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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Comments

@129 DNA_Jock
...the final sentence is obviously untrue,...
Are you certain that your (above quoted) statement is true?Dionisio_{January 1, 2015
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#129 DNA_Jock
...the final sentence is obviously untrue,...
Are you certain that your (above quoted) statement is true?Dionisio_{January 1, 2015
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#129 DNA_Jock I have more questions, which will try to post later. :)Dionisio_{January 1, 2015
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DNA_Jock @129
Hence the caveat “as I see it”, which makes it clear that I am only offering up my personal impression, not anything that I know to be true.
Q1. Then why did you make it sound as if it is true? Q2. Why did you make all those personal attacks based on 'personal impression' which you didn't know if it was true? Q3. Is that the way you treat everyone, including your relatives and friends?Dionisio_{January 1, 2015
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@129 DNA_Jock
Hence the caveat “as I see it”, which makes it clear that I am only offering up my personal impression, not anything that I know to be true.
Q1. Then why did you make it sound as if it is true? Q2. Why did you make all those personal attacks based on 'personal impression' which you didn't know if it was true? Q3. Is that the way you treat everyone, including your relatives and friends?Dionisio_{January 1, 2015
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#129 DNA_Jock
Hence the caveat “as I see it”, which makes it clear that I am only offering up my personal impression, not anything that I know to be true.
Q1. Then why did you make it sound as if it is true? Q2. Why did you make all those personal attacks based on 'personal impression' which you didn't know if it was true? Q3. Is that the way you treat everyone, including your relatives and friends?Dionisio_{January 1, 2015
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DNA_Jock @129
All I can say is that you make these “my mind is slow” statements, but (based on your behavior) it appears to me that the “my mind is slow” statements are insincere, and merely made as part of your “Socratic” questioning.

(based on your behavior)
Q1. Please, would you mind to quote the exact text that illustrate what behavior you are referring to?
...it appears to me that...
Q2. Could that be a misperception? Appearances could be deceiving, couldn't they?
...are insincere
Q3. How do you know they are not sincere?
...your “Socratic” questioning.
Q4. Why do you use that term in reference to my simple questions? Thank you in advance for trying to answer my questions.Dionisio_{January 1, 2015
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@129 DNA_Jock
All I can say is that you make these “my mind is slow” statements, but (based on your behavior) it appears to me that the “my mind is slow” statements are insincere, and merely made as part of your “Socratic” questioning.

(based on your behavior)
Q1. Please, would you mind to quote the exact text that illustrate what behavior you are referring to?
...it appears to me that...
Q2. Could that be a misperception? Appearances could be deceiving, couldn't they?
...are insincere
Q3. How do you know they are not sincere?
...your “Socratic” questioning.
Q4. Why do you use that term in reference to my simple questions? Thank you in advance for trying to answer my questions.Dionisio_{January 1, 2015
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#129 DNA_Jock
All I can say is that you make these “my mind is slow” statements, but (based on your behavior) it appears to me that the “my mind is slow” statements are insincere, and merely made as part of your “Socratic” questioning.

(based on your behavior)
Q1. Please, would you mind to quote the exact text that illustrate what behavior you are referring to?
...it appears to me that...
Q2. Could that be a misperception? Appearances could be deceiving, couldn't they?
...are insincere
Q3. How do you know they are not sincere?
...your “Socratic” questioning.
Q4. Why do you use that term in reference to my simple questions? Thank you in advance for trying to answer my questions.Dionisio_{January 1, 2015
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#129 DNA_Jock
Re 131, No, not really.
Why couldn't you answer the question posted @131?Dionisio_{January 1, 2015
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DNA_Jock @129
The problem, as I see it, is that you are D-K blissfully unaware of these shortcomings: when you make these self-deprecating statements, you consider them merely part of your lame Socratic shtick, and you do not actually believe them to be true, sadly.
Can you explain in easy to understand terms and with as many details as necessary, how do you know that what you wrote (above quoted text) is true? Thank you.Dionisio_{January 1, 2015
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@129 DNA_Jock
The problem, as I see it, is that you are D-K blissfully unaware of these shortcomings: when you make these self-deprecating statements, you consider them merely part of your lame Socratic shtick, and you do not actually believe them to be true, sadly.
Can you explain in easy to understand terms and with as many details as necessary, how do you know that what you wrote (above quoted text) is true? Thank you.Dionisio_{January 1, 2015
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#129 DNA_Jock
The problem, as I see it, is that you are D-K blissfully unaware of these shortcomings: when you make these self-deprecating statements, you consider them merely part of your lame Socratic shtick, and you do not actually believe them to be true, sadly.
Can you explain in easy to understand terms and with as many details as necessary, how do you know that what you wrote (above quoted text) is true? Thank you.Dionisio_{January 1, 2015
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#134 DNA_Jock
So why include all this superfluous science-y stuff, unless in an attempt to appear erudite?
Q1. Could there be other reasons? Q2. Why do you call that information superfluous?Dionisio_{January 1, 2015
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#134 DNA_Jock
Your 132 acknowledges the condescending part.
Please, can you quote the specific text that supports your statement? Thank you.Dionisio_{January 1, 2015
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Dionisio, Re 130, Your 132 acknowledges the condescending part. As to the “erudite” part, the text
and optics and refraction and reflection and light spectrum and wave length and wave amplitude and wave frequency and geometry and the eyes mechanisms and the neuroscience mechanisms that transmit and process the light information in the brain, and all that stuff
can safely be omitted from your paragraph without any loss of meaning. So why include all this superfluous science-y stuff, unless in an attempt to appear erudite? Re 131, No, not really. All I can say is that you make these “my mind is slow” statements, but (based on your behavior) it appears to me that the “my mind is slow” statements are insincere, and merely made as part of your “Socratic” questioning. Hence the caveat “as I see it”, which makes it clear that I am only offering up my personal impression, not anything that I know to be true. Re 133, What you wrote to me @99 was
Have you heard of the spliceosome and all that stuff in post-transcriptional regulation, before the translation in the ribosomes. Have you heard of the post-translational regulation, before the protein folding takes place? At the end of those intermediate processes the final sequence of amino acids may not exactly reflect the original sequence of nucleotide in the protein coding portion of the DNA that was transcribed into the initial pro-mRNA making the mRNA. I don’t know much about this, hence any correction is welcome!
Given that “ I’m not trying to learn biology from DNA_Jock”, the final sentence is obviously untrue, even if you choose to redefine “much” to mean “as much as I would like”. By your own definitions, you are not a “sincere interlocutor” (see 113). Now I cannot know what is in your mind, obviously, but the way you alternate between “curious idiot” mode and “erudite and condescending” mode (see 129) leads me to the conclusion that you think you are lying when you profess the depth of your ignorance. The idea that you are indulging in a little “role-play” for Socratic effect is the most charitable explanation for this pattern, and would explain why you are unable to keep track of whether you are interested in learning biology from wd400 or not (see 122). And the good news is that you are not, in fact, lying when you say “I don’t know much about this”.DNA_Jock_{January 1, 2015
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#129 DNA_Jock
So when you write “I don’t know much about this” you only think you are lying.
How do you know that I think that I'm lying? I don't want to lie because that's a very sinful action. God knows when I'm lying. He does not like when I lie. Why don't you want to believe me when I write that I don't know much about something? How do you know what 'much' means to me? Please, would you explain all this in easy to understand terms? Thank you. PS. I'm not an ID proponent, or a YEC, or OEC, or any acronym of any kind. I'm a miserable sinner who has been saved by God, even though I don't deserve it at all. My only identity is in Christ, my Savior and my Lord. That's all. When I say I don't know much of something, I really mean it. Specially when I read a few posts written by other folks here, perhaps including you too, and I have very little idea, if any, of what is being discussed. Biology has fascinated me since a few years ago. I retired early, so that I could have more tome to learn some new software development techniques for 3D interactive animation development, which I did not know, and also certain aspects of biology associated with information-processing within the bio systems. My mother-in-law doesn't like when I say that I'm worse than most people I know personally. She doesn't want to understand that I don't compare myself with other people, but with the absolute standard of purity, Christ, and I can't even start the comparison. That's why Paul the apostle wrote that he is the chief of sinners. Likewise, I compare my knowledge with what is unknown to me, which is practically infinite. When I write that I don't know much about something, I'm not comparing my knowledge level with other people's. I'm comparing it with what I would like to know. Perhaps I can't explain this in a clear way that is understandable. But I'm very interested in ensuring that you do understand me. I pray that we can have a serious conversation. But that's not under my control. Actually, very little is under my control. I wish you a Happy New Year and many blessings in the days to come. To you and to your family and to your friends. Perhaps the story of my former boss and I can repeat with you and me.Dionisio_{December 31, 2014
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#129 DNA_Jock
I am still willing to cut you a little slack regarding English-not-your-first language – my apologies for confusing you with the colloquial phrase “my understanding is neither here nor there” – so here’s a piece of friendly advice : ending your pontification with “Do you grasp what I just wrote?” is rude.
I didn't know that. Please, accept my apologies for saying something that was rude. Really appreciate that you have brought this up to my attention. I think my former boss used to say that to me, but I'm not completely certain about that. However, if he really did, I didn't take it as offensive back then. In a way I'm glad I wasn't aware of the correct meaning of that expression in those days. Actually, at some point my supervisor, who was the head of development, told me he was wasting time when dealing with me, because I did not understand much of what he was trying to tell me and he did not understand much of what I was trying to tell him. Eventually I learned just enough English to keep a very basic communication with my supervisor and colleagues. I guess my knowledge of English has not progressed much further from that level since then. But God is gracious and took me through a long and winding road to this point. Can't complain at all. I've been blessed. :) BTW, my former supervisor is a good friend of mine now. Isn't that great? Perhaps you're familiar with this biblical passage, which I believe somehow applies to this case:
...not many of you were wise according to worldly standards,[c] not many were powerful, not many were of noble birth. 27 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; 28 God chose what is low and despised in the world, even things that are not, to bring to nothing things that are, 29 so that no human being[d] might boast in the presence of God. 30 And because of him[e] you are in Christ Jesus, who became to us wisdom from God, righteousness and sanctification and redemption, 31 so that, as it is written, “Let the one who boasts, boast in the Lord.”
Dionisio_{December 31, 2014
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#129 DNA_Jock
The problem, as I see it, is that you are D-K blissfully unaware of these shortcomings: when you make these self-deprecating statements, you consider them merely part of your lame Socratic shtick, and you do not actually believe them to be true, sadly.
Can you explain in easy to understand terms and with as many details as necessary, how do you know that what you wrote (above quoted text) is true? Thank you.Dionisio_{December 31, 2014
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#129 DNA_Jock Please, can you explain in easy to understand terms what exactly reveals an “erudite and condescending” mode in the below quoted text?
If the daddy knows very well why the sky is looks blue, and he is really interested in explaining it to the child, and he has the time and conditions to do it, then he should be able to explain it to a 6-yo child in a manner that is easily understood. However, if daddy doesn’t have a good grasp of physics and optics and refraction and reflection and light spectrum and wave length and wave amplitude and wave frequency and geometry and the eyes mechanisms and the neuroscience mechanisms that transmit and process the light information in the brain, and all that stuff, or daddy doesn’t care about the child’s question, or he does not have time or conditions to do it, then daddy can’t explain that phenomenon to anyone between zero and 110-yo. Do you grasp what I just wrote?
Thanks.Dionisio_{December 31, 2014
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Honestly, Dionisio, you don’t upset me. You crack me up. You wrote:
But please, keep in mind that, as I have stated before (yes, maybe in other threads), my reading comprehension is poor, my communication skills are almost nonexistent, English is not my first language, my mind is slow…
I am mindful of these attributes, Dionisio, since they shine through your prose. Nobody with any knowledge of the subjects under discussion could read your interactions with reality-based posters here and fail to notice your shortcomings. I was quite willing to help you overcome these handicaps and learn some biology, if you were interested. The problem, as I see it, is that you are D-K blissfully unaware of these shortcomings: when you make these self-deprecating statements, you consider them merely part of your lame Socratic shtick, and you do not actually believe them to be true, sadly. This is revealed when you make the switch from “curious idiot” mode into “erudite and condescending” mode, e.g.
If the daddy knows very well why the sky is looks blue, and he is really interested in explaining it to the child, and he has the time and conditions to do it, then he should be able to explain it to a 6-yo child in a manner that is easily understood. However, if daddy doesn’t have a good grasp of physics and optics and refraction and reflection and light spectrum and wave length and wave amplitude and wave frequency and geometry and the eyes mechanisms and the neuroscience mechanisms that transmit and process the light information in the brain, and all that stuff, or daddy doesn’t care about the child’s question, or he does not have time or conditions to do it, then daddy can’t explain that phenomenon to anyone between zero and 110-yo. Do you grasp what I just wrote?
The above is not the writing of someone who believes their comprehension poor, communication skills non-existent and their mind slow. It is the writing of someone trying to show off. You even changed “is blue” to “looks blue” so that you could add some superfluous tripe about biology. But you failed to mention “light scattering”. Ooops. I am still willing to cut you a little slack regarding English-not-your-first language – my apologies for confusing you with the colloquial phrase “my understanding is neither here nor there” – so here’s a piece of friendly advice : ending your pontification with “Do you grasp what I just wrote?” is rude. When it comes to biology, the gap between your level of understanding and what you think is your level of understanding is rather wide:
Have you heard of the spliceosome and all that stuff in post-transcriptional regulation, before the translation in the ribosomes. Have you heard of the post-translational regulation, before the protein folding takes place? At the end of those intermediate processes the final sequence of amino acids may not exactly reflect the original sequence of nucleotide in the protein coding portion of the DNA that was transcribed into the initial pro-mRNA making the mRNA. I don’t know much about this, hence any correction is welcome!
The above paragraph takes some really basic, introductory level biology and tries to make it sound complicated. Given that you know my background and even tried to make fun of the fact that I used to be a molecular biologist, the “Have you heard” questions are rather condescending. Before you wrote this, I was ready to discuss formylglycine and other mechanisms that might not get covered an intro to biochem course; we could have had a “serious discussion” about biology. But you would rather ask childish “Have you heard?” questions and lecture me on pedagogical technique. Your choice, I guess. And yet again, hilariously, your attempt at sounding erudite fails: there is a basic error in your paragraph. So when you write “I don’t know much about this” you only think you are lying.DNA_Jock_{December 31, 2014
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Ok, let's wrap up this discussion. Again, here's a list of some (not all) interesting posts in this thread: https://uncommondescent.com/genetics/paul-giem-on-overlapping-genetic-codes/#comment-539425Dionisio_{December 30, 2014
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5for @125
Go home Dinisio, you’ve been shown up badly.
Hmm... What do you mean? Why did you write that? Thank you.Dionisio_{December 30, 2014
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#122 DNA_Jock Why do you like to write so many personal attacks? Why are you so upset? Can't you calm down? Obviously, older comments I posted in other threads could not refer to specific names associated with newer posts in this thread. Why have you made such a big deal of that obvious detail you have failed to understand? However, now looking back at my comments, I think I realize what could have caused so much confusion, itching and hype. Perhaps I should take some blame for not communicating my thoughts correctly. If that's the case, then I apologize for that mistake. But please, keep in mind that, as I have stated before (yes, maybe in other threads), my reading comprehension is poor, my communication skills are almost nonexistent, English is not my first language, my mind is slow - when someone tells a joke on the weekend, I may get it by Tuesday, after my wife explains it to me. Now you have a better idea who you're dealing with. :) All that said, below you may see a few examples of my comments in other threads, where I wrote about similar situations, that have to do with folks that get easily upset, apparently because they don't seem to like having to answer certain number of questions (though I really don't know the exact reason for their bad mood): Post #45 in this thread: https://uncommondescent.com/intelligent-design/an-attempt-at-computing-dfsci-for-english-language/#comment-527201 Post #137 in this thread: https://uncommondescent.com/intelligent-design/an-attempt-at-computing-dfsci-for-english-language/#comment-527458 Post #138 in this thread: https://uncommondescent.com/intelligent-design/an-attempt-at-computing-dfsci-for-english-language/#comment-527461 Post # 846 in this thread: https://uncommondescent.com/intelligent-design/an-attempt-at-computing-dfsci-for-english-language/#comment-532823 Perhaps there are more threads where I have posted similar comments. Is the situation more clear to you now? Relax. Calm down. :)Dionisio_{December 30, 2014
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Go home Dinisio, you've been shown up badly.5for_{December 30, 2014
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#122 DNA_Jock
So it is clear from the context that “our discussions” includes your querying of wd400 @87.
No, that's not accurate, you've misunderstood it. My questions were required before we could get into a serious discussion. Hence, they were not part of a serious discussion yet. Unfortunately, we never reached that desired 'serious discussion' level. For example, I have been able to reach that 'serious discussion' level with gpuccio on various occasions, because gpuccio is very helpful and careful about answering my questions clearly and accurately. Sometimes he has corrected my misunderstandings with refined pedagogical skills. I've heard he's a medical doctor, but I won't be surprised if I find that he's also an academic professor. Apparently some folks can't or don't want to do the same. But that's not my problem. If there's anything I could do to help, I would definitely do it. :)Dionisio_{December 30, 2014
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#122 DNA_Jock
my understanding is neither here or there,...
Yes, it's obvious that your understanding seems to be nowhere. :) Glad to see you're aware of that too. :)Dionisio_{December 30, 2014
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Oh dear. Do try to keep up.
None. Both are accurate. Your lack of understanding confirms them.
Unfortunately for you, Dionisio, my understanding is neither here or there, since as I pointed out to you in 119 both statements were made to wd400: In post 87, you asked wd400 a series of ~13 questions about basic biology. Post 88 was your ‘addendum’ to post 87, in which you stated :
@88, addressing wd400: Please, be aware that I’m a student (autodidact), hence I’m interested in learning many things I still don’t know about biology. Any useful information I can gather from our discussions is very appreciated.
So it is clear from the context that “our discussions” includes your querying of wd400 @87.
@103, addressing wd400: As I have stated very clearly before, I’m not trying to learn biology from DNA_Jock or from you or from any of your comrades and fellow travelers
where did you make this “very clear” statement that you allude to?
In another thread. Why are you so interested in that?
For the following reason: unless you made that “very clear” statement in the 3 hour 7 minute window between your posts 88 and 103, it represents a prior statement that you are NOT trying to learn biology from DNA_Jock or wd400. Therefore your lame ”No one can’t learn much of anything from anyone who is not interested in serious discussions” attempt to weasel out of being caught in a lie fails miserably. According to you, you stated (on another thread) that you were NOT interested in learning biology from wd400, then stated @88 that you were, then stated @103 that you were not. “Serious discussions”: you keep using that phrase, I do not think that it means… I am happy to discuss biology with anyone who is interested.DNA_Jock_{December 30, 2014
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#119 DNA_Jock
Which of the following two statements are you going to retract?
None. Both are accurate. Your lack of understanding confirms them. :) No one can't learn much of anything from anyone who is not interested in serious discussions. See gpuccio as a contrasting example of someone who patiently explains things with details and is always willing to answer all questions, even my childishly dumb ones. :) You may want to learn from him too.
where did you make this “very clear” statement that you allude to?
In another thread. Why are you so interested in that? :)
How can one avoid the conclusion that you are, by your own definitions, insincere? How can one avoid the conclusion that either 88 or 103 must be a lie?
Perhaps one way to avoid that conclusion is to read carefully what I wrote and to have a desire to really understand it. However, it may take a miracle for that to occur. :)
It’s okay if you don’t want to answer these questions.
Yes, it's ok if one doesn't answer questions. You have not answered some questions in this thread, but then you claimed that you did answered them. That's fine. ¡Feliz Año Nuevo! :)Dionisio_{December 30, 2014
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I'm certainly confident that onlookers will be able to understand why you won't respond, Dionisio.wd400_{December 30, 2014
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