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

PS. Post #113 was loaded with so much vitriolic ad hominem nonsense that it’s not worth commenting on it, besides post #114.
LOL Vitriol: Yes Ad hominem: No. That phrase does not mean what you think it means... Nonsense: Why are you suddenly so shy about pointing out nonsense? Isn't that the ultimate goal of your brilliant inquisitorial method? But your lack of any response is noted. My response to 114 : "Yes, I am sure". Now for the fun bit: Which of the following two statements are you going to retract, Dionisio?
@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.

@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
Furthermore, where did you make this "very clear" statement that you allude to? In the same post (103) you also, very helpfully, defined a common goal of "sincere interlocutors" thus:
In any case, the sincere interlocutors will try their best to keep the discussion moving smoothly toward a mutually beneficial common goal: shedding more light on the discussed subject and ultimately learning more about it.
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? It's okay if you don't want to answer these questions. I'll understand. LMAODNA_Jock_{December 30, 2014
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PS. Post #113 was loaded with so much vitriolic ad hominem nonsense that it's not worth commenting on it, besides post #114.Dionisio_{December 30, 2014
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http://1.bp.blogspot.com/-gKHud3Kib0E/UhYvnhwz5XI/AAAAAAAAHyk/DdOVpjw-Xe4/s1600/quien+rie+ultimo+rie+mejor.jpgDionisio_{December 30, 2014
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Reminding some (not all) important information that was posted in this thread (leaving aside the distracting senseless debate that pointed nowhere): #14
Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution DOI: 10.1126/science.1243490 Genomes contain both a genetic code specifying amino acids and a regulatory code specifying transcription factor (TF) recognition sequences. We used genomic deoxyribonuclease I footprinting to map nucleotide resolution TF occupancy across the human exome in 81 diverse cell types. We found that ~15% of human codons are dual-use codons (“duons”) that simultaneously specify both amino acids and TF recognition sites. Duons are highly conserved and have shaped protein evolution, and TF-imposed constraint appears to be a major driver of codon usage bias. Conversely, the regulatory code has been selectively depleted of TFs that recognize stop codons. More than 17% of single-nucleotide variants within duons directly alter TF binding. Pervasive dual encoding of amino acid and regulatory information appears to be a fundamental feature of genome evolution. http://www.sciencemag.org/content/342/6164/1367.abstract?sid=10ce3b98-d907-4d26-be90-89ffa3a245fb
#15
Exploiting hidden information interleaved in the redundancy of the genetic code without prior knowledge doi: 10.1093/bioinformatics/btu797 Dozens of studies in recent years have demonstrated that codon usage encodes various aspects related to all stages of gene expression regulation. When relevant high-quality large-scale gene expression data are available, it is possible to statistically infer and model these signals, enabling analysing and engineering gene expression. However, when these data are not available, it is impossible to infer and validate such models. http://bioinformatics.oxfordjournals.org/content/early/2014/12/24/bioinformatics.btu797.abstract
#16
Multiple roles of the coding sequence 5? end in gene expression regulation doi: 10.1093/nar/gku1313 The codon composition of the coding sequence’s (ORF) 5? end first few dozen codons is known to be distinct to that of the rest of the ORF. Various explanations for the unusual codon distribution in this region have been proposed in recent years, and include, among others, novel regulatory mechanisms of translation initiation and elongation. However, due to the fact that many overlapping regulatory signals are suggested to be associated with this relatively short region, its research is challenging. Here, we review the currently known signals that appear in this region, the theories related to the way they regulate translation and affect the organismal fitness, and the debates they provoke. http://nar.oxfordjournals.org/content/early/2014/12/12/nar.gku1313.abstract
#17
Different types of secondary information in the genetic code doi: 10.1261/rna.044115.113 Whole-genome and functional analyses suggest a wealth of secondary or auxiliary genetic information (AGI) within the redundancy component of the genetic code. Although there are multiple aspects of biased codon use, we focus on two types of auxiliary information: codon-specific translational pauses that can be used by particular proteins toward their unique folding and biased codon patterns shared by groups of functionally related mRNAs with coordinate regulation. AGI is important to genetics in general and to human disease; here, we consider influences of its three major components, biased codon use itself, variations in the tRNAome, and anticodon modifications that distinguish synonymous decoding. AGI is plastic and can be used by different species to different extents, with tissue-specificity and in stress responses. Because AGI is species-specific, it is important to consider codon-sensitive experiments when using heterologous systems; for this we focus on the tRNA anticodon loop modification enzyme, CDKAL1, and its link to type 2 diabetes. Newly uncovered tRNAome variability among humans suggests roles in penetrance and as a genetic modifier and disease modifier. Development of experimental and bioinformatics methods are needed to uncover additional means of auxiliary genetic information. http://rnajournal.cshlp.org/content/20/7/977.abstract
#18
Overlapping genes and variability of the genetic code DOI: 10.1023/A:1026631030516 the finding that the meanings of some codons of the mitochondrial genetic code differ from the usual ones was unexpected. http://www.researchgate.net/publication/12118880_Overlapping_genes_and_variability_of_the_genetic_code
#19
Computation of the genetic code DOI: 10.1134/S1064562410040095 The author has conducted mathematical analysis of genetic decoding for a number of years. Overlapping genes, discovered in 1976, were one of the main objects of the study. These are cases where the same segment of DNA encodes two or more protein sequences. Numerous cases of identified genetic overlaps allowed setting a number of mathematical problems that have been successfully solved. A detailed exposition of these problems is given in the author’s monograph Mathematical Analysis of Genetic Code (BINOM, Moscow, 2010). Such problems have made it possible to penetrate deeply enough into the structure of the genetic code and its relationship with the overlapping genes. As a result, a new problem was set: the computation of the genetic code on the basis of the amino acid sequences that record overlapping genes. One approach to this problem is described in this paper. http://www.researchgate.net/publication/243092380_Computation_of_the_genetic_code
#20
Some new characteristics of large genomes DOI: 10.1134/S2070048213030071 http://www.researchgate.net/publication/257865080_Some_new_characteristics_of_large_genomes
#21
Scientists Discover Another Genetic Code Overlapping language seems to help direct DNA activity in cells, researchers report Another code within DNA has been discovered by scientists — a finding that the researchers say sheds light on how changes to DNA affect health. Since the genetic code was first deciphered in the 1960s, scientists have believed it was used solely to write information about proteins. But this new study from University of Washington scientists found that genomes use the genetic code to write two separate languages. One language describes how proteins are made, and the other helps direct genetic activity in cells. One language is written on top of the other, which is why this other language went undiscovered for so long, according to the report in the Dec. 13 issue of Science. “For over 40 years, we have assumed that DNA changes affecting the genetic code solely impact how proteins are made,” team leader Dr. John Stamatoyannopoulos, an associate professor of genome sciences and of medicine, said in a university news release. “Now we know that this basic assumption about reading the human genome missed half of the picture,” he said. http://health.usnews.com/health-news/news/articles/2013/12/12/scientists-discover-another-genetic-code
#23
Scientists discover double meaning in genetic code Scientists have discovered a second code hiding within DNA. This second code contains information that changes how scientists read the instructions contained in DNA and interpret mutations to make sense of health and disease. http://www.washington.edu/news/2013/12/12/scientists-discover-double-meaning-in-genetic-code/
#25
Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells The classic organization of a gene structure has followed the Jacob and Monod bacterial gene model proposed more than 50 years ago. Since then, empirical determinations of the complexity of the transcriptomes found in yeast to human has blurred the definition and physical boundaries of genes. Using multiple analysis approaches we have characterized individual gene boundaries mapping on human chromosomes 21 and 22. Analyses of the locations of the 5? and 3? transcriptional termini of 492 protein coding genes revealed that for 85% of these genes the boundaries extend beyond the current annotated termini, most often connecting with exons of transcripts from other well annotated genes. The biological and evolutionary importance of these chimeric transcripts is underscored by (1) the non-random interconnections of genes involved, (2) the greater phylogenetic depth of the genes involved in many chimeric interactions, (3) the coordination of the expression of connected genes and (4) the close in vivo and three dimensional proximity of the genomic regions being transcribed and contributing to parts of the chimeric RNAs. The non-random nature of the connection of the genes involved suggest that chimeric transcripts should not be studied in isolation, but together, as an RNA network. Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, et al. (2012) Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells. PLoS ONE 7(1): e28213. doi:10.1371/journal.pone.0028213 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0028213
#26
Scientists discover double meaning in genetic code Scientists have discovered a second code hiding within DNA. The second code contains information that changes how scientists read the instructions contained in DNA and interpret mutations to make sense of health and disease. Genomes use the genetic code to write two separate languages. One describes how proteins are made, and the other instructs the cell on how genes are controlled. One language is written on top of the other. http://www.sciencedaily.com/releases/2013/12/131212142151.htm
#30 by gpuccio
“Overlapping genes referred in post #19 are not exactly the same as the overlapping languages referred in post #21. They seem like two different concepts, don’t they? The former refers to overlapping protein code, which apparently was discovered in 1976, while the latter has to do with the alleged recent discovery of another DNA-related language used for the operating logic. Is this correct?!” Yes, it is correct. the first paper is about possible alternative reading frames which use the same nucleotides to code for different aminoacid sequences. While there is overlapping, the symbolic code is the same. The second paper is about the role of nucleotides in promoting the binding of transcription factors. That function can be found anywhere in the genome, including coding exons. So, those nucleotides in coding exons which are also involved in TF binding seem to have a double function: they retain their meaning in the traditional genetic code as symbols of AAs, and at the same time they have a role in interacting with TFs. Here the code is not the same: two different codons can code for the same aminoacid, but only one of them can be active in TF binding. For example, Fig. 2 A of the paper shows that both AAC and AAT code for asparagine, but AAC seems to be preferred in TF interaction, while AAT is not. “BTW, do posts #21 & 23 somehow relate to the TAD concept that you brought up in the ‘third way’ discussion thread?” Only indirectly, in a sense. TADs are divisions of the genome which are determined by specific boundaries which limit long distance interactions between genomic regions when TFs bind to DNA and generate loops. So, in a sense, all that influences TF binding has probably some relationship with TAD architecture.
#33 by gpuccio
hrun0815:
“the overlapping code was discovered in the late seventies”
OK, but the epigenetic levels of regulation are being clarified only now. The contributions of DNA sequences to cell differentiation and regulation by multiple parallel and interacting “codes” (like the methylome, the histone codes, the TF networks and their combinatorial effects, all the post-transcriptional interventions by non coding RNAs, and so on) are hot new subjects of scientific research. They are new, exciting information. And the genome is at the center of those multiple, parallel interactions. So excuse us, poor ID fools, if we are discussing those interesting things that you apparently “failed to notice”.
#63 by gpuccio
“Is the OP video talking mainly about the genetic code specifying amino acids or a regulatory code specifying transcription factor (TF) recognition sequences, or both, or none of them, or something else?” Well, in the video Paul Giem comments (very well, IMO) a paper by George Montañez, Robert J. Marks II, Jorge Fernandez and John C. Sanford. The paper is about the mathematical modeling of beneficial mutations when nucleotides are involved in multiple codes, and does not refer to specific examples. However, there are references in the bibliography. For example, this work by Trifonov: Trifonov EN (1989) Multiple codes of nucleotide sequences. Bull of Mathematical Biology 51:417–432. The original paper is in Russian, but here is the abstract: “Apart from the classical RNA-protein translation code, the genomic DNA sequences carry many other, nontriplet codes of different nature. Those of them which are at least partly deciphered are discussed in this review in the order of their estimated occupancy in the eukaryotic genome. Each of the codes is degenerate, like the triplet code. This is the basis for their coexistence in one and the same sequence, so that the same base often (if not always) belongs to several different overlapping sequence patterns. The genomic DNA sequence is, therefore, an unusual example of natural sequence compression where, apparently, each single symbol not only is not wasted, but is also used simultaneously in many superimposed messages.” So, the idea is that if some nucleotides are functional at different levels and in different codes, that implies extreme functional constraint, and extreme improbability of evolving the result by random beneficial mutations. That seems to be the main point of the paper. The recent paper you referenced in your post: “Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution” http://www.sciencemag.org/content/342/6164/1367 is another good example. I think that any multiple function at the nucleotide level is a special constraint for that position. Multicode functionality is a special kind of information compression, ad it generates extreme limitations. The codes can be of the protein coding type, or just regulatory: the concept remains the same. We can have multiple overlapping ORFs, or an ORF overlapping with non coding regulatory sequences, and so on. Look at this page, for example: http://www-sequence.stanford.edu/group/yeast_deletion_project/overlapping.html
Dionisio_{December 30, 2014
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It's been said that it ain't over 'til is over. Well, apparently this thread is over. Well, it lasted much longer than one could have expected at its start. :) Happy New Year! ¡Feliz Año Nuevo!Dionisio_{December 30, 2014
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#113 DNA_Jock
Ironically, all daddy needs to understand is “Light-scattering”,...
Are you sure? That limited knowledge won't help, when dealing with the questions a curious child could ask, which could cover all areas of knowledge at some point sooner than later. You see, children have a sense of wonder that gets lost as we grow older and let the mundane things of live to take over our original curiosity. Every answer may provoke new questions. The process may continue until it's time to take a break or something (external signal, physiological need, etc.) distracts the child's attention away from the original curiosity. Obviously, different children act differently. But generally, that's the expected behavior. That's the way we should approach science research too. With child-like mentality, not sparing any question, no matter how dumb it may sound. On the other hand, children (as well as adults) complain when required to deal with larger volumes of information in order to understand a problem. When my children were in high school, they took AP calculus. They asked me to help them to learn how to resolve the problems they had for homework. When I tried to explain to them a practical method to resolve the problems, I noticed they could not grasp it well. Every time they faced a different problem, with a slight change of conditions, they had hard time trying to figure out what was what. So I started to ask them very basic mathematical questions, going from the most elementary issues and gradually moving up to more complex concepts and principles. Then they complained that I'm asking them so many stupid questions about things they already knew well. I told them I needed to ask them those questions so that I could find what they didn't know, in order to take it from there. Well, to make the story shorter, they reluctantly submitted to my interrogation until I detected the weak spots in their knowledge, which then I explained to them carefully, using all kinds of illustrations and examples. Apparently the method worked, because they passed those AP calculus courses. That was long ago. They are now medical doctors, which is far beyond what my wife and I reached educationally or professionally. :) Ironically, it was a human development textbook, which one of my children left at home after finishing medical school, that activated my curiosity for biology, when I tried -unsuccessfully- to read a few pages on the cellular processes that take place in the first couple of weeks after conception. The few paragraphs I barely could read blew up my mind into pieces. I have not recovered since them. The sense of wonder, which I experienced so intensively in my childhood, but had lost as I grew older, suddenly was back, even more intensive and passionate than ever before. I gradually paid less attention to my software development work, as my mind got consumed in trying to understand other arts of that book. I started to ask questions to relatives and friends in biomedical fields. But my questions had a heavy information-processing flavor, most probably influenced by my software development background, hence the scientists I consulted were not sure they understood the bottom line of my questioning (well, most probably it was also because I did not know and perhaps still don't know how to ask questions correctly).Dionisio_{December 29, 2014
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Dionisio, I know you think you are applying the Socratic method brilliantly, but your failure to read for comprehension and actually engage with your interlocutors on the subject matter makes you look more like an ignorant six-year-old. I did enjoy this:
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?
You sound very erudite, if a bit condescending. Ironically, all daddy needs to understand is “Light-scattering”, which, much to my amusement, did not make it onto your list… You claim that this thread is clear testimony to the fact that I have not answered all your questions (excluding the ‘not even wrong’ one). Here’s the problem: given that I had already answered the question
Do you know approximately when was the “regulatory code specifying transcription factor (TF) recognition sequences” first referenced in textbooks?
with the response “No” (@89), then your questions at 93
When was the overlapping between two distinct codes first mentioned in textbooks? Since the eighties? Earlier? Later? It hasn’t been mentioned at all? Don’t know?
have been answered before you ever asked them. And Socrates would never ask them, because he would make the effort to comprehend the answers he receives. In a similar vein, your other questions have already been answered. Q: “What is it that you don’t like about gpuccio’s final sentence @33?” A: “It’s asinine.” Maybe you meant to ask a different question. :) I have no motivation to keep answering questions that have already been answered, merely because my inquisitor isn't paying attention. Your comment 103 is the conversation-ender, however:
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
Please provide a link to your “very clear” statement with respect to myself. I must have missed it. But if you are not interested in learning any biology, then I will stop trying to help you learn.
I’m trying to make you and your comrades show your real motives in this discussion, so everyone sees them openly. Those interested in having serious discussions will try to answer all questions.
Well, all relevant questions. I am happy to discuss biology with anyone who is interested in discussing biology.
In any case, the sincere interlocutors will try their best to keep the discussion moving smoothly toward a mutually beneficial common goal: shedding more light on the discussed subject and ultimately learning more about it.
So, by your own definition [in bold above], you are not a sincere interlocutor. ‘Nuff said.DNA_Jock_{December 29, 2014
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#111 bornagain77 Yes, that's the ultimate reason that explains the ultimate reality. But I don't want to push the interlocutors into that area at the beginning of the discussion. I believe most evidences discussed in a serious discussions should eventually lead us all to that ultimate realization.Dionisio_{December 29, 2014
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Dionisio, the sky is blue because God made it that way! :) ,,,These specific frequencies of light (that enable plants to manufacture food and astronomers to observe the cosmos) represent less than 1 trillionth of a trillionth (10^-24) of the universe’s entire range of electromagnetic emissions. Extreme Fine Tuning of Light for Life and Scientific Discovery – (Privileged Planet excerpt)video https://vimeo.com/114136732 Fine Tuning Of Universal Constants, Particularly Light - Walter Bradley - video https://vimeo.com/114137127 Fine Tuning Of Light to the Atmosphere, to Biological Life, and to Water - graphs http://docs.google.com/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMTljaGh4MmdnOQ Michael Denton: Remarkable Coincidences in Photosynthesis - podcast http://www.idthefuture.com/2012/09/michael_denton_remarkable_coin.htmlbornagain77_{December 29, 2014
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#108 fifthmonarchyman
Socratic method (also known as method of elenchus, elenctic method, or Socratic debate), named after the classical Greek philosopher Socrates, is a form of inquiry and discussion between individuals, based on asking and answering questions to stimulate critical thinking and to illuminate ideas.
Excellent point. Thank you. Glad to see a thinking person here! :)Dionisio_{December 29, 2014
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#107 Aurelio Smith
It’s pretty clear Dionisio doesn’t know the answers to many questions. He is like a six-year-old asking “why is the sky blue, daddy,?” Such questions are easy for a six-year-old to ask but the answers are impossible for him to grasp.
Please, read posts # 99, 103, 105, 106 for my comments related to what you just wrote. 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? :)Dionisio_{December 29, 2014
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Aurelio Smith says, He is like a six-year-old asking “why is the sky blue, daddy,?” I say, quote: what do they teach at these schools? end quote: CS Lewis ....... Socratic method (also known as method of elenchus, elenctic method, or Socratic debate), named after the classical Greek philosopher Socrates, is a form of inquiry and discussion between individuals, based on asking and answering questions to stimulate critical thinking and to illuminate ideas. .......... peacefifthmonarchyman_{December 29, 2014
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#104 wd400
You mean you waste people’s time asking them questions you know the answers to, then claim others are not interested in a serious discussion?
No, quite on the contrary. I don't want to waste anyone's time. I don't have any rights nor desire to do so. That's why I ask questions that may lead to a productive discussion or completely shutdown the whole exchange for good. It all depends on the interest shown by each party involved in the discussion. I don't know the exact answer to all the questions I ask. I have studied the subject, but see contradictions between different statements written by various folks in the thread or outside the blog. So I ask for clarification on the subject, while giving the interlocutors the opportunity to easily reveal their true motives for engaging in the given discussion, before the discussion proceeds too far, trying to keep it from turning into a wasted senseless debate. I don't know many details and terminology, but just enough to discuss and to collaborate in multidisciplinary teamwork approach, which is very common in research these days. Computer scientists, electrical engineers, biologists, all collaborate in multidisciplinary teams working on biology or biotechnology research. None of the members are experts in everything. They complement one another. Their union has much more knowledge and expertise than the total sum of their individual knowledge and expertise. I have seen excessively long debates in this blog, that ultimately have led nowhere. That's a waste of time I prefer to avoid. My initial questioning may quickly help to reveal the true motives of both parties, before the debate extends further into waste territory. That's saved time. Perhaps if others in this blog take a similar approach, many excessively long debates would have stopped much earlier than they actually did. That would have translated into saved time for everyone. But some folks in this blog don't mind the long senseless debates, because they could benefit the onlookers/lurkers out there. See post #105 for more on this.Dionisio_{December 29, 2014
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Obviously some interlocutors in this blog don't seem interested in serious discussions. Perhaps my rare 'blitzkrieg' interrogation approach is uncomfortable to those who just want to mock others and have fun. Some interlocutors called me 'exorcist' and 'Spanish inquisitor' in this blog, because I was asking many simple childish questions to help them reveal to me their true motives. If that's your case, too bad. Just ignore my posts, so you go undetected to me. :) Again, I'm trying to have serious discussions, but need to know if my interlocutors are interested too. They are the only ones who can reveal their true motives. I can't. Hence I ask simple questions, which sometimes seem kind of dumb, just to let the interlocutors react and thus reveal their own motives. That's all. I rejoice when I find someone like gpuccio, who sticks to the questions I ask, and goes an extra mile for the sake of explaining to me anything I have asked that he knows. He has never told me to go out and look for that information somewhere else, except when he himself has provided the links to the papers he recommends. And you know what? I'm not sure if gpuccio and I are on the same page theologically speaking. Probably not exactly. But he is very respectful and always willing to share what he knows, which seems to be a lot more than I and many other folks in this blog do. Gpuccio explains things in a very respectful manner, in very simple terms, and doesn't make fun of my lack of knowledge or my dumb-sounding questions or my sometimes repetitive style. Also, gpuccio has demonstrated possessing the gift of patience, which I miserably lack. He has engaged in discussions with stubborn interlocutors that obviously have little or no interest in their discussions. Definitely I was not endowed with such a virtue. I believe gpuccio is a very dedicated medical doctor, with additional extensive studies in biological sciences, but he could do very well as a professor lecturing at a university. But that's my personal perception of his strong pedagogical skills. Just wanted to comment on two contrasting extremes seen in this blog. :)Dionisio_{December 29, 2014
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You mean you waste people's time asking them questions you know the answers to, then claim others are not interested in a serious discussion?wd400_{December 29, 2014
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#101 wd400
Biology is weird, for any general rule there will be exceptions. There are a few cases in which genomic DNA doesn’t fully specify a protein, as later modifications change the mRNA or amino acid sequence. More generally, most of the questions you are asking are the things you’d expect to learn in the first week of a molecular biology course, if you don’t understand these you have no hope of understanding the papers you link to. It’s really not DNAjock’s (or anyone else’s) job to teach you elementary biology, and making snide comments about there not answering all of your many questions is not becoming.
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. That would be like trying to swim across the ocean nonstop without any assistance. Well, perhaps the latter is not as difficult as the former. :) There are plenty of resources to learn biology these days. Online courses at reputable universities is just one of the many ways to acquire the information. Been there, done that. I'm trying to make you and your comrades show your real motives in this discussion, so everyone sees them openly. Those interested in having serious discussions will try to answer all questions. If they don't know the answer, they humbly will admit it. In any case, the sincere interlocutors will try their best to keep the discussion moving smoothly toward a mutually beneficial common goal: shedding more light on the discussed subject and ultimately learning more about it. That's all. It's that simple. Relax. Cool down. :)Dionisio_{December 29, 2014
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Apparently this could be the post #101
#89 DNA_Jock
Dionisio: Does that nucleotide sequence in the DNA always tell you the final sequence of amino acids? DNA_Jock: Almost always. Dionisio: Why not always? In which case(s) the two sequences don’t correspond directly?
#95 DNA_Jock
DNA_Jock: re 94, google formylglycine.

I'm not asking for specific examples at this point, just general concepts, principles. See Joe's post #97. Can you summarize general concepts, principles? If examples are required, they should be given upon request. Although voluntarily providing them is ok too, but after the general concepts, principles, are presented in a compacted manner. Does this make sense? However, many folks don't like to engage in this kind of serious discussions. That's fine. If you're in that group, just say it, so those who might be interested in having such a discussion know that they have to find another interlocutor. :)Dionisio_{December 29, 2014
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Dionisio, Biology is weird, for any general rule there will be exceptions. There are a few cases in which genomic DNA doesn't fully specify a protein, as later modifications change the mRNA or amino acid sequence. More generally, most of the questions you are asking are the things you'd expect to learn in the first week of a molecular biology course, if you don't understand these you have no hope of understanding the papers you link to. It's really not DNAjock's (or anyone else's) job to teach you elementary biology, and making snide comments about there not answering all of your many questions is not becoming.wd400_{December 29, 2014
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Ok, this is just a post to reach the #100 mark! :)Dionisio_{December 29, 2014
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#89 DNA_Jock
Dionisio: Does that nucleotide sequence in the DNA always tell you the final sequence of amino acids? DNA_Jock: Almost always. Dionisio: Why not always? In which case(s) the two sequences don’t correspond directly?
#95 DNA_Jock
DNA_Jock: re 94, google formylglycine.

I'm not asking for specific examples at this point, just general concepts, principles. See Joe's post #97. 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! Can you summarize general concepts, principles? If examples are required, they should be given upon request. Although voluntarily providing them is ok too, but after the general concepts, principles, are presented in a compacted manner. Does this make sense? However, many folks don't like to engage in this kind of serious discussions. That's fine. If you're in that group, just say it, so those who might be interested in having such a discussion know that they have to find another interlocutor. :)Dionisio_{December 29, 2014
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#95 DNA_Jock
Your other questions have been answered (except for the ‘not even wrong’ one)
No, you haven't answered several questions. This thread is an obvious testimony. But that's fine, you don't have to answer all the questions. The onlookers/lurkers will have the opportunity to review this thread and arrive at their own conclusions. :)Dionisio_{December 29, 2014
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Dionsio- The DNA is transcribed into mRNA which is then processed, meaning the nucleotide sequence can change. Think of alternative splicing. What our opponents are not saying is that unguided evolution cannot account for any of it.Joe_{December 29, 2014
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#89 DNA_Jock Please, don't send me out to enroll in classes (posts #88 and 90 comment on that subject), let's discuss here. I'm trying to engage in a serious discussion. If you don't want to discuss this, then simply skip my questions or state it openly that you are not interested in this kind of discussion. I will respect your preference. But I've been told that in this and other blogs the onlookers/lurkers are important too. Hence, even if you ignore some questions, the onlookers/lurkers may still read the posts and arrive at their own conclusions. :)Dionisio_{December 29, 2014
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re 94, google formylglycine. Your other questions have been answered (except for the 'not even wrong' one): try reading for comprehension. Get a biology degree.DNA_Jock_{December 29, 2014
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#89 DNA_Jock
Does that nucleotide sequence in the DNA always tell you the final sequence of amino acids?
Almost always.
Why not always? In which case(s) the two sequences don't correspond directly?Dionisio_{December 29, 2014
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#89 DNA_Jock
Do you know approximately when was the “regulatory code specifying transcription factor (TF) recognition sequences” first referenced in textbooks?
No.
Could it have been since the eighties? Do you know if the “regulatory code specifying transcription factor (TF) recognition sequences” sometimes may at least partially overlap with the "genetic code specifying amino acids"? Have you heard or read anything on this subject lately? When was the overlapping between two distinct codes first mentioned in textbooks? Since the eighties? Earlier? Later? It hasn't been mentioned at all? Don't know?Dionisio_{December 29, 2014
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#89 DNA_Jock
See insightful post #63 by gpuccio. Optionally, posts #30 and 33, also by gpuccio, shed more light on this discussion.
Post #30 is a good explanation. So is post 33, except for its asinine final sentence. However, the Sanford paper gp refers to in #63 (and the OP itself) fall into the ‘not even wrong’ category.
What is it that you don't like about gpuccio's final sentence @33? Why do you say that the paper gpuccio refers to @63 is 'not even wrong'?Dionisio_{December 29, 2014
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#89 DNA_Jock
Does the OP somehow (directly or indirectly) refer to the “regulatory code specifying transcription factor (TF) recognition sequences” too?
I think so, but…
but what?Dionisio_{December 29, 2014
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#89 DNA_Jock You didn't answer all the questions written in post #87, just some of them. Any particular reason why? BTW, post #88 could be a comment on your last statement in post #89. The online courses I took are provided by reputable universities. Since you didn't answer all the questions, can I say you should enroll in a biology course at a reputable university? No! I don't know why you did not answer all of my questions. But the answers to some biology questions may not be in any biology course at any reputable university. The answer my friend is blowing in the wind. :)Dionisio_{December 29, 2014
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Does the OP somehow (directly or indirectly) refer to the “regulatory code specifying transcription factor (TF) recognition sequences” too?
I think so, but…
See insightful post #63 by gpuccio. Optionally, posts #30 and 33, also by gpuccio, shed more light on this discussion.
Post #30 is a good explanation. So is post 33, except for its asinine final sentence. However, the Sanford paper gp refers to in #63 (and the OP itself) fall into the ‘not even wrong’ category.
Do you know approximately when was the “regulatory code specifying transcription factor (TF) recognition sequences” first referenced in textbooks?
No.
Look where? in the DNA? what coding sequence? the nucleotide sequence within the DNA?
Yes
Does that nucleotide sequence in the DNA always tell you the final sequence of amino acids?
Almost always.
Does that nucleotide sequence in the DNA always translate into a sequence of amino acids?
More often than not.
Do portions of the DNA nucleotide sequence get involve in regulatory or controlling mechanisms?
Occasionally. Again, I would encourage you to actually enroll in a biology course at a reputable university.DNA_Jock_{December 29, 2014
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