of any sort. Of course there will be chemical affinities. No one says that it works via magic.

    Yes, the non-randomness would be a common trait. The article addresses the possibility that the genetic ‘code’ at least partially arose through sheer chemical means; I would consider those blind processes. And we certainly agree about magic!!

    There is still a 10 million dollar prize that remains unclaimed. The prize will go to anyone who can demonstrate that chemical processes are up to the task.

    Yup! Maybe someday someone will put in a claim. Or maybe not. It’s kind of an exciting time to be alive.

  62. 62
    ET says:

    JVL:

    The article addresses the possibility that the genetic ‘code’ at least partially arose through sheer chemical means

    Lip service doesn’t make it a possibility. The article still is lacking a means to produce the components required. For example, tRNA’s are out of the reach of blind and mindless processes.

    And people have already put in claims for the prize. All failures so far.

  63. 63
    kairosfocus says:

    JVL, as predicted. There you go, suggesting that the genetic code and linked systems in part assembled themselves out of presumably blind Chemical affinities. It has already been pointed out that existing materials, properties and forces of nature are a normal part of design. In this case also the fact is that the tRNA CCA tip that holds the AAs is a universal joint, one that chemically could bind any AA. It is a specific, controlled loading process that leads to the anti-codon AA match, and such can be reprogrammed. In short, there is no determination by chemical affinity, for things at opposite ends of the tRNA. Where, the CCA tip joins the common COOH end of Amino Acids. In short, a modular, universal joint. You just are not going to get DNA and protein families from blind forces. And if the laws and circumstances are thought to arise from the physics and circumstances of our cosmos, that would be fine tuning on steroids. KF

  64. 64
    JVL says:

    Kairosfocus: There you go, suggesting that the genetic code and linked systems in part assembled themselves out of presumably blind Chemical affinities.

    It’s not me! I’m just passing on some information that suggests other people think it’s a viable hypothesis. I don’t know if they are right; I’ll wait and see what they come up with. After that I’ll make up my mind.

    You just are not going to get DNA and protein families from blind forces.

    I don’t know if that’s true. I’m going to wait and see what the research comes up with.

    And if the laws and circumstances are thought to arise from the physics and circumstances of our cosmos, that would be fine tuning on steroids.

    Different topic. One I’m happy to engage in if you like.

  65. 65
    JVL says:

    ET: Lip service doesn’t make it a possibility.

    No it doesn’t. But an experimental result might. Let’s see what they come up with.

    The article still is lacking a means to produce the components required.

    The Wikipedia article is just a pointer to the real research so . . . are you commenting on one of the papers behind the Wikipedia article?

    And people have already put in claims for the prize. All failures so far.

    There may never be a winner. But I’m happy to let people hypothesis and test. Do some science. That’s good isn’t it? There’s no such thing as negative information so knowing something doesn’t work is valuable.

  66. 66
    Barry Arrington says:

    JVL

    There may never be a winner.

    Dear readers, JVL has demonstrated how materialists insulate themselves from reality. Sure, materialists do not even have plausible speculations about how to account for the rise of the genetic code through blind unguided natural causes. And they may never. That’s OK with JVL just so long as he doesn’t have to reexamine his metaphysical commitments.

  67. 67
    JVL says:

    Barry Arrington: Sure, materialists do not even have plausible speculations about how to account for the rise of the genetic code through blind unguided natural causes.

    I’m not sure that’s true. That’s why I linked to the Wikipedia article which discusses some of the hypothetical cases and the references behind the article point to some of the work already done.

    And they may never. That’s OK with JVL just so long as he doesn’t have to reexamine his metaphysical commitments.

    Of course it’s okay with me. I’m happy to work with the data and results we’ve got. And if we don’t have the data or results to support a particular conclusion then it will stay a hypothesis at best.

    I don’t think that’s insulating from reality. That’s acknowledging that sometimes we can’t say one way or another.

    I do not understand why you are so dismissive of real scientific work being done just to see if it’s possible that the genetic ‘code’ partially arose via chemical affinities. What’s wrong with checking that out? It might not pan out, fair enough. But what’s wrong with testing it to see?

    You believe in the power of science and scientific reasoning so why aren’t you supportive of work being done to test the limits of what basic chemical affinities can accomplish? Especially since it might, in the end, support your view.

    Are you fighting the work or a view? Those are separate things.

  68. 68
    Barry Arrington says:

    JVL

    I’m not sure that’s true.

    Which demonstrates nothing but willfully obdurate denial of the plain facts. Which, in turn, demonstrates very powerfully the point of my last post: Materialists will go to astonishing lengths to deny reality if it means not having to reexamine their metaphysical commitments. Thank you.

  69. 69
    Barry Arrington says:

    JVL

    I’m happy to work with the data and results we’ve got. And if we don’t have the data or results to support a particular conclusion then it will stay a hypothesis at best.

    Two untruths in successive sentences. The results we’ve got point unequivocally to “design” as the best abductive answer. You are not happy with that result and reject it out of hand.

    And we don’t have the data or results to support a particular conclusion

    Nonsense. The data overwhelmingly support a particular conclusion. That conclusion is at odds with your metaphysical commitments so you say “damn the data; I’m not budging.”

  70. 70
    Barry Arrington says:

    JVL

    You believe in the power of science and scientific reasoning so why aren’t you supportive of work being done to test the limits of what basic chemical affinities can accomplish? Especially since it might, in the end, support your view.

    Again, nonsense. I completely support the work that is being done for the very reason to which you allude. That work is hopelessly mired. After decades of research they’ve got nothing. So it is not “in the end” that it supports my view. It overwhelmingly supports my view at this very moment. It is you who do not support the conclusions of the work. That work demonstrates that researchers haven’t the foggiest notion of how to even begin developing a “blind unguided” route to the genetic code. That means that, at present, by an overwhelming margin, the inference to best explanation (the root of all scientific conclusions) is that the best explanation lies elsewhere. And that elsewhere is “design.” And you can’t stand that, so you reject the results, saying “maybe tomorrow they will develop a naturalistic explanation, but even if they never do my metaphysical prejudices prohibit me from accepting the best explanation currently on the table.”

  71. 71
    orthomyxo says:

    Hi Upright,

    You don’t have to do anything, it’s only Barry who decided this had to be a fight.

    Barry was incredulous at the idea that the genetic code can work through a series of chemical reactions. I don’t see how saying the reactions involved in the code are discontinuous changes the face they are a series of reactions. So I don’t this very compelling.` I’m not sure I can say much more. Except…

    Regardless of your answer to that question, when you say that it is ”absolutely the case that the next amino acid in a developing protein is determined by chemistry” you are wrong. That chain of events from DNA to binding is undeniably discontinuous, just as it is from the “A” key on your computer to the letter “A” appearing on your screen.

    Why does it matter if it is discontinuous? If there is a pool of tRNA-amino-acids available, the next amino acid in the chain will be determined by the affinity of a specific tRNA to the mRNA codon, right? The fact that the tRNAs had to be available hardly changes the fact that a series fo chemical reactions make the genetic code work.

    It’s possible that I don’t know what you mean by “discontinuous”, because this word seems to be dong a lot of heavy lifting in your posts.

  72. 72
    ET says:

    Yes, the genetic code wouldn’t work without chemical reactions. Sending a Morse code via telegraph wouldn’t work without electrical reactions. But the electrical and chemical reactions don’t make the code that they are carrying out.

    Discontinuous- with a typewriter the key directly moves the arm with the proper letter. There isn’t any discontinuity there. With a computer keyboard the discontinuity is clear. All keyboard strokes are coded and must be processed before being displayed.

    With the genetic code the discontinuity is in the fact the codons represent amino acids. Codons are not involved in some chemical reaction that makes the amino acid they represent. There isn’t any law that dictates the pairing- codon to amino acid

  73. 73
    ET says:

    JVL, there isn’t any research into nature’s ability to spontaneously produce tRNA’s. tRNA’s are useless without the proper ligase(s) already in place.

    And the proteins required to get it all accomplished is the old chicken vs egg problem. You need proteins for transcription and translation to work but to get those proteins you need a working transcription and translation system.

    People would have a better chance of showing that nature produced Stonehenge. We know that nature is a good stone maker. So that hypothesis at least has that. And don’t go on about Stonehenge can’t reproduce. Biological reproduction is the very thing your side needs to account for.

  74. 74
    JVL says:

    Barry Arrington: Which demonstrates nothing but willfully obdurate denial of the plain facts.

    I think the information I linked to was addressing plausible accounts of the development of the genetic ‘code’ via blind processes. But I guess we’ll have to differ on that.

    Materialists will go to astonishing lengths to deny reality if it means not having to reexamine their metaphysical commitments.

    I just linked to some information. I’m not sure what astonishing lengths that took.

    Two untruths in successive sentences. The results we’ve got point unequivocally to “design” as the best abductive answer. You are not happy with that result and reject it out of hand.

    I’m not doing so. I’m just pointing out some work looking at the possible development of the genetic ‘code’ via basic chemical affinities. Let’s wait and see what that research tells us.

    Nonsense. The data overwhelmingly support a particular conclusion. That conclusion is at odds with your metaphysical commitments so you say “damn the data; I’m not budging.”

    I don’t agree but I guess you’re going to brand me with that view even if I don’t hold it. Trust me, it has nothing to do with my metaphysical commitments. Would you like it if I made such broad and comprehensive assumptions about your stance?

    I completely support the work that is being done for the very reason to which you allude. That work is hopelessly mired. After decades of research they’ve got nothing. So it is not “in the end” that it supports my view. It overwhelmingly supports my view at this very moment. It is you who do not support the conclusions of the work.

    I am far from alone when I disagree with you on this point. And I was talking exclusively about the development of the genetic ‘code’.

    That means that, at present, by an overwhelming margin, the inference to best explanation (the root of all scientific conclusions) is that the best explanation lies elsewhere. And that elsewhere is “design.” And you can’t stand that, so you reject the results, saying “maybe tomorrow they will develop a naturalistic explanation, but even if they never do my metaphysical prejudices prohibit me from accepting the best explanation currently on the table.”

    Again, I don’t agree. I don’t mind you putting the assumption of design on the table but it does entail a lot of other assumptions which have not been supported. We are talking about science here not philosophy or theology.

    I don’t want to be antagonistic, and we both agree that it’s good to pursue scientific questions. If you’re right then I’m sure those who are looking for a blind process development of the genetic ‘code’ will fail. It may take some time but what’s the rush? It’s better for your case to let them fail isn’t it?

  75. 75
    JVL says:

    ET: Yes, the genetic code wouldn’t work without chemical reactions. Sending a Morse code via telegraph wouldn’t work without electrical reactions. But the electrical and chemical reactions don’t make the code that they are carrying out.

    Of course not. But the development of the genetic ‘code’ is not analogous to a telegraph code really. A telegraph code is just the flipping of electrical states on a line. The genetic ‘code’ constructs structures.

    With the genetic code the discontinuity is in the fact the codons represent amino acids. Codons are not involved in some chemical reaction that makes the amino acid they represent. There isn’t any law that dictates the pairing- codon to amino acid

    I think you’ll find that there is research to suggest it might be the case that there IS some possible chemical reactions that dictates the pairings. That was one of the points of the information I linked to.

    JVL, there isn’t any research into nature’s ability to spontaneously produce tRNA’s. tRNA’s are useless without the proper ligase(s) already in place.

    I’m not sure that is true. I think that is an active area of research. Perhaps we should wait and see how that work plays out.

    And the proteins required to get it all accomplished is the old chicken vs egg problem. You need proteins for transcription and translation to work but to get those proteins you need a working transcription and translation system.

    Yes, of course. But you don’t want to be making one of those “it’s all too complicated for unguided processes’ arguments do you? Why not wait and see what they discover?

    People would have a better chance of showing that nature produced Stonehenge. We know that nature is a good stone maker. So that hypothesis at least has that. And don’t go on about Stonehenge can’t reproduce. Biological reproduction is the very thing your side needs to account for.

    Again, why not let the research progress and then draw a conclusion?

  76. 76
    OLV says:

    This discussion has gone far… 🙂
    UB’s argument is right on target.

  77. 77
    OLV says:

    Quantification of mRNA translation in live cells using single-molecule imaging

    mRNA translation is a key step in gene expression. Proper regulation of translation efficiency ensures correct protein expression levels in the cell, which is essential to cell function. Different methods used to study translational control in the cell rely on population-based assays that do not provide information about translational heterogeneity between cells or between mRNAs of the same gene within a cell, and generally provide only a snapshot of translation. To study translational heterogeneity and measure translation dynamics, we have developed microscopy-based methods that enable visualization of translation of single mRNAs in live cells. These methods consist of a set of genetic tools, an imaging-based approach and sophisticated computational tools. Using the translation imaging method, one can investigate many new aspects of translation in single living cells, such as translation start-site selection, 3?-UTR (untranslated region) translation and translation-coupled mRNA decay. Here, we describe in detail how to perform such experiments, including reporter design, cell line generation, image acquisition and analysis. This protocol also provides a detailed description of the image analysis pipeline and computational modeling that will enable non-experts to correctly interpret fluorescence measurements. The protocol takes 2–4 d to complete (after cell lines expressing all required transgenes have been generated).

     

  78. 78
    kairosfocus says:

    JVL, you cited with implicit approval, hence my inference that your comment suggested. That is tangential. What is core is that the structure of tRNA with a modular CCA tip that binds to the COOH acid side of an AA . . . a standard part of the AA along with its NH2 and R group . . . is modular. It is how it is loaded that makes the difference, and then how that loading matches the anticodon at the opposite end. tRNA serves as a “taxi” and position-arm machine element in the ribosome, so that under mRNA tape control, there is stepwise, controlled extension of a peptide chain, towards folding, agglomeration and adding metal atoms etc, leading to a key-lock fitting, functioning protein, including particularly enzymes. Where, there are start, next step and finitely remote halt stages, i.e. an algorithm using a 4-state per base triplet base frame machine code; which is immediately linguistic and goal-directed. All of which depends on existing supportive RNA, protein and enzyme structures. That is, this is a chicken-egg loop. The FSCO/I involved sets up an island of function deeply isolated in the space of possible molecule and atom configurations. The mRNA and DNA chains of codons carry linguistic, coded, goal-directed information in string data structures. All of these are strong signs of intelligently directed configuration, design. There is no plausible blind chance and/or mechanical necessity driven means to bridge from atoms and molecules in some allegedly plausible prebiotic soup and such a system, the search challenge vs atomic resources and time in the sol system or the observed — the only actually observed — cosmos puts that on the table. But as your own comments show, coded linguistic structures well beyond 500 – 1,000 bit thresholds for FSCO/I, are routinely produced by intelligent design. Where there is no good reason to suppose that we exhaust possible designers. KF

  79. 79
    ET says:

    JVL:

    But the development of the genetic ‘code’ is not analogous to a telegraph code really.

    Larry Moran disagrees with you. And stop putting scare quotes around the word code in genetic code. It only exposes your ignorance. The genetic code is a code in the same sense as Morse code- Larry Moran.

    I’m not sure that is true.

    It is true. No one is trying to figure out if nature can produce tRNA’s or their required ligases.

    But you don’t want to be making one of those “it’s all too complicated for unguided processes’ arguments do you?

    It has nothing to do with mere complexity. It has everything to do with specified complexity. And it still remains that you and yours have nothing bit wishful thinking.

    Yes, let the research waste money and get nowhere. It isn’t as if there aren’t more pressing problems the world requires attention to.

    You and yours live by means of promissory notes. There will never be enough negative findings to thwart your PoV.

  80. 80
    ET says:

    The genetic code is a real code. It is a real code in the same sense that the Morse code is a real code. So seeing JVL put ‘ ‘ around the word code in genetic code proves that he doesn’t understand the basic fact. But then again anyone who thinks that nature can produce codes from the bottom up isn’t all there to begin with.

    Talk about irrational…

  81. 81
    OLV says:

    More ID:

    Imaging Translation Dynamics of Single mRNA Molecules in Live Cells

    mRNA translation is a key step in decoding the genetic information stored in DNA. Regulation of translation efficiency contributes to gene expression control and is therefore important for cell fate and function. Here, we describe a recently developed microscopy-based method that allows for visualization of translation of single mRNAs in live cells. The ability to measure translation dynamics of single mRNAs will enable a better understanding of spatiotemporal control of translation, and will provide unique insights into translational heterogeneity of different mRNA molecules in single cells.

     

     

  82. 82

    .
    Ortho at #71 (sorry for the delay)

    You don’t have to do anything, it’s only Barry who decided this had to be a fight.

    I think it is virtually impossible to not know that this is a contentious ongoing competition of ideas. The systems under debate have been fully documented in the literature, and that documentation unambiguously supports the minority position over the majority position. Allow me to repeat that: Science supports the minority. In response, the majority position is forced to use poor reasoning, avoidance, and (most often) deceptive and underhanded means to maintain their position. You entered that competition.

    Barry was incredulous at the idea that the genetic code can work through a series of chemical reactions.

    I addressed this from my perspective in comment #23 and repeated it again in comment #51. This is the cop-out that was used by Ed to avoid the issues at hand. And, it worked – you won’t find Ed (or Seversky or JVL for instance, or a long list of names before them) on these pages actually dealing with the empirical observations recorded in the literature. These are the avoidance maneuvers of the majority, which can be very easily demonstrated by turning the statement around and saying that the genetic code MUST work through a series of chemical reactions, including observations X and Y and Z – and suddenly the room will clear of the Eds and Severskys, and JVLs of the world. Actually confronting the documented material conditions required for life to appear on earth does not serve their purposes (i.e. Popper’s conventionalist stratagem, and all that).

    Why does it matter if it is discontinuous? If there is a pool of tRNA-amino-acids available, the next amino acid in the chain will be determined by the affinity of a specific tRNA to the mRNA codon, right?

    No this in incorrect. The next amino acid in the chain will the determined by the shape and properties of the aaRS that loaded the tRNA. Let us say the cell needs to construct a polypeptide with 100 amino acids. We can ask: “How is this polypeptide specified from memory”. The sequence of codons in DNA (matured in mRNA) will determine that there are 100 positions in the polypeptide, and will determine the pattern of 20 different amino acids which will occupy each those 100 positions. But it is the protein aaRS that will determine which specific amino acids occupy that pattern. So, when the peptide is complete, you can say there is an aspartic acid (for instance) appearing in positions #22, #42, #54-58, #69, and #75 – but it will be the aaRS that determined aspartic acid occupies those positions. The codons are the quiescent symbol vehicles in the DNA memory and the aaRS are the interpretive constraints that establish the code and enable the system to function as it does.

  83. 83
    orthomyxo says:

    I don’t really know what else to say, I think this is a very underwhelming defence of Barry’s position. Articulating which chemical reactions are essential for translation, and where an when they happen in relation to each other, doesn’t do much to change the fact the genetic code works through a series of chemical reactions.

    I find your last point to be a distinction without a difference. I say if a pool of loaded tRNAs are available then next a/a is determined by the codon, you say the relationship between tRNA and a/a is determined by different chemical reaction. True enough, I guess. But what does that add up to?

  84. 84
  85. 85
    ET says:

    Barry’s question allows for semantic games. The question should have been:

    Are you suggesting that the genetic code is reducible to and originated from a series of chemical reactions?

  86. 86
    OLV says:

    More ID:

    Multi-Color Single-Molecule Imaging Uncovers Extensive Heterogeneity in mRNA Decoding

    mRNA translation is a key step in decoding genetic information. Genetic decoding is surprisingly heterogeneous because multiple distinct polypeptides can be synthesized from a single mRNA sequence.

    We find that start site selection is largely stochastic but that the probability of using a particular start site differs among mRNA molecules and can be dynamically regulated over time. This study provides key insights into translation start site selection heterogeneity and provides a powerful toolbox to visualize complex translation dynamics.

    more recent work has shown that translation of many if not most mRNAs is far more complex and that different regions of an mRNA can be translated.

     

    Specialized ribosomes and the control of translation

    The control of translation is increasingly recognized as a major factor in determining protein levels in the cell. The ribosome — the cellular machine that mediates protein synthesis — is typically seen as a key, but invariant, player in this process. This is because translational control is thought to be mediated by other auxiliary factors while ribosome recruitment is seen as the end-point of regulation. However, recent developments have made it clear that heterogeneous ribosome types can exist in different tissues, and more importantly, that these ribosomes can preferentially translate different subsets of mRNAs. In so doing, heterogeneous ribosomes could be key regulatory players in differentiation and development. Here, we examine current evidence for the existence of different ribosome types and how they might arise. In particular, we will take a close look at the mechanisms through which these ribosomes might mediate selective mRNA translation. We also summarize recently developed techniques/approaches that will aid in our understanding of the functions of such specialized ribosomes.

    given the bulk of evidence over the years, the ribosomes themselves do merit a closer look as potential regulatory players in protein synthesis.

  87. 87
    Ed George says:

    O

    May 7, 2020 at 4:08 pm
    I don’t really know what else to say, I think this is a very underwhelming defence of Barry’s position.

    I agree. Frankly, I don’t understand the ire raised over me answering the following question:

    Are you suggesting that the genetic code works through a series of chemical reactions?

    Yes is the only correct answer possible. Anyone who thinks otherwise either has no knowledge of biochemistry or is incapable of understanding the very plain meaning of the question. The question was not about the origin of life or the origin of DNA. It simply asked if DNA works through a series of chemical reactions. Which it most certainly does.

  88. 88

    .
    Ortho at 83

    I don’t really know what else to say

    I see that.

    … doesn’t do much to change the fact the genetic code works through a series of chemical reactions.

    Yes, that is the cop out in question.

    I find your last point to be a distinction without a difference. I say if a pool of loaded tRNAs are available then next a/a is determined by the codon

    You did say that, and you were incorrect.

    you say the relationship between tRNA and a/a is determined by different chemical reaction.

    Yes, I did indeed say that. Those associations (collectively referred to as the Genetic Code) are determined by the set of protein aaRS. They are not determined by base pair complimentary.

    True enough

    Yes again … which means your “difference without a distinction” comment was incoherent at the very point that you typed it out.

    But what does that add up to?

    Well, in the most obvious and immediate sense, it means that the materialist who is (with Ed firmly by his side) copping out on the question of how the genetic code works is clearly incorrect about how the genetic code works – that is, of course, if how the code is established is considered part of how it works.

    In another sense, it is one of the many documented universal observations confirming the model predicted and described in the literature, where the capacity to specify a protein from heritable memory requires one arrangement of matter to act as a symbol and a separate arrangement of matter to act as a constraint to independently establish what is being specified. Welcome to the world of irreducible complexity in the core requirement of life on earth, just as it was predicted to be.

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    kairosfocus says:

    UB (attn EG): It seems it has not registered with EG, that the tRNA tip that holds an AA through its COOH end, is a universal joint, CCA-. That immediately points to the importance of the enzymes that load the AA. It also calls to mind cases such as H pylori, where a chemically related AA is loaded and then modified to the correct AA by further enzyme action. That underscores the universal joint point. I suspect EG thinks he knows the right answers and is just disposing of IDiots with clever quips. Instead, he is inadvertently showing some of the dangers of ideological blinkering and contempt-laced polarisation. Such a state is not without consequences; we saw it biasing minds against and leading to oh there’s no evidence assertions in the face of mounting evidence of effective treatments by cocktails that help to stave off immune system over-reaction and buy time for natural defences to work. At last count we were looking at 90+% reductions relative to expected fatality rates with the de facto standard, on a cumulative base of thousands of cases. It is coming down to a point where gross, entrenched errors need to visibly fail to meet their intellectual and policy IOUs, for there to be a sea-change. That may be beginning, across the board. KF

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