Paul Giem on overlapping genetic codes

_{Denyse O'Leary

December 24, 2014

Genetics, News}

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In the book “Biological Information: New Perspectives” Chapters 6 and 9 (at least) argue that stretches of DNA can have multiple functions encoded into them. We will partially evaluate the strength of the evidence behind that argument.

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Anyway, a more effective way to collaborate here is to provide references to research papers that show how quickly the magic ‘n-D e’ formula RV+NS+HGT+T=E is failing to explain the origin of the elaborate cellular and molecular choreographies orchestrated within the biological systems.
Here's one fish from the oven: unexpected mechanism of protein synthesis, in which a protein—not an mRNA—determines tRNA recruitment
Science 2 January 2015: Vol. 347 no. 6217 pp. 75-78 DOI: 10.1126/science.1259724 Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains In Eukarya, stalled translation induces 40S dissociation and recruitment of the ribosome quality control complex (RQC) to the 60S subunit, which mediates nascent chain degradation. Here we report cryo–electron microscopy structures revealing that the RQC components Rqc2p (YPL009C/Tae2) and Ltn1p (YMR247C/Rkr1) bind to the 60S subunit at sites exposed after 40S dissociation, placing the Ltn1p RING (Really Interesting New Gene) domain near the exit channel and Rqc2p over the P-site transfer RNA (tRNA). We further demonstrate that Rqc2p recruits alanine- and threonine-charged tRNA to the A site and directs the elongation of nascent chains independently of mRNA or 40S subunits. Our work uncovers an unexpected mechanism of protein synthesis, in which a protein—not an mRNA—determines tRNA recruitment and the tagging of nascent chains with carboxy-terminal Ala and Thr extensions (“CAT tails”). http://www.sciencemag.org/content/347/6217/75.abstract?sid=e0929331-cb7c-4b8a-9c12-e00c68795868
Dionisio_{January 2, 2015
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#207 wd400 Normally I don't post comments for you or your comrades, except when I mistakenly get engaged in senseless debates with y'all, which become a tremendous waste of time I later regret. You and your fellow travelers have not been in the main list of intended recipients of my posts. Actually, most of my posts are simply references to research papers I find interesting enough to share with others here. They are not mine. I don't qualify to write anything worth reading. :)Dionisio_{January 2, 2015
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#206 Aurelio Smith
Don’t let UB bully you.
UB asked me very nicely to change my approach, giving me clear to understand reasons. You may want to try learning from UB. It won't hurt you to know how to present information in a nice and easy to understand manner. Perhaps UB can teach you that. I should learn that too. :)Dionisio_{January 2, 2015
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Not whining, Dio. What you've done is exceedingly childish and rude and your questions are inane. I fail to see how having you spam these threads serves any purpose, let alone gets you the the "serious discussion" you started out claiming to seek. You can't behave as you have and expect others to treat you with respect or politeness. The best I can offer is to add you the BA/Joe class and scroll past your comments, but I still question why your spam should clog up these threads at all.wd400_{January 2, 2015
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#204 wd400 Whining? You, your comrades and fellow travelers do the same all the time, but in a more subtle manner, scattering your nonsense comments through the threads, in order to get away with it by flying under the radar. What I did was more obvious, kind of like a short-timed blitzkrieg offensive. I gave you your own medicine, but on larger dose, so you knew how bad it tastes. Now you know. But I have good news for you. UB nicely asked me to stop it and I immediately did it. You see? It works when people talk nicely. You may want to try learning that style too, though it's probably unknown to you. Now run and tell your comrades the good news! But don't think you're off the hook. Questions will keep coming your way, but not in an unnecessary 'Dresden bombardment' style. Just one at a time. :) Just be careful and don't try to setup another money exchanging business in the main portal. Someone could come and overturn your tables again. :) Anyway, a more effective way to collaborate here is to provide references to research papers that show how quickly the magic 'n-D e' formula RV+NS+HGT+T=E is failing to explain the origin of the elaborate cellular and molecular choreographies orchestrated within the biological systems. In a way now think that I wasted too much time trying to play by your dirty rules. Looking back I have to admit that I didn't enjoy it. Another lesson learned. I should learn to ignore y'all. :)Dionisio_{January 2, 2015
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Are the mods on holiday? What value does Dinisio's spam add to this thread, or indeed this site? How long would an pro-evolutionary biology poster last here if they spammed threads with the same sort of inane questions repeated so many times?wd400_{January 2, 2015
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#200 Upright BiPed
Dio, you’ve now posted 60 of the last 62 posts on this thread, including the last 37 posts straight. Many of your posts are seemingly repeats (or almost identical to) adjacent posts you’ve made. You are effectively killing the threads. This is ineffective. Please consider altering your approach.
Ok, will change the posting approach. Didn't know this affected the thread so badly. The 'third way' thread is much larger than this and no one has mentioned this kind of critical problem. Thank you for bringing this up to my attention. Happy New Year!Dionisio_{January 2, 2015
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DNA_Jock: Did you respond my questions posted @163 yet? I don’t recall seeing it, but perhaps it was posted after you left on vacation? Anyway, in case you have time, here’s a link to post #163 in this thread: https://uncommondescent.com/genetics/paul-giem-on-overlapping-genetic-codes/#comment-539937Dionisio_{January 2, 2015
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DNA_Jock, Did you respond my questions posted @163 yet? I don’t recall seeing it, but perhaps it was posted after you left on vacation? Anyway, in case you have time, here’s a link to post #163 in this thread: https://uncommondescent.com/genetics/paul-giem-on-overlapping-genetic-codes/#comment-539937Dionisio_{January 2, 2015
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Dio, you've now posted 60 of the last 62 posts on this thread, including the last 37 posts straight. Many of your posts are seemingly repeats (or almost identical to) adjacent posts you've made. You are effectively killing the threads. This is ineffective. Please consider altering your approach.Upright BiPed_{January 2, 2015
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DNA_Jock: Why do you like to write so many personal attacks? BTW, I asked the same question @126, but don’t recall seeing your answer anywhere? Maybe you tried to answer this @159 to no avail? You may want to try to make your explanation more understandable to people who are not as sharp and don't think as fast as you do. Make it understandable to a 6-yo child. :) @162 I asked this: Please, would you mind to show me where you answered that specific question, if you did? Thank you.Dionisio_{January 2, 2015
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DNA_Jock, Why do you like to write so many personal attacks? BTW, I asked the same question @126, but don’t recall seeing your answer anywhere? Maybe you tried to answer this @159 to no avail? You may want to try to make your explanation more understandable to people who are not as sharp and don't think as fast as you do. Make it understandable to a 6-yo child. :) @162 I asked this: Please, would you mind to show me where you answered that specific question, if you did? Thank you.Dionisio_{January 2, 2015
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DNA_Jock Why do you like to write so many personal attacks? BTW, I asked the same question @126, but don’t recall seeing your answer anywhere? Maybe you tried to answer this @159 to no avail? You may want to try to make your explanation more understandable to people who are not as sharp and don't think as fast as you do. Make it understandable to a 6-yo child. :) @162 I asked this: Please, would you mind to show me where you answered that specific question, if you did? Thank you.Dionisio_{January 2, 2015
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DNA_Jock, RE: #161 Did you respond my questions posted @161 yet? I don't recall seeing it, but perhaps it was posted after you left on vacation? Anyway, in case you have time, here's a link to post #161 in this thread: https://uncommondescent.com/genetics/paul-giem-on-overlapping-genetic-codes/#comment-539935Dionisio_{January 2, 2015
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DNA_Jock, Did you respond my questions posted @161 yet? I don't recall seeing it, but perhaps it was posted after you left on vacation? Anyway, in case you have time, here's a link to post #161 in this thread: https://uncommondescent.com/genetics/paul-giem-on-overlapping-genetic-codes/#comment-539935Dionisio_{January 2, 2015
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DNA_Jock: Did you respond my questions posted @161 yet? I don't recall seeing it, but perhaps it was posted after you left on vacation? Anyway, in case you have time, here's a link to post #161 in this thread: https://uncommondescent.com/genetics/paul-giem-on-overlapping-genetic-codes/#comment-539935Dionisio_{January 2, 2015
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#159 DNA_Jock:
Re 147, 151 I’m off on vacation soon, so I may not respond. You might consider taking a break too.
Glad you're off on vacation soon. It's good to take time off and rest. Thank you for suggesting that I do the same. Will consider it.Dionisio_{January 2, 2015
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#159 DNA_Jock,
Re 147, 151 I’m off on vacation soon, so I may not respond. You might consider taking a break too.
Glad you're off on vacation soon. It's good to take time off and rest. Thank you for suggesting that I do the same. Will consider it.Dionisio_{January 2, 2015
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#159 DNA_Jock
Re 147, 151 I’m off on vacation soon, so I may not respond. You might consider taking a break too.
Glad you're off on vacation soon. It's good to take time off and rest. Thank you for suggesting that I do the same. Will consider it.Dionisio_{January 2, 2015
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DNA_Jock: If you wonder why I mentioned the idea of repeating a post 3 or 7 times, it's just related to old history. It has been said that in some ancient cultures they repeated 3 times what they considered important for others to note. Additionally, the number 7 was considered a symbol of completeness. Most probably you already knew this. But perhaps some onlookers/lurkers don't know it. BTW, it's possible that the multiple postings have attracted more attention to the affected thread. Thus, the stats of the thread may have improved. :)Dionisio_{January 2, 2015
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DNA_Jock, If you wonder why I mentioned the idea of repeating a post 3 or 7 times, it's just related to old history. It has been said that in some ancient cultures they repeated 3 times what they considered important for others to note. Additionally, the number 7 was considered a symbol of completeness. Most probably you already knew this. But perhaps some onlookers/lurkers don't know it. BTW, it's possible that the multiple postings have attracted more attention to the affected thread. Thus, the stats of the thread may have improved. :)Dionisio_{January 2, 2015
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DNA_Jock If you wonder why I mentioned the idea of repeating a post 3 or 7 times, it's just related to old history. It has been said that in some ancient cultures they repeated 3 times what they considered important for others to note. Additionally, the number 7 was considered a symbol of completeness. Most probably you already knew this. But perhaps some onlookers/lurkers don't know it. BTW, it's possible that the multiple postings have attracted more attention to the affected thread. Thus, the stats of the thread may have improved. :)Dionisio_{January 2, 2015
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DNA_Jock: You have called me a liar but have not been able to produce a proof to support your accusation. It was just based on your own misperceptions. Can't you understand that I admit to my lack of knowledge and my slow thinking sincerely? Still you haven't been able to explain your position clearly. Can any directed explanation be considered effective if the addressed audience doesn't understands it? Can you make it more understandable to me? If you can't, could it be that my mental capacity to understand (regardless of language considerations) is lower than what you assume or expect according to your presupposed standards? Is it that difficult for you to accept that someone can sincerely reveal not being as sharp as others may expect, not being as fast thinking as others may expect, not knowing as much as others may expect? Why do you keep adding unfounded insults just based on your apparent misperception? Why do you keep stating that I'm lying, just because you don't want to accept my sincere explanation? Are you familiar with the following biblical passage? [just a portion of it]. How do you understand it?
…not many of you were wise according to worldly standards, not many were powerful, not many were of noble birth. But God chose what is foolish in the world to shame the wise; God chose what is weak in the world to shame the strong; God chose what is low and despised in the world, even things that are not, to bring to nothing things that are, so that no human being might boast in the presence of God. And because of him you are in Christ Jesus, who became to us wisdom from God, righteousness and sanctification and redemption, so that, as it is written, “Let the one who boasts, boast in the Lord.” [1 Corinthians 1:26-31]
How many times should I repeat this post so that you consider it seriously? 3? 7?Dionisio_{January 2, 2015
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DNA_Jock, You have called me a liar but have not been able to produce a proof to support your accusation. It was just based on your own misperceptions. Can't you understand that I admit to my lack of knowledge and my slow thinking sincerely? Still you haven't been able to explain your position clearly. Can any directed explanation be considered effective if the addressed audience doesn't understands it? Can you make it more understandable to me? If you can't, could it be that my mental capacity to understand (regardless of language considerations) is lower than what you assume or expect according to your presupposed standards? Is it that difficult for you to accept that someone can sincerely reveal not being as sharp as others may expect, not being as fast thinking as others may expect, not knowing as much as others may expect? Why do you keep adding unfounded insults just based on your apparent misperception? Why do you keep stating that I'm lying, just because you don't want to accept my sincere explanation? Are you familiar with the following biblical passage? [just a portion of it]. How do you understand it?
…not many of you were wise according to worldly standards, not many were powerful, not many were of noble birth. But God chose what is foolish in the world to shame the wise; God chose what is weak in the world to shame the strong; God chose what is low and despised in the world, even things that are not, to bring to nothing things that are, so that no human being might boast in the presence of God. And because of him you are in Christ Jesus, who became to us wisdom from God, righteousness and sanctification and redemption, so that, as it is written, “Let the one who boasts, boast in the Lord.” [1 Corinthians 1:26-31]
How many times should I repeat this post so that you consider it seriously? 3? 7?Dionisio_{January 2, 2015
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DNA_Jock You have called me a liar but have not been able to produce a proof to support your accusation. It was just based on your own misperceptions. Can't you understand that I admit to my lack of knowledge and my slow thinking sincerely? Still you haven't been able to explain your position clearly. Can any directed explanation be considered effective if the addressed audience doesn't understands it? Can you make it more understandable to me? If you can't, could it be that my mental capacity to understand (regardless of language considerations) is lower than what you assume or expect according to your presupposed standards? Is it that difficult for you to accept that someone can sincerely reveal not being as sharp as others may expect, not being as fast thinking as others may expect, not knowing as much as others may expect? Why do you keep adding unfounded insults just based on your apparent misperception? Why do you keep stating that I'm lying, just because you don't want to accept my sincere explanation? Are you familiar with the following biblical passage? [just a portion of it]. How do you understand it?
…not many of you were wise according to worldly standards, not many were powerful, not many were of noble birth. But God chose what is foolish in the world to shame the wise; God chose what is weak in the world to shame the strong; God chose what is low and despised in the world, even things that are not, to bring to nothing things that are, so that no human being might boast in the presence of God. And because of him you are in Christ Jesus, who became to us wisdom from God, righteousness and sanctification and redemption, so that, as it is written, “Let the one who boasts, boast in the Lord.” [1 Corinthians 1:26-31]
How many times should I repeat this post so that you consider it seriously? 3? 7?Dionisio_{January 2, 2015
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If you want, we can all agree to stop it here. Or you may continue the old rotten style, if that's what you prefer. Let's make a deal? If we agree, we'll try to refrain from commenting on anything we all write from now on. At this point one of my main interests is to gather references to research papers for review using Zotero + Mind Meister + private WordPress web logs, some of which I share here in this blog.Dionisio_{January 2, 2015
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wd400 & DNA_Jock My recent postings are intended to show you and your comrades along with your fellow travelers how bad your own medicine tastes. I don't like it. Maybe you’ll finally realize that it’s better to get serious. It would be more pleasant. Let's be nice. It'll make difficult discussions a little easier.Dionisio_{January 2, 2015
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Onlookers/lurkers: If you'd prefer to skip the ongoing chat, here’s a list of some (not all) serious posts in this thread: https://uncommondescent.com/genetics/paul-giem-on-overlapping-genetic-codes/#comment-539425Dionisio_{January 2, 2015
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Onlookers/lurkers: If you'd prefer to skip the ongoing chat with wd400 and DNA_Jock, here’s a list of some (not all) serious posts in this thread: https://uncommondescent.com/genetics/paul-giem-on-overlapping-genetic-codes/#comment-539425Dionisio_{January 2, 2015
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Onlookers/lurkers: Here's a list of some (not all) serious posts in this thread: https://uncommondescent.com/genetics/paul-giem-on-overlapping-genetic-codes/#comment-539425Dionisio_{January 2, 2015
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