Stunning Levels of Ignorance Regarding the Genetic Code

_{Barry Arrington

May 5, 2020

Intelligent Design

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Intelligent Design}

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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.

Comments

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. KFkairosfocus_{May 10, 2020
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. 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.Upright BiPed_{May 7, 2020
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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.Ed George_{May 7, 2020
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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.
OLV_{May 7, 2020
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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?ET_{May 7, 2020
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Ortho, you clearly know or should know better than your talking points. Cf here https://uncommondescent.com/intelligent-design/orthomyxo-types-on-keyboard-when-letters-appear-on-screen-its-physical/#comment-701028 KFkairosfocus_{May 7, 2020
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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?orthomyxo_{May 7, 2020
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. 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.Upright BiPed_{May 7, 2020
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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.
OLV_{May 7, 2020
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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...ET_{May 7, 2020
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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.ET_{May 7, 2020
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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. KFkairosfocus_{May 7, 2020
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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).
OLV_{May 6, 2020
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This discussion has gone far... :) UB's argument is right on target.OLV_{May 6, 2020
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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?JVL_{May 6, 2020
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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?JVL_{May 6, 2020
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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.ET_{May 6, 2020
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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 acidET_{May 6, 2020
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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.orthomyxo_{May 6, 2020
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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."Barry Arrington_{May 6, 2020
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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."Barry Arrington_{May 6, 2020
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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.Barry Arrington_{May 6, 2020
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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.JVL_{May 6, 2020
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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.Barry Arrington_{May 6, 2020
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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.JVL_{May 6, 2020
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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.JVL_{May 6, 2020
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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. KFkairosfocus_{May 6, 2020
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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.ET_{May 6, 2020
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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.JVL_{May 6, 2020
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JVL:
We all support science and scientific methods.
All evidence to the contrary, of course.ET_{May 6, 2020
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03
AM
PDT}

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