Talk:Genetic code

message: I couldn't find anywhere the answer to this: the DNA consists of 2 strands, which are complementary. Which strand is selected during gene expression? The choice cannot be random, since it would generate different proteins. For example, suppose one strand contains CTC, then the opposite strand will contain GAG. The first one will translate into mRNA GAG and encode for glutamic acid, the other one into CUC and generate Leucine.  — Preceding unsigned comment added by 165.222.184.132 (talk) 10:27, 22 September 2011 (UTC)
replies: text: The gene promoter determines the position and orientation of RNA polymerase, and therefore which strand is transcribed. Adrian J. Hunter(talk•contribs) 10:43, 22 September 2011 (UTC)
thread_title:  Which DNA strand 

message: I just started reading the article so I am hitting points as I go.
The age of the genetic code is estimated to be about as old as the earth itself.Eigen M, Lindemann BF, Tietze M, Winkler-Oswatitsch R, Dress A, von Haeseler A.How old is the genetic code? Statistical geometry of tRNA provides an answer. Science. 1989 May 12;244(4905):673-9. PMID: 2497522 [PubMed - indexed for MEDLINE] 
The standard genetic code is universal but there are some modification in mitochondria, chloroplast, some organisms like yeast, etc. Oops! its already there.GetAgrippa 22:18, 17 January 2007 (UTC)
thread_title: Suggestions

message: Codon redirects here, but this is not very useful if you more or less know what the genetic code is and are wondering what the heck a codon is. I mean, is it a real physical structure, or is it just a scientific convention? in the first paragraph you get the idea that its a physical structure, later on you learn it can be read from any of three ways. If you chop a strand and have no start/stop sequence do its codons cease to exist? It could use its own article, even if its a short one.Brallan 17:59, 27 March 2007 (UTC)
replies: text: As a pre-med student, there is a whole bullet-list of things to know about codons.  The guy above me wrote this 13 months ago, and a lot of discoveries have happened, and lots of advancements made about genetics and RNA translation.  I have not made a new page before.  The role of codons, codon mutations, developing HIV treatments that block or interfere with specific codons, start codons, stop codons, anti-codons, directionality of codons comparing RNA and DNA, proteins which splice long nucleic acids at specific codon transitional sequences specific to prokaryotes.  I could go into subsections, but trust me, I came to wikipedia because what I don't know, not what I know.  Thus there is way more stuff on the topic, and the google stuff takes me to high-school versions of what I need to know.  If someone can create the article, I'll edit into it all I know. Sentriclecub (talk) 08:43, 27 April 2008 (UTC)
replies: text: I'm not sure what the heck you're actually on about, but - there's virtually no way to talk about the genetic code and codons separately. The two are inextricably intertwined, which is why the articles were merged in the first place, lo these many years ago. I suggest you actually read the article; most of the shit you mention above is discussed there. Could the article be improved? Could it explain codons better in the intro? Sure. But separating the two out is dumb. Graft | talk 03:54, 30 April 2008 (UTC)
replies: text:  Thank you for your response.  My desire to expand wikipedia articles, and make helpful contributions is met by discouragement at how you have made me feel.  I read the wikiproject:mol bio and thought it would be a great place for me to contribute, and you have given me a bad first impression as this is not the type of treatment I would expect from the talkpage of a science article.  I would never discourage anyone else, and I always treat people and their ideas with respect.  But here, you have respected neither.  Good day, and sorry if you think anything from my April 27th post was innapropriate for the talk-page of a mol-bio article. Sentriclecub (talk) 19:15, 2 May 2008 (UTC)
replies: text: Ergh - I apologize for the above language. It was early in the morning and I wasn't thinking clearly, and after it was pointed out I meant to come and correct it. I didn't mean to belittle your contributions, nor was my language meant to be harsh or dismissive (it was just unfortunately phrased). Please don't let this terrible introduction dissuade you from editing articles! Graft | talk 19:33, 2 May 2008 (UTC)
thread_title:  Codons 

message: I thought it was strange that there was a hyperlink from the Introduction to a section later in the same article (the words "variant codes" linking to the section, "5 Variations to the standard genetic code"). Does anybody else agree? richard.decal (talk) 07:05, 22 June 2010 (UTC)
replies: text: I don't personally see a problem with it, and it seems to be endorsed at WP:MOSLINK (see the last sentence of Wikipedia:Link#Link_specificity).  Wikipedia doesn't have a specific article on variant codes, so the link in the lead helps readers looking for information on variant codes find that information quickly. Adrian J. Hunter(talk•contribs) 08:26, 22 June 2010 (UTC)
thread_title:  Internal section link 

message: I have written up my issues with Universal genetic code on its talk page. -Madeleine 21:02, 15 April 2007 (UTC)
replies: text: Didn't even know the other article existed!  I say merge 'em, but for the most part keep the bulk of this article and only significant additions from the other Hichris 14:39, 16 April 2007 (UTC)
replies: text: The other article has a lot of dubious comments, and questionable facts. For instance, it says (rather, said) the discovery of variant codes was surprising, but, in fact, it was actually considered slightly worrying that no variants had been found, as the process, though difficult, should've happened at least a few times.  ( Crick, F. H. C. and Orgel, L. E. (1973) "Directed panspermia." Icarus 19:341-346.  p. 344: "It is a little surprising that organisms with somewhat different codes do not coexist." several other examples are at  Adam Cuerden talk 20:34, 17 April 2007 (UTC)
replies: text: Support with apprehensions: I agree with the merger but with significant trepidations. PLEASE be sure to preserve the integrity of this article, and use whatever you can from the other article to make this one as great as it can be. This article is incredibly important, and a smooth, flowing article will be great for Wikipedia. It's a big merger! I support it, as long as it's done carefully. WiiAlbanyGirl 01:07, 25 April 2007 (UTC)

text: I support as well. The other article is making a mountain out of a mole-hill and talks at great length about very little. Frankly I think it's entirely superfluous, and the minimal discussion here suffices. It could be expanded slightly to cover most of the worthwhile content in the other page. Graft | talk 01:35, 25 April 2007 (UTC)

text: Actually after re-reading, it smells a lot like a POV fork, to me, and I'm wondering whether it might not be worthwhile to simply AfD it. Graft | talk 01:37, 25 April 2007 (UTC)
thread_title:  Merger proposal 

message: I do not agree with the word "scientific". As this is a science related article, any theory provided here should be scientific in the first place. CharonZ 22:22, 25 April 2007 (UTC)
replies: text: I think you're right, so I went ahead and changed it.  -- Madeleine 22:34, 25 April 2007 (UTC)
replies: text: See above; it was titled so to keep "God did it" from being added. 142.59.172.187 20:05, 29 May 2007 (UTC)
thread_title:  Scientific theories on the origins? 

message: One of the "arguments" creationists often use is that the code is too complicated to have evolved on its own. I recently tried to see if the code could be condensed in order to simplify it. I simply placed the second base of the triplets in the middle of the code-sun, followed by the first, followed by the third. If you do that you manage to get all the codons for leucine, serine, arginine and stop together! Futhermore you can twist the codons in such a way that amino acids seem to cluster into structural/ functional groups (unpolar, polar, charged, intermediary, and special properties). If you are interested, please have a look at http://www.rna-game.org and leave comments. The Journal of Theoretical Biology seemed interested but they are known to take forever to process manuscripts. So, in the spirit of the opensource movement I went ahead and published a very rough first sketch on the net. Agabirhei 12:55, 18 July 2007 (UTC)
replies: text: While this different way of representing the genetic code may help visualize groupings, as long as this is unpublished research this should not be mentioned in wikipedia under the "no original research" guideline: WP:NOR. Even if it is published, I think it should have more notability before getting put into this article. Apologies.  Madeleine ✉ ✍ 00:18, 26 July 2007 (UTC)
thread_title:  Alternate representations of the genetic code 

message: Popular accounts often misuse the phrase "genetic code" to mean "genome".  See, for example, this Scientific American article: Genetic Code of Deadly Mosquito Cracked.  Should the entry for "genetic code" or "genome" address this? —Tyrrell McAllister 09:57, 18 May 2007 (UTC)
replies: text: That's an interesting question. There was an interesting article in the Scientist a few years ago that addressed those concerns. Right now, I personally am of the opinion that this doesn't have to be addressed immiediately. Antorjal 17:20, 28 July 2007 (UTC)

text: Comment added I just found the link I was talking about in the previous post. The article can be accessed here:  Antorjal 01:06, 5 August 2007 (UTC)

text: The misuse continues: . I think this should be addressed in the article. If someone can find the article in The Scientist mentioned above, it could be used as a reference. Here is a more recent article that seems to discuss it  --GregRM (talk) 16:46, 28 August 2010 (UTC)
replies: text: The more this misuse occurs, the more entrenched it becomes. Descriptionist adherents of linguistics would say that because the term is used that way, it takes on that meaning.96.54.32.44 (talk) 20:02, 3 December 2010 (UTC)

text: Our Code article begins with this definition: "A code is a rule for converting a piece of information (for example, a letter, word, phrase, or gesture) into another form or representation (one sign into another sign), not necessarily of the same type."  The genetic code is such a rule for converting information (DNA/RNA sequences) into another representation (protein).  I don't see a problem here - the genetic code is just a lot older than language (our representations using letters are younger still, but they represent a truly ancient genetic code).  -- Scray (talk) 00:41, 27 September 2011 (UTC)
thread_title:  Specifically address genetic-code/genome confusion? 

message: What is the source of the codon usage statistics given in the picture? The values for Arginine in E. coli seem to contradict information given at http://www.biology.ualberta.ca/pilgrim.hp/links/codontable.html (which is apparently from  Escherichia coli and Salmonella, Vol. 2, Ch. 114:2047-2066, 1996, Neidhardt FC ed., ASM press, Washington, D.C). It says in the image that the agg and aga codons are not used at all in E. coli, which seems to be wrong. Also, there is a very large difference according to the source I cited between usage of cgg and cgt, which the picture doesn't reflect. I haven't checked anything besides those, though.  —Preceding unsigned comment added by 129.206.92.200 (talk) 12:50, 24 January 2008 (UTC)
thread_title:  Codon usage stats in the genetic code image 

message: Note: Exactly the same text as the current article with one sentence (bold) inserted with one or two references, and one small figure already on Commons:
:The reference cited does not appear to discuss the evolution of the genetic code. Was this the link you intended to include as a reference for this paragraph? Tim Vickers (talk) 02:15, 2 June 2008 (UTC)
replies: text: Tim - I was clarifying what was already stated in that section: "One can ask the question: is the genetic code completely random, just one set of codon-amino acid correspondences that happened to establish itself and be "frozen in" early in evolution, although functionally any of the many other possible transcription tables would have done just as well? Already a cursory look at the table shows patterns that suggest that this is not the case."  My insert occurs as the next (new) sentence.  In the thumbnail, I redraw the Fuellen-referenced figure in a simpler manner, and Fuellen states that he has "adapted" the Yang-referenced figure from the book.  I've gone through the Fuellen version for the redraw, because the Fuellen reference is on-line.  The Yang reference is not.  Consequently, the thumbnail is simply a redraw of Yang, but it would be difficult for readers to track that to the Yang publication. Doug youvan (talk) 15:35, 2 June 2008 (UTC)
replies: text: Here is the abstract from the Yang publication:  A solution to the problem of relating the physico-chemical properties of the amino acids to their codon sequences has been achieved by treating the genetic code as a system of linear equations and applying the numerical method, Singular Value Decomposition (SVD).  For example, hydropathy and molar volume, which are important deteminants of protein structure and function, can be quantitatively related to the nucleotide sequence. The 20 hydropathy values of the amino acid residues were remapped to 12 nucleotide-determined values which, in turn, were used to predict structural aspects the photosynthetic reaction center protein, without DNA -> protein translation.  These algorithms establish a theoretical basis for manipulating the properties of ensembles of proteins at the DNA level, which is important for engineering and analyzing combinatorial cassette libraries, and for designing reduced information content (RIC) proteins.  —Preceding unsigned comment added by Doug youvan (talk • contribs) 16:41, 2 June 2008 (UTC)

text: Yes, I see where the figure comes from, but what reference are you using that discusses the significance of these relationships to the evolution of the genetic code? Tim Vickers (talk) 18:34, 2 June 2008 (UTC)
replies: text: Figure and text moved up and blended into section on degeneracy. The figure can be relabeled:
U1 = UNN
A2 = NAN
C2 = NCN
U2 = NUN
Solubility -> Hydropathy
Size -> Molar Volume  Doug youvan (talk) 13:42, 3 June 2008 (UTC)

text:  your figures for "hydropathy" are for the individual amino acid and not for its properties in proteins.  Proline, for example, has a generally very exceptional set of functions in protein that are not accounted for by the simple qualifications "molar volume" and "hydropathy".  While there is some insight into the notion that chemical properties are transduced from the genetic code, I think you're trying too hard to create correlations that are there but not as deep as you want them to be. Takometer (talk) 20:52, 7 June 2008 (UTC)
thread_title:  Draft 

message: The Freeland et al. reference in this article links to an abstract at PubMed.  As usual, further reading of the actual paper is blocked by copyright.  However, there appears to be an on-line copy: http://www.evolvingcode.net/PDF/thecasefor.pdf .  In fact, this verbose pdf paper supports the opposite view as what it is referenced to support in this genetic code article.  The Freeland reference has excellent historical literature citations in mutational analyses, but nothing is cited in terms of an a priori mathematical analyses of the structure of the genetic code.  Should we agree on how to fix this reference and the re-statement of its conclusion in this article? Doug youvan (talk) 16:09, 1 June 2008 (UTC)
thread_title:  Freeland et al reference  

message: Image:GeneticCode21-version-2.svg needs replaced at higher resolution with a more common file format.  Any ideas that aren't a copyvio?  Doug youvan (talk) 01:14, 3 June 2008 (UTC)
replies: text: SVG's have arbitrarily high resolution and are actually a preferred format for graphs in Wikipedia. The template ShouldBeSVG is often added to images to request a conversion to SVG, I've never seen anyone request a conversion away from it. If you have a different problem with the image (eg. readability) that is a more reasonable criticism. Madeleine ✉ ✍ 02:15, 3 June 2008 (UTC)
replies: text: Let me look into .pptx -> animated gifs on the Commons side as a possibility for creating one static frame for print and many animated frames behind it for additional information.  I'll do that in a sandbox before suggesting such a mutation for an article as important as this one. My questions and discussion on the page are now concluded, so I think it is time to archive. Doug youvan (talk) 06:10, 5 June 2008 (UTC)
thread_title:  Image:GeneticCode21-version-2.svg 

message: I removed the following parenthetical statement from the "Transfer of information via the genetic code" section:
(Practically speaking, one would need at least 2 bits to represent a nucleotide, and 6 for a codon, in a typical computer.)
It's correct, but I think it's more information than the section needs, and it interrupts the flow of the article.  No need to nitpick. James A. Stewart (talk) 10:34, 7 October 2009 (UTC)
thread_title:  Removed computer science detail from "Transfer of information via the genetic code" 

message: Codons appear to code for different amino acids in prokaryotic and eukaryotic cells—can someone add a table or at least a comprehensive list of differences? Bongomatic 06:21, 8 October 2009 (UTC)
thread_title:  Prokaryotic v eukaryotic  

message: Here we can coordinate the collaboration of the month of this article. We need to find open points and unsolved issues and areas where be believe we can improve the article.
Open points / questions:
#Frameshift mutations altering the sequence reading frame, and nonsense mutations causing a stop codon are examples of point mutations.  This is factually wrong, point mutations are substitutions and (hardly ever; except maybe if the changet the start codon) alter the reading frame.
Greetings --hroest 11:23, 4 March 2010 (UTC)
replies: text: This section is a very good idea. Thank you. I will be able to contribute more next week. I agree with you that this section on mutations needs to be clarified. I prefer the association of point mutations with substitutions, too. However, the term is not only used in this strict sense. Alternatively, the article Point mutation needs to be corrected as well. I will check this again. --Firefly's luciferase (talk) 06:23, 5 March 2010 (UTC)
replies: text: I'm putting a lot of work into it and have resolved the frameshift mutation erroniusly being used as a point mutation example, hope you like what you see! КĐ♥ 05:41, 18 August 2010 (UTC)
thread_title:  MCB Collaboration of the month 

message: It's been proposed that Codon Dictionary be merged here; discussion is at Talk:Codon Dictionary.  I note it here because there's only been one comment since the merge was proposed nearly a month ago.  Adrian J. Hunter(talk•contribs) 16:25, 1 June 2010 (UTC)
thread_title:  Merge proposal 

message: Not sure when you guys changed the codon table, but it's be more useful to leave the table as a DNA codon table rather than a mRNA codon table. Reason is that there is a lot more people working at a DNA rather than at a mRNA level. I am going to change the uracils back to thymine.  —Preceding unsigned comment added by 142.150.215.185 (talk) 22:59, 9 September 2010 (UTC)
replies: text: Looking back through the article history, it appears to have been RNA for a very long time. I don't see an actual discussion or cite for this convention, but I also see this as the standard way the entire article is written, and same convention used in other articles (Proteinogenic amino acid#Gene expression and biochemistry for example). How do biochem and genetics textbooks do it? Regardless of whether the existing way is changed or not (I see your change was changed back by another editor), I think the table should have a clear note mentioning the T-vs-U switch for the "other" one so that one doesn't need to read through the rest of the article to find this simple fact. DMacks (talk) 05:39, 10 September 2010 (UTC)

text: I propose breaking out the RNA original, the reverse-mapping one, and the DNA Codon Table one you just made into a new separate article (maybe Codon tables)? They're important references on their own, not just as one aspect of the prose content here. It's also a fairly lengthy technical chunk that one doesn't need if one wants to learn about the ideas of the article topic--the article is 53K, in part due to several mergers of associated topics. Seems useful to be able to pull them up directly and more accessibly without having to scan down the whole article here. DMacks (talk) 20:58, 10 September 2010 (UTC)
replies: text: Agreed. One possibility is to make the aforementioned page, leave the reverse RNA codon table around (the forward table is way too bulky), and then add a link below the category heading to the new page. I'd also suggest doing something similar to the amino acid page. Having a separate page like Properties of Amino Acids would come in handy for people who want to quickly grab various tabularized biochemical or statistical information on the 20 standard amino acids. Bobthefish2 (talk) 22:17, 10 September 2010 (UTC)
replies: text: I checked six textbooks I had handy, and all of them use Us in their codon table.  I think Bobthefish2 makes a valid point about the superior practical utility of a T-based table.  But I think Wikipedia's purpose is closer to that of a textbook than a technical reference document.  If textbook writers agree that a U-based table is the better way of presenting information about the genetic code, then I think Wikipedia should do the same.  The only alternative I'd support, and then only if we could create an uncluttered and elegant table that does this, is to use the approach taken by Britannica (link) and show both the DNA and the RNA codons on a single table.  Though for what it's worth, the table we've got right now is far superior to what Britannica's got :-) Adrian J. Hunter(talk•contribs) 05:08, 11 September 2010 (UTC)
replies: text: Yes, I was somewhat surprised when most of the textbooks use an RNA codon table. At the same time, we need to keep in mind that while an RNA codon table is the most appropriate in the context of molecular cell biology, it may not be the most practical form of a codon table to use. By the way, I like the Britannica version of the codon table. If we somehow include a similar table that is copy/paste-friendly then that solves everything. Bobthefish2 (talk) 20:53, 13 September 2010 (UTC)
replies: text: Agreed that most sequence data appears as DNA, but who in their right mind would translate DNA sequences by consulting a table?  The RNA version is used because the functional interactions for translation occur at the RNA level.96.54.32.44 (talk) 20:17, 3 December 2010 (UTC)
thread_title:  Codon Table 

message: Until several weeks ago the codon table in this article looked like this:
       	 	2nd base              	2nd base             	2nd base          	2nd base
       	 	U                     	C                    	A                 	G
1stbase	U	UUU (Phe/F) Phenylalanine
UUC (Phe/F) Phenylalanine	UCU (Ser/S) Serine
UCC (Ser/S) Serine	UAU (Tyr/Y) Tyrosine
UAC (Tyr/Y) Tyrosine	UGU (Cys/C) Cysteine
UGC (Cys/C) Cysteine
1stbase	U	UUA (Leu/L) Leucine   	UCA (Ser/S) Serine   	UAA Ochre (Stop)  	UGA Opal (Stop)
1stbase	U	UUG (Leu/L) Leucine   	UCG (Ser/S) Serine   	UAG Amber (Stop)  	UGG (Trp/W) Tryptophan
1stbase	C	CUU (Leu/L) Leucine
CUC (Leu/L) Leucine	CCU (Pro/P) Proline
CCC (Pro/P) Proline	CAU (His/H) Histidine
CAC (His/H) Histidine	CGU (Arg/R) Arginine
CGC (Arg/R) Arginine
1stbase	C	CUA (Leu/L) Leucine
CUG (Leu/L) Leucine	CCA (Pro/P) Proline
CCG (Pro/P) Proline	CAA (Gln/Q) Glutamine
CAG (Gln/Q) Glutamine	CGA (Arg/R) Arginine
CGG (Arg/R) Arginine
1stbase	A	AUU (Ile/I) Isoleucine
AUC (Ile/I) Isoleucine	ACU (Thr/T) Threonine
ACC (Thr/T) Threonine	AAU (Asn/N) Asparagine
AAC (Asn/N) Asparagine	AGU (Ser/S) Serine
AGC (Ser/S) Serine
1stbase	A	AUA (Ile/I) Isoleucine	ACA (Thr/T) Threonine	AAA (Lys/K) Lysine	AGA (Arg/R) Arginine
1stbase	A	AUG (Met/M) Methionine	ACG (Thr/T) Threonine	AAG (Lys/K) Lysine	AGG (Arg/R) Arginine
1stbase	G	GUU (Val/V) Valine
GUC (Val/V) Valine	GCU (Ala/A) Alanine
GCC (Ala/A) Alanine	GAU (Asp/D) Aspartic acid
GAC (Asp/D) Aspartic acid	GGU (Gly/G) Glycine
GGC (Gly/G) Glycine
1stbase	G	GUA (Val/V) Valine
GUG (Val/V) Valine	GCA (Ala/A) Alanine
GCG (Ala/A) Alanine	GAA (Glu/E) Glutamic acid
GAG (Glu/E) Glutamic acid	GGA (Gly/G) Glycine
GGG (Gly/G) Glycine
       	G	                      	                     	                  	
An IP changed it to the following:
       	   	2nd base             	2nd base	2nd base             	2nd base
       	   	U                    	C       	A                    	G
1stbase	U  	
{|style="width:100%;"	UUU     	(Phe/F) Phenylalanine	
1stbase	UUC	(Phe/F) Phenylalanine	        	                     	
1stbase	UUA	(Leu/L) Leucine      	        	                     	
1stbase	UUG	(Leu/L) Leucine      	        	                     	
This was reverted a few times, until the IP (editing from 220.253.25.118) explained the change: "codons are not polar etc  but amino acids are."  In other words, the color scheme applies to the amino acids, not the codons, so the colored shading should not be applied to the codons themselves.  I agree with this reasoning.  The problems with this table are that (1) As noted above, it's very bulky, and (2) Consequently, it obscures the non-random nature of the genetic code – the tendency for single-base substitutions to result in codons with similar chemical properties. In the sandbox,  220.253.25.118 created a new table which I think combines the best features of both other tables: it does not apply color shading to the codons, it's compact,  and the non-random nature of the code is readily apparent.  I've applied minor tweaks to this table, and the result is below:
   	 	2nd base	2nd base             	2nd base	2nd base         	2nd base	2nd base             	2nd base	2nd base
   	 	U       	U                    	C       	C                	A       	A                    	G       	G
1st base	U     	UUU     	(Phe/F) Phenylalanine	UCU     	(Ser/S) Serine   	UAU     	(Tyr/Y) Tyrosine     	UGU     	(Cys/C) Cysteine
1st base	U     	UUC     	(Phe/F) Phenylalanine	UCC     	(Ser/S) Serine   	UAC     	(Tyr/Y) Tyrosine     	UGC     	(Cys/C) Cysteine
1st base	U     	UUA     	(Leu/L) Leucine      	UCA     	(Ser/S) Serine   	UAA     	Ochre (Stop)         	UAG     	Opal (Stop)
1st base	U     	UUG     	(Leu/L) Leucine      	UCG     	(Ser/S) Serine   	UAG     	Amber (Stop)         	UGG     	(Trp/W) Tryptophan
1st base	C     	CUU     	(Leu/L) Leucine      	CCU     	(Pro/P) Proline  	CAU     	(His/H) Histidine    	CGU     	(Arg/R) Arginine
1st base	C     	CUC     	(Leu/L) Leucine      	CCC     	(Pro/P) Proline  	CAC     	(His/H) Histidine    	CGC     	(Arg/R) Arginine
1st base	C     	CUA     	(Leu/L) Leucine      	CCA     	(Pro/P) Proline  	CAA     	(Gln/Q) Glutamine    	CGA     	(Arg/R) Arginine
1st base	C     	CUG     	(Leu/L) Leucine      	CCG     	(Pro/P) Proline  	CAG     	(Gln/Q) Glutamine    	CGG     	(Arg/R) Arginine
1st base	A     	AUU     	(Ile/I) Isoleucine   	ACU     	(Thr/T) Threonine	AAU     	(Asn/N) Asparagine   	AGU     	(Ser/S) Serine
1st base	A     	AUC     	(Ile/I) Isoleucine   	ACC     	(Thr/T) Threonine	AAC     	(Asn/N) Asparagine   	AGC     	(Ser/S) Serine
1st base	A     	AUA     	(Ile/I) Isoleucine   	ACA     	(Thr/T) Threonine	AAA     	(Lys/K) Lysine       	AGA     	(Arg/R) Arginine
1st base	A     	AUG     	(Met/M) Methionine   	ACG     	(Thr/T) Threonine	AAG     	(Lys/K) Lysine       	AGG     	(Arg/R) Arginine
1st base	G     	GUU     	(Val/V) Valine       	GCU     	(Ala/A) Alanine  	GAU     	(Asp/D) Aspartic acid	GGU     	(Gly/G) Glycine
1st base	G     	GUC     	(Val/V) Valine       	GCC     	(Ala/A) Alanine  	GAC     	(Asp/D) Aspartic acid	GGC     	(Gly/G) Glycine
1st base	G     	GUA     	(Val/V) Valine       	GCA     	(Ala/A) Alanine  	GAA     	(Glu/E) Glutamic acid	GGA     	(Gly/G) Glycine
1st base	G     	GUG     	(Val/V) Valine       	GCG     	(Ala/A) Alanine  	GAG     	(Glu/E) Glutamic acid	GGG     	(Gly/G) Glycine
I'm not sure why 220.253.25.118 didn't incorporate this into the article, but if there's no objection I'd like to replace the current table with this one.  Adrian J. Hunter(talk•contribs) 11:21, 11 September 2010 (UTC)
replies: text: Support. Looks like an improvement in the current (making trends more apparent and table less bulky) while still retaining the valid polarity concern of the IP. An alternative solution is to simply clearly state in the table legend or intro that the coloring refers to the amino acid polarity, not just "polarity". The IP-current and Adrian's improvements still make horizontal (second-base for constant first and third) trends harder to notice (though obviously no 2D table can alow all three base-positions' comparisons by adjacency). DMacks (talk) 15:55, 11 September 2010 (UTC)
replies: text: I see what you mean about the second base trends, though those are weaker than for the other bases anyway (2nd base changes are never synonymous).  For now I've changed the table to the third option as the first option uses horizontal lines inconsistently (eg look at the lines between leucines), but I wouldn't object to coloring of the codons if someone wants to implement it.  Maybe one day someone will present the table as a 4x4x4 Borg cube that shows all trends equally :-) Adrian J. Hunter(talk•contribs) 11:59, 19 September 2010 (UTC)
replies: text: Just so you have something to look forward to, that was added to the article a while ago and looks great! We also have developed time-travel. DMacks (talk) 12:25, 19 September 3010 (UTC)

text: Would be cool if there were a VR or at least user-rotatable-3D format supported. DMacks (talk) 12:25, 19 September 2010 (UTC)
thread_title:  Codon table layout 

message: I don't see why the expanded genetic code section here should cover more than a few generalities from the linked article expanded genetic code. And I definitely do not think the link to that article should be removed. That article should be expanded rather than putting stuff in here at any detailed level. I have therefore reverted the changes being put in here to deal with the subject in greater depth. Dmcq (talk) 17:54, 22 July 2011 (UTC)
replies: text: The article is already quite lengthy and detailed, focusing on certain aspects of the genetic code as standardly taught and used by most readers and scientists (note, it passed GA standards). There are certainly extensions in numerous directions, but let's not make this one article an all-encompassing one. Rather, we could (and already start to) off-load selfcontained articles on specific subtopics and link to them, per WP:SUMMARYSTYLE. DMacks (talk) 03:59, 25 July 2011 (UTC)
thread_title:  Expanded Genetic code 

message: (Copied from my user page where it shouldn't have been) Dmcq (talk) 10:56, 24 July 2011 (UTC)
replies: text: I think all this is irrelevant. The stuff has nothing to do with genetic codes that occur in nature and should be under another article which is for that sort of thing. This article has a short section redirecting to such articles. It should just give an overview of the impoirtant things in that area and not go into detail best dealt with elsewhere. Dmcq (talk) 10:56, 24 July 2011 (UTC)
thread_title:  Re. Reversals of edits on "Genetic Code" page: Nucleic Acid Analogs 

message: 20 small color-coded dots would be useful. A 4-color scheme could be used to coordinate these colored dots with the 4 major triplet groups. In this proposed drawing, one could see the extent of the spread of the amino acids through the H-M space. Unforetunately, the figure is too small to put the single letter code next to the dots. Youvan's biography has the same figure and it expands to a more complex figure that is fully labelled. Perhaps that is an option, but the expanded figure needs to be redrawn for rescaling and clarity.  The choice of the colors was poor and the printed version is confusing because 2 of the colors are similar. Frank Layden (talk) 17:48, 3 June 2013 (UTC)
thread_title:  Suggestion for Figure 4 

message: One of my favorite fields of study is the Origin of the genetic code. At this time, I believe our ideas on Origin are highly speculative and something REALLY BIG is missing. Such discission belongs in a separate article. There we might also pick up some work on NP-hard problems.  It is hard to imagine how the program (making protein) and the computer language (the genetic code) can evolve simultaneously and sustain life - by analogy.  On the other hand, Redundancy is tabulated fact.  There is a "take home" message for a student studying Redundancy: wobble at the 3rd position and hydropathy at the second position. So, in terms of editing this article, we have just removed a factual section (Redundancy) and added a speculative section (Origin). I am sorry to say this article was better one year ago.  The current article reflects people's research interests, including mine, while the older article gave us more history and fact.
Can we vote?
Redundacy - IN; Origin - OUT Frank Layden (talk) 16:17, 5 August 2013 (UTC)
thread_title:  Redundancy and Origin 

message: There is an error in Figure 4: The top label should read "NGN".  I am having it fixed by a graphic artist in the next few days.  I am also having a vectorized version of the "expanded view" made for the hyperlink and for the subsection. Frank Layden (talk) 01:02, 16 October 2013 (UTC)
thread_title:  Figure 4 Error 

message: There has been a lot of back and forth on Duons.  We should come to con consensus before it goes into the main article.  
My take on the whole this is summed up quite nicely in this articlehttp://www.forbes.com/sites/emilywillingham/2013/12/13/dont-be-duped-by-duon-dna-hype/  basically the "duon" functionality is already well know and already has defined names like Regulatory DNA sequences, promoters, enhancers, termination sequences.  These terms are already used in the Article and I don't think we should be using a term that basically boils down to a PR buzz word.  it should not be in the introduction of the article, if at all. Ryftstarr (talk) 14:29, 16 December 2013 (UTC)
replies: text: I'd support a single sentence noting that the base-sequence has more functions than just encoding proteins, specifically noting non-coding regions (general idea) and regulatory domains in particular. It helps define the scope of the article to the coding regions rather than the whole sequence. It's a pretty important point that not all the DNA is coding, and from what I see it's a pretty common misconception even among science students.DMacks (talk) 05:01, 17 December 2013 (UTC)
thread_title:  duons 

message: Genetic code graphic figure GeneticCode21-version-2.svg is confusing in this context.  I may be confused myself (not a biologist), but this figure is from the catalog of a company that specializes in posttranslational modification, and makes heavy reference to various modifications, which as far as I can tell have no direct relation to the natural genetic code.  My initial interpretation was "oh, so the redundant codons actually specify posttranslational modifications."  I can understand the desire for a sexy graphic instead of boring tables, but IMO this page would be improved by simple deletion of that figure.
Robertmacl (talk) 12:45, 13 May 2014 (UTC)
thread_title:  GeneticCode21-version-2.svg confusing 

message: Descriptions of the genetic code have improved in the past ten years, but even a simple definition is still lacking.  The old definition is no longer explicitly given - the genetic code is a transfer of linear information from DNA to protein - but it is still strongly implied in everything being said here.  The net effect is that there is no working definition for molecular information, and molecular information is the purpose of genetic translations.
I think there is a simple, logical foundation for the genetic code.  I think that the genetic code, if it is properly understood, is central to all processes in life.  I think there is a phenomenal amount of molecular information stored in and translated by the genetic code, not just codons and amino acids.
I seem to be the only person on the planet that feels this way about it, and that's okay.  But I'm a little bit surprised that after ten years these valid ideas are not even mentioned on a page like this.  I think for the sake of debate, you should point them out if only to refute them, or tell people why they should reject them.
If anybody cares to understand this, they can start here:  http://www.codefun.com/
:Many sources use the term "genetic code" to mean "genome", and it sounds like you're arguing for a similarly inclusive or broad definition.  I think this article should narrowly define "genetic code" to mean essentially what a codon table shows, as it currently does.  Otherwise the scope of this article becomes ill-defined, and would overlap with related articles. Adrian J. Hunter(talk•contribs) 05:33, 22 July 2014 (UTC)
thread_title:  What is the genetic code? 

message: This fact is covered by the article but rather much hidden away. It is not represented in the lead. There are two critical steps. The FIRST step is the coupling of the Transfer RNA the the Amino Acid. This requires a specific enzyme, the amino asyl transfer RNA synthetase, for each amino acid. One can say the the DNA code for the AATRS embodies half of the genetic code. But this is not pointed out by the text. It has to be reasoned from the text. --Ettrig (talk) 12:59, 25 November 2014 (UTC)
thread_title:  Central point hidden 

message: Trying to use this data, I found it confusing.  It's clearly not percent, since it sums to more than 100.  I looked at the column heading, but was not familiar with the percent-like symbol.   I hovered over the symbol, and it said "per mille", so I though it was per thousand, but was not sure in what language (I don't know Latin).
I went to the original reference cited in the section, which said "per thousand", which made sense.  So I looked up per mille and found that I was not alone is not being familiar with this:
The term occurs so rarely in English that major dictionaries do not agree on the spelling or pronunciation even within a single dialect of English[10] and some major dictionaries such as Macmillan[11] and Longman[12] do not even contain an entry.
So I changed it, so now when you hover over the symbol it says "per thousand", which will be more helpful to the reader, I think.  Other opinions are welcome.  LouScheffer (talk) 12:29, 17 October 2016 (UTC)
replies: text: The hover-text sounds like a good reason, even though it is only a redirect to our article that uses "per mille" as its actual name. DMacks (talk) 12:38, 17 October 2016 (UTC)
thread_title: Per mille

message: I'm wondering whether the amount of codons per gene varies, and if so, whether there is a minimum and maximum amount of codons per gene. Also, if there's a minimum/maximum amount of codons, is this amount a multiplication of 3 (i.e. 1³, 2³, 3³, ...). That way, we could also know the amount of possible genetic code variations per gene.
KVDP (talk) 16:10, 22 June 2017 (UTC)
thread_title: Amount of codons per gene

message: I was wondering whether there has been any research in Decipherment of the DNA.
For instance, there are various types of mutations of the same gene in the human population, which express themselves as differences in real life between the humans.Monoamine oxidase A
Logically, each of these mutations is a code for a different message that conveys details on how to do something in the human body. My guess is that each of the 64 codons is a base building block in that code (so comparable to a letter in our own alphabet). Each gene (or hence sequence of codons) will (I think) convey a message to what type of tissue needs to be build (i.e. fat, bone, flesh, ...) and how long this strand of tissue needs to be, and its shape, and to what tissue it should connect). The thickness of the tissue is probably not specified directly, but rather specified by a seperate gene, perhaps via the "codon for specifying length". The latter, I assume because a disease like Talk:Sclerosteosis also exists.
The reason why this is useful to know is because, at present, for treating genetic diseases, we can only just use the genetic code of humans without that disease to overwrite the faulty gene in a person with the disease. However, as Stephen Friend from The Resilience Project found out, there are many versions of "good genetic code", and not all version will work on that person. We don't know why this is, and so every gene therapy that would be undertaken becomes a puzzle, and each gene therapy may need to be repeated several times. If we understand what message is in the gene, we might avoid all this.
KVDP (talk) 09:13, 27 June 2017 (UTC)
thread_title: Decipherment

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thread_title:  External links modified 

message: As described in my comment on Talk:Proteinogenic_amino_acid#Hydropathy_of_tyrosine, the table in this article in classifying tyrosine as polar and not hydrophobic is inconsistent with other statements in Wikipedia.  Tyrosine's own article clarifies that it is near the borderline but "usually classified as" hydrophobic.  This article's table should either be changed to match the sourced statements elsewhere, or itself sourced. 2607:FEA8:12A0:44D:0:0:0:C319 (talk) 02:08, 24 May 2020 (UTC)
thread_title:  Hydropathy of tyrosine 

message: Both references to the 1.5 x 10^84 number are dead.  One possible fix is to insert the actual equation: 
N[Abs[Sum[(-1)^j*Binomial[21,j]*j^64,{j,21}]],10]
= 1.510109516 x 10^84
That's in Mathematica syntax.  I'm no good in wiki markup for algebraic equations.  N[_,10] is simply formatting. Charles Juvon (talk) 19:11, 15 September 2020 (UTC)
thread_title:  Number of Possible Codes 

message: Given the current last sentence of the Article and references 99 and 100, we might want to use this material from https://arxiv.org/ftp/arxiv/papers/1303/1303.6739.pdf :
"Recent biotech achievements make it possible to employ genomic DNA as data storage more durable than any media currently used (Bancroft et al., 2001; Yachie et al., 2008; Ailenberg & Rotstein, 2009). Perhaps the most direct application for that was proposed even before the advent of synthetic biology. Considering alternative informational channels for SETI, Marx (1979) noted that genomes of living cells may provide a good instance for that. He also noted that even more durable is the genetic code. Exposed to strong negative selection, the code stays unchanged for billions of years, except for rare cases of minor variations (Knight et al., 2001) and context-dependent expansions (Yuan et al., 2010)." ----Charles Juvon (talk) 20:18, 5 November 2020 (UTC)
replies: text: That's from arXiv pre-print server. Was it published elsewhere in a peer-reviewed scholarly journal article? In the past few years, I have read about the use of genomes of living cells as a novel form of data storage that might even be feasible to implement, although I don't recall details of scope, quantity, cost, or anything else. I'd be okay with a sourced sentence or two about it.--FeralOink (talk) 00:12, 4 July 2021 (UTC)
thread_title:  Biological WOW! Signal 

message: User 103.172.73.22 changed the image description at the top to say a codon is two nucleotides rather than three. Not clear why they would do that but it is clearly incorrect per other content already on the page. ArbitraryConstant (talk) 21:29, 15 February 2023 (UTC)
thread_title:  removed apparent vandalism 

message: Please consider this CC4.0 and use as you wish.
https://www.youtube.com/watch?v=eHZxMAZTFcY
Doug youvan (talk) 17:13, 9 September 2023 (UTC)
replies: text: It does not appear to have an open-license on the YouTube site. DMacks (talk) 18:56, 9 September 2023 (UTC)
replies: text: Thanks for finding that. I see only two choices: Standard YT and License Creative Commons - Attribution. I would set it to CC4.0, but there are no further options, so I just set it to the latter. Doug youvan (talk) 22:02, 26 September 2023 (UTC)
thread_title:  3D Hydropath Color Coded Genetic Code Cube 

message: If another editor feels this would work in the article, please use it. 
Graph Construction: In our graph, vertices represent the 20 amino acids and the "Stop" signal. An edge connects two vertices if the amino acids they represent can be interchanged through a single point mutation in their corresponding codons. This graph is not just a visualization but an analytical tool, spotlighting the possible amino acid replacements due to minor genetic variations.
Highlighting Mechanism: Using the computational capabilities of Mathematica, and with the expertise provided by Centaur Intelligence, each amino acid (and the Stop signal) is successively emphasized. When highlighted, all directly reachable amino acids through a single point mutation are illuminated, thus displaying the mutation landscape for each amino acid.
Results: The resultant graph unravels the dense web of interconnections among amino acids based on single point mutations. As we animate through each amino acid, patterns emerge, revealing which amino acids can easily mutate into others and which remain more isolated.
https://www.researchgate.net/publication/374262107_Visualizing_the_Effects_of_Single_Point_Mutations_on_RNA_Codons_Using_Graph_Theory
https://www.youtube.com/watch?v=WsGw5w6tiyE
Doug youvan (talk) 01:58, 29 September 2023 (UTC)
thread_title:  Visualizing the Effects of Single Point Mutations on RNA Codons Using Graph Theory 

message: It's more accurate, but it would need some work by a graphic artist for scaling. Serine (S) is properly represented. CC 4.0.
https://www.researchgate.net/publication/374911250_Amino_Acids_Are_Segregated_in_Hydropathy_-_Molar_Volume_Space_by_the_Second_Position_of_the_Codon Doug youvan (talk) 01:27, 23 October 2023 (UTC)
thread_title:  New Hydropath - Molar Volume Image ? 

message: https://www.researchgate.net/publication/374973672_Codon_Cluster_Analysis_With_Hydropathy_Written_by_GPT-4_in_Python Doug youvan (talk) 19:38, 25 October 2023 (UTC)
thread_title:  Codon Cluster Analysis With Hydropathy 

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thread_title:  Copyright problem removed