Talk:Genetic code/Archive 1

Archive 1

Archive 2

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Does anybody have a reference for "This was first discovered in the 1960's.", it would be nice to add by who it was discovered, the DNA article states that it was Crick's group. A reference to a paper would be ideal. New299 15:49, 21 August 2006 (UTC)

Someone should write about all exception from basic scheme. Taw

The article was kind of hard to read, so I'm doing some significant modifications. Let me know if these are ok. I'd really like to take the start codons out of the table, since they have considerably more variability than the rest of the code (differ between eukaryotes and prokaryotes), and aren't really sufficient for a start anyways. Also, why do we always capitalize STOP and START?

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So DNA is not in "genetic code?" Also, DNA and genes are not organized into codons? This needs clarification; also, ought not the article to define intron and exon? Slrubenstein

Not sure what you mean by DNA not being in "genetic code", DNA is mentioned in the second paragraph and is the medium in which genetic encodings are written. Also, yes, DNA and genes are organized into codons; a codon is simply a group of three nucleotides, like the way a byte is a group of 8 ones and zeroes. As for introns and exons, they might be worth a mention but I don't think they're really directly relevant to an article about the genetic code. introns and exons are dealt with in "preprocessing", before RNA gets to the protein-translating machinery. Bryan

Intron and exon belong in a more general article on translation, imo. This should have the tables and a bit of closely relevant explanation. -- dsws 03:01, 12 July 2005 (UTC)

The first sentence reads:

The genetic code is the code used to translate a sequence of RNA nucleotides into protein.

Now, I assume that this is how biologists talk -- trust me, a non-biologist would eagerly look to the next sentence to find out what "translate" means in this context (or might just give up; remember, this is not a textbook, readers do not have professors or TA's to explain things, it has to be all here). So, not being sure what the technical meaning of translation is here, all I see is that there is no mention of DNA in the first sentence, only mention of RNA. Even knowing a fair amount of biology, this sentence leads me to think that the code is used in the RNA itself. There is nothing in the first sentence to suggest that the RNA is forming complementary bases from a strand of DNA which uses the same code. Look, I am not trying to be argumentative. I think the first sentence needs to be clear to leaypeople, and provide a good general definition. I really think a layperson would be pretty confused. Also, concerning codons, according to the first part of the article, codons are parts of RNA -- the implication is that they are not parts of DNA. Don't you see what I mean? The article may provide an accurate description of the process of transcription, which may be the main function of "genetic code," but it is not introducing the lay-person to what words like "genetic code" and "codon" mean in a clear way. Slrubenstein

Err.. actually, the non-biologist is supposed to CLICK the translate to find out what it means.

Absolutely agree with Slrubenstein if I understood him correctly. A mention of the genetic material as DNA or RNA is essential IMO, and I've changed the lead sentence to reflect that. --Antorjal 04:57, 21 September 2006 (UTC)

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Translation starts with a chain initiation or START codon, but unlike STOP codons these are not sufficient by themselves to begin the process; nearby initiation sequences are also required to induce transcription into mRNA and binding by ribosomes

What are "nearby initiation sequences"? Are we talking about cell processes that get DNA transcription/translating going, or are we talking about special sequences of codons? If the latter, why isn't it more accurate to drop talk about "start codons" and speak only of "start sequences" of codons? --Ryguasu 01:45 Jan 31, 2003 (UTC)

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I edited the bit about redundancy a bit and removed the insinuation that met only has one codon because it is the start site; since the start site is recognized by a separate tRNA than the met-tRNA for normal elongation, it is not necessary that these two properties be coupled. That is, met could have redundant codons, and only one of them need specify the start site. Graft 18:30, 13 Jul 2004 (UTC)

non-AUG START codons

(first moving material from above down here to a heading)

What's with all these alternate starts? I can find one reference on pubmed that talks about GUG starts, in mtDNA. Nothing for CUG. Why are they given simply as 'start', with no annotation or caveats? For all practical purposes there's really only one start codon, the rest are basically just novelties, and the text ought to emphasize this. Unless someone has a reference saying otherwise? Graft 16:14, 9 Apr 2004 (UTC)

Wup. Never mind, found lots about alternate initiation. But I still think the text should emphasize that AUG is the norm. Graft 16:15, 9 Apr 2004 (UTC)

I used to work on a family of mammalian transcription factors that are thought to initiate at a non-AUG codon (AUU=>I). There is evidence still lacking for a proof-positive concrete this-is-fact conclusion on that family, though, in particular amino-terminal peptide sequencing, exclusion of RNA-editing as a factor, and demonstration of either cross-recognition by a MET-encoding charged tRNA or the existence of a properly charged AUU anti-codon tRNA. I believe the evidence is concrete for plants, organelles, and microorganisms for known exceptions to their respective stereotypical START codons. For vertebrates (though I've been out of related research for going on 6 years) the hard-core biochemistry just isn't there to convince one that non-AUG initiation occurs in vivo. I would suggest that the non-AUG options for vertebrates (and man) be included in th translation or a translation initiation article and to refer to that article. Courtland 03:07, 2005 Feb 11 (UTC)

What are start and stop codons?

There is no explanation in the text. ··gracefool |☺ 01:56, 27 Sep 2004 (UTC)

The defintion is in the article, but rather implicit: Translation starts with a chain initiation codon (start codon). But unlike stop codons, these are not sufficient to begin the process; nearby initiation sequences are also required to induce transcription into mRNA and binding by ribosomes. The most notable start codon is AUG, which also codes for methionine. CUG and UUG, and in prokaryotes GUG and AUU, also work.

Pjacobi 11:08, 27 Sep 2004 (UTC)

What does this mean?

I'm not sure exactly what this means (diff link):

Note that if the number of amino acids coded for was eight or less, also the number of different bases needed would -- assuming a three base codon -- be only two: "generic purine" and "generic pyrimidine".

Can anyone clarify? If so, I'll add it back into the article. --bdesham 14:03, 21 Dec 2004 (UTC)

This means simply that we would have eight different codons: RRR RRY RYR RYY YRR YRY YYR and YYY. Enough to code eight different amino acids (R = purine, Y = pyrimidine). It would be a binary code, not base-4 as we have now. Note that purines are two-ring molecules and pyrimidines one-ring, so this is a strong geometric expression. Differences within these two groups are more subtle and would have been added to the code later in evolution. You can still see the "generic purine/pyrimidine" patterns in the code table...

If you now understand and agree that it is of interest, please explain it better on the page :-) - mv Tue Dec 21 18:01:15 EET 2004

Look at purine-pyrimidine scheme of the genetic code

Yo!

Okay, there's some serious problems with what we're doing here. We have DNA, we have translation (genetics), we have codon, and we have genetic code. All of these are redundant to some extent, but far more than they need to be. This article is easily the most nested of the set; in order to grasp it, one must understand the information-storing nature of DNA, the basics of protein synthesis, and what a codon is. In its current form, the article attempts to recapitulate all this information. This seems the wrong attitude to take, especially as some of these are unwieldy topics that don't lend themselves to quick exposition. So, I propose that we simply take a hardass line and say up front, "Look, if you want to understand the genetic code, you MUST know what DNA is first. go read that article and when you grasp the information storage mechanism whereby DNA operates, come back here." (etc.) Such steps will prevent the article from filling up with useless and abbreviated twaddle, and will allow it to present the code itself succintly and discuss it in greater detail, as it deserves. Graft 04:01, 23 Dec 2004 (UTC)

Err, it seems codon is now a redirect here. Mentally amend the above paragraph as necessary. Graft 04:02, 23 Dec 2004 (UTC)

If you think you can make this better, then by all means. I tried myself and IMHO made it better, but not good. Still, remember that all articles have this problem: they all assume background knowledge that the reader may or may not have. Only in this case the knowledge is more technical and less likely to be found in any particular reader.

Putting a warning at the start to this effect may be a good idea. Still, even after that the article should remain self-contained in a meaningful way. So that somebody that is familiar with these backgrounds can read it and say 'ah yes, that's how it was'. - mv Fri Dec 24 02:01:41 GMT+2 2004

Graft: yes, this looks clearly better! - mv Sat Dec 25 18:49:04 EET 2004

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Good job on this page guys. I just thought it would be a good idea, as suggested below, to have a list of exceptions. Also- it may be worth someones time to being to put in exceptions do different species, either on this page and like to the species or on the species page and like from here to there. Keep up the good work! --DavidMendoza

Codon bias

A section should be added that talks about codon bias across organisms as an evolutionary change as well as codon bias between genes in one organsism as a subtle way of altering the rate of translation (a short presentation that popped up as the #1 Google hit against "codon bias"). I'll put it on my own list of things to do, but one of the others of you would likely get to it before me. Courtland 03:17, 2005 Feb 11 (UTC)

the real picture

After a quick perusal, I'd say this explanation is pretty good. What irritates me in media explanations of the genetic code is that they imply that the code is read exactly as such! (i.e. ATTCGG etc.) If I were 100% layperson hearing that I would be confused. They don't make clear that it is a sequence of amino acids which we then convert into letters. I've even heard reporters say something like "when they discovered the sequence of letters that make up the human genome"!! (as if there are small A's G's and T's visible somewhere! --62.254.0.38 17:33, 2 Apr 2005 (UTC)

First sentence is wrong

The genetic code is a set of rules, which maps DNA sequences to proteins in the living cell, and is employed in the process of protein synthesis.

This is an incorrect assertion. The code does not, in amy way shape or form, map anything (unless you have a strange definition of the word map). Surely it is more accurate to say that The genetic code is a set of instructions or even The genetic code is a set of rules. One can then go on to explain that the instructions are used to make proteins, which provide structure and function. So the code is the set of instructions, written in triplets which tell the cell how to build proteins.

There are many mistakes in this article. Note a gene is not the same as a cistron. Not everyone would agree that the definition of a gene is that it codes for one product (be it RNA or protein). Many would argue that a gene is a heritable unit. Try to use words which have a specific meaning, like cistron.

I also think that it should be made apparent that there are other instructions which are not part of the code, no detail need be given, but it could be explained that they are similar to switches, turning genes on and off.

It is difficult to explain concepts such as this to non biologists, but it is a technical article. I understand little of many othe technical pages, such as computer pages. One cannot be expected to go into the complexities of chemistry and protein structure/function in the same article, this is why articles are linked. For example if one wants to know what translation means to a biologist, then there should be a separate article about it. Alternatively this article could be the basis for one about protein synthesis and a link from genetic code to the article could be made. After all the genetic code is simply an explanation of how protein synthesis works in vivo

This article seems to cover much irrelevant ground.--Alun 11:07, 12 May 2005 (UTC)

Come on... no one uses the word "cistron" any more, except in idiosyncratic technical usages. Also, the use of the word "map" is the mathematical one. Borrowing a definition, a map is "The correspondence of elements in one set to elements in the same set or another set.", and "to map" is "To establish a mapping of (an element or a set)." With that definition the first sentence is perfectly fine.

Also, I'm not sure what you mean by "switches". Are you talking about gene regulation? If so, that's definitely out of the scope of this article. Graft 16:16, 12 May 2005 (UTC)

So are you disputing that the code is a set of instructions? And is it not a more accessible way of defining it. This is not a mathematical article, so why use mathematical terminologies? I never said that gene regulation should be part of the article, just that it should be mentionned that the code is not the only purpose of DNA. I dispute the word gene because it is ambiguous. It does have different meanings in different disciplines. The word gene is as over used and as often misused as the word evolution. Being accurate leads to less confusion, and there seems to be plenty of confusion here. If no one uses the word cistron any more then more fool them, as it's a perfectly good word with an unambiguous meaning. Also the word map is used extensively already in molecular biology in terms of chromosome mapping, which will lead to even greater confusion.--Alun 17:55, 12 May 2005 (UTC)

I don't dispute that the code is a set of instructions. But "mapping" precisely captures what the genetic code is: a relationship between two separate encodings or alphabets. Certainly, a mapping is also a set of instructions - "set of instructions" is a rather broad term.

I'm not particularly unhappy about the use of the word "gene" - most people understand what it means in specific contexts. "Cistron" is unnecessary jargon. Graft 18:26, 12 May 2005 (UTC)

Well I disagree, I think the term map causes much confusion, and I disagree that it precisely captures what the genetic code is, quite the reverse. But I don't want to get into a dispute about it, if people are generally happy then fine. Again with the word 'gene', if the consensus is that it's OK then fair enough, though people do use it to mean other things like 'allele' and 'locus' and even 'phenotype' (for example eye colour), it is over used and I was merely attempting to be more accurate.

It is still true that much of what is in this article should really be in an article about protein synthesis. Remember that the article is about the genetic code, and not about transcription or translation, these should have their own articles. Also an article about protein synthesis (is ther one?) could include things like differences between prokaryotic and eukaryotic synthesis, how transcription and translation are linked in prokaryotes, but occur in seperately in eukaryotes. This is where there should be some mention of the differing roles of DNA and RNA in protein synthesis. After all the code is just one small part of protein synthesis, it merely allows us to predict a protein's primary structure from a citronic or mRNA sequence. What do you think?--Alun 05:26, 13 May 2005 (UTC)

The first sentence is also wrong as many viruses do not use DNA as a genome e.g. influenza, hepatitis C virus use RNA (no DNA stage). However in the interests of keeping it simple (if not accurate) I have made this point lower down in genomes. This is consistent with what is in the [genome]s article.

User [[User::TransControl]] 26 July 2006.

Reasons for redundancy

The codons attempt to ensure that minor errors in the genetic code either only causes a silent mutation or an error that would not affect the amino acid's hydrophilic/hydrophobic property

How can codons attempt to do anything, are they sentient? I will change this to

A practical consequence of redundancy is that minor...etc

as it seems more accurate to me.

The code is redundant because it has to be, two bases are two few to code for all amino acids (4²=16), so it has to be three at a minimum (4³=64). One consequence of this is the occurence of silent mutations. --Alun 06:34, 27 May 2005 (UTC)

four-fold degenerate codons can tolerate any mutation at the third position; two-fold degenerate codons can tolerate one out of the three possible mutations at the third position

This sentence is also clearly wrong. A four fold degenerate codon could not tolerate a deletion in the third position I have changed any mutation to any point mutation--Alun 06:49, 27 May 2005 (UTC)

Names of stop codons

My copy of Biochemistry (Voet & Voet, second edition) says, "... amber, ochre, and opal codons ... were so named as the result of a laboratory joke: the German word for amber is Bernstein, the name of an individual who helped discover amber mutations (mutations that change some other codon to UAG); ochre and opal are puns on amber." -- dsws 03:02, 12 July 2005 (UTC)

I, too, found that in-passing statement odd, if for no other reason than if there are genes named amber, ochre and opal, I'd like more details on what the genes normally do. I've found these web pages confirming dsws view:

http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/rev-sup/amber-name.html

http://www.sciencenews.org/articles/20000603/bob9.asp

And some proposing a different origin:

http://www.madsci.org/posts/archives/mar2000/954367704.Mb.r.html

In my short web search, I found no reference to the "gene name" theory, short of copies of this Wikipedia article. If no one has a reference for the "gene name" theory, I'd suggest a change. 19:30, 18 April 2006 (UTC)

I deleted the last link, because it was also related to some religious topics such as Kabala.

To the original question a fairly likely explation for all 3 name is at: http://www.madsci.org/posts/archives/2000-03/954367704.Mb.r.html

The picture is good, but...

Most people are more familiar with DNA than RNA. If possible, a picture of DNA would be preferable. Also, the first sentence says that codons are in DNA. Shouldn't it say nucleic acids, or DNA and RNA? Twilight Realm 00:06, 4 January 2006 (UTC)

EDIT: When I wrote this, I thought the article was about codons. Codon redirects to this article. It definitely deserves its own article. Just because codons are part of genetic code doesn't mean they shouldn't have their own article. Google and Yahoo are search engines, but if you type their names in, you aren't redirected to search engine. Congress is a part of the US government, but it has its own article. Same thing here. Twilight Realm 00:11, 4 January 2006 (UTC)

EDIT YET AGAIN: Actually, this page doesn't have much more than information on codons. Maybe the redirect should be reversed? Maybe some non-codon information is needed? Or maybe I'm just wasting my time and it's fine how it is. Consider it, at least. Twilight Realm 00:15, 4 January 2006 (UTC)

That redirect resulted from the fact that it's simply impossible to discuss either the genetic code or codons without discussing the other. That is, the concepts are so intertwined that they might as well occupy the same article. Graft 01:05, 4 January 2006 (UTC)

Start Codon Inconsistancies

In Table 1 and Table 2 the codones for start are inconsistant. Table 2 lists only AUG & GUG as start codons, but Table 1 lists AUG, UUG, & CUG as start codons for prokaryotes, and GUG & AUU as start codons for Prokaryotes only. Which is is? --Matthew 18:31, 24 February 2006 (UTC)

Actually I think we should not label anything but AUG as a start. Only a handful of non-AUG starts exist; this certainly isn't reflected by the current tables, which say 'AUG, GUG' are both starts. WTF? Justification, anyone? Otherwise I'm cleaning it up and including a footnote about alternative starts. Graft 18:38, 24 February 2006 (UTC)

Beyond amino acids

I understand the part that explains how codons relate to amino acids. What the article currently misses is an explanation how groups of codons lead to a whole protein, that is: are the amino acids chained together one after one? Thanks, --Abdull 20:20, 20 May 2006 (UTC)

Oh, it's already in: This in turn is translated by mediation of a machinery consisting of ribosomes and a set of transfer RNAs and associated enzymes into an amino acid chain (polypeptide), which will then be folded into a protein.

5' to 3'

nobody mentioned the direction of the code If i'm wrong, please correct me.

"Code" metaphor criticisms

I don't know enough about them at the moment to write it up, but a section on criticisms from biologists and others (notable cryptologists) against the "code" metaphor is probably appropriate here. There is a great discussion of this in Lily Kay's book, Who Wrote the Book of Life: A History of the Genetic Code. --Fastfission 15:06, 1 August 2006 (UTC)

Genocode

Hello, all. As many of you have noticed, Doctor Faust (talk · contribs) has been suggesting that we should add the word "genocode" to our discussion of the genetic code because it is "the de facto single-word term replacing 'genetic code'. Yesterday, he wrote me an email asking that we allow this addition. I have posted the body of that email below. – ClockworkSoul 12:35, 8 September 2006 (UTC)

Greetings,

Below is a sample of the term "Genocode" references of both common and technical usage. The user who originated the Genetic Code page might consider keeping abreast of the evolution of the language of evolution and genetics.

I most respectfully request permission to add the term "Genocode" to the Genetic Code page.

Warmest regards,

Doctor Faust

1. Article Title: Random Amplification of Polymorphic DNA and Microsatellite Genotyping of Pre- and Posttreatment Isolates of Candida spp. from Human Immunodeficiency Virus-Infected Patients on Different Fluconazole Regimens -

http://jcm.asm.org/cgi/content/full/36/8/2308 - See Heading: Materials and Methods, Sub-Heading: Rapd Analysis: "...Single band differences are identified by signscript numbers for the "genocode"...

2. Article Title: Genocodes for Genetic Algorithms -

http://216.239.51.104/search?q=cache:GKOa1d3pVv8J:www.csis.ul.ie/staff/jjcollins/mendel97.ps.gz+horse+genocode&hl=en&gl=us&ct=clnk&cd=4&client=firefox-a

3. Common/Popular Usage:

www.cafepress.com/buy/biology/-/pv_design_prod/pg_10/p_storeid.72897363/pNo_72897363/id_14305866/opt_/fpt_/c_360/

4. Common/Popular Usage: http://valy8851.livejournal.com/
5. Rabbit Genetics/Scientific/Common Usage: http://www.geocities.com/rah_rabbitry/QuikSilver.html

"Genocode: aaBbC-D-E-..."

6. Common/Scientific Usage: "Spider's Genocode" - http://www.da.wvu.edu/archives/021903/news/021903,01,03.html

"...He went on to talk about how in Canada, some scientists took a spider’s genocode and inserted it into the cell of a goat."

I chose to reply here, rather than by the original medium, for two reasons. First, because it is more appropriate to discuss such a subject here in the open with the entire community, and second, because I think that his logic is seriously flawed. A search returns exactly zero uses of the term "genocode" in the abstracts scientific literature (the one that he listed is the sole paper that mentions it in the body, and then only one time, buried in the methods section). Furthermore, citing highly obscure personal websites is more suggestive of the terms obscurity than its ubiquity. I am forced to conclude that the mention of the term "genocode" in this article is not appropriate, and that the existing redirect from Genocode to Genetic code is entirely sufficient. – ClockworkSoul 12:41, 8 September 2006 (UTC)

None of these usages have anything to do with the actual genetic code. Graft 18:09, 8 September 2006 (UTC)

As opposed to the imaginary genetic code. Doctor Faust 05:53, 13 September 2006 (UTC)

As many of you may not have noticed, ClockworkSoul's refusal to accept the new usage for the term, Genocode is not based on logic or the facts, but rather is personal and proprietary. Essentially, he is on a power trip. His ego apparently can not tolerate the possibility that there may be something about this subject of which he was unaware. Doctor Faust 20:52, 8 September 2006 (UTC)

The reason people may not have noticed is that this is entirely in your head. The reasons given are quite clear, and the consensus lies with those opposing this change. If you really wish for this to be added to the article, please make your case stronger by providing more evidence of the common use of this term, as opposed to weakening it by making uncommented reverts which go against article consensus. Thanks. Chris Cunningham 10:01, 15 September 2006 (UTC)

• Apparently it is acceptable, after all, to denigrate a contributor. And I beg your forgiveness for going "against article consensus." LOL Thanks. Doctor Faust 22:02, 20 September 2006 (UTC)

I only find about 1500 ghits for the term so it doesn't seem to be in common popular/lay press usage either (corresponds with ClockworkSoul's pondering on the need to cite an obscure website to find it). It may someday come into common use in scientific or non-scientific circles—if and when it does (assuming its meaning is as Doctor Faust proposes it is) it'll be appropriate to include it here. DMacks 06:32, 13 September 2006 (UTC)

As far as I am aware the term "genocode" is an obscure neologism and most of the hits are for misspellings of "genocide". --Antorjal 16:19, 19 September 2006 (UTC)

• Neologism: a new word or usage. Yes, I agree. It is a new usage for the term genetic code. Doctor Faust 21:50, 20 September 2006 (UTC)

Wikipedia is not the place to promote neologisms. It should identify them if and when they are commonly-enough used that there is encyclopedic value in explaining them. Wikipedia policy explicitly disproves of the inclusion of such terms. Chris Cunningham 23:14, 20 September 2006 (UTC)

• You sound so authoritative. I understand now: Wikipedia is uninterested in the most recent contributions to the evolution of language. Thank you so much for clarifying that for us. I also find it interesting that your postings are contributions, and mine are "promotions." Doctor Faust 01:00, 23 September 2006 (UTC)

It sounds like you're being sarcastic. What you've stated is in fact actually policy. And yes, your contribution is an attempt to promote the use of a neologism. My contributions might very well be seen as attempting to promote the use of post-grade school level English; I doubt I'd argue with that. I try not to edit articles to actually influence the reader though. Chris Cunningham 15:10, 23 September 2006 (UTC)

• Cunningham: Your most recent contribution might also be seen as "promoting" smug, presumptuous, insulting, comments. "Post-grade school level English?" LoL Yes, the rest of us are semi-literate chimps beside your luminous intellect. You know perfectly well that your usage of "promote" in the aforementioned context was intended to be pejorative. My response was certainly sarcastic, and responsive, but not passive-aggressive. I defer to you in all matters related to passive-aggression and the sly put-down. This is, of course, the preferred sport of academia. And if, as you state, a disinterest in "recent contributions to the evolution of language" is Wikipedia policy, then it becomes clear why many question this alleged encyclopedia's credibility. Doctor Faust 05:08, 25 September 2006 (UTC)

I don't understand how omission of this term affects WP's credibility. Searching for "Genocode" directs to the page here. But Chris is (still) right...WP is generally opposed to the use of neologisms. DMacks 04:57, 25 September 2006 (UTC)

• Look. I did NOT say the omission of the term Genocode affected WP's credibility. I clearly stated that a "policy of disinterest in recent contributions to the evolution of language" (which is what Cunningham stated) affects credibility. Doctor Faust 05:05, 25 September 2006 (UTC)

This talk page is for dicsussion about the "Genetic code" page: how to improve it and keep it in compliance with estanblished WP policies and guidelines. So if you're not talking about that, then you should find some other place that discusses whatever-you-are-talking-about. A debate on WP policies themselve and their effect on credibility or public perception of WP really needs more (and more diverse) minds than just those who read the talk pages of science pages. DMacks 05:30, 25 September 2006 (UTC)

Extensive edit-session

I know this is an A-Class article but I believe that we might have been a little lenient on this one. ;-) I've done a lot of editing (close to 100 edits), but still I'm personally not completely happy with the "incomplete" product. Anyways, I've got a lot of editing to do over the next couple of days provided I get time from the job (that pays the bills). I apologize for not explaining every single edit but I have done so more out of appreciation of my fellow editors who I'm sure will understand most of the changes I've made. However, if you do have the time to go through the history, I'd be very happy to address any concerns/comments/anger at any edit or edits I might have made during the course of the last few hours. Thanks and regards. --Antorjal 04:43, 21 September 2006 (UTC)

I had probably bludgeoned the intro a bit with excessive jargonese, thanks Graft for the changes. I've added some comments on viruses and the universal nature. Looks pretty good IMO. I agree with ClockworkSoul it's definitely GA status and needs references now. I wish there was Endnote for wikipedia... lol. I think with some work, this one might even make FA status. I'll hack at it for a bit but would love all the help I can get. Thanks again. --Antorjal 17:39, 21 September 2006 (UTC)

Some further tidying suggestions

I know the article is at GA status for the content, but it's still a tad overbearing in parts. That whole table could do with being de-linked for starters. The article generally suffers from both problems related to linking; it links too often, and it links instead of using less jargonated language. I'm sooo not the most qualified to correct this, but I'll have a go at re-linking duplicates and unnecessary things in a bit.

Other than that, the second half reads rather like a dead-tree: it uses some inappropriate second-person and makes further reading recommendations in-line.

Suggestions

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)

Now that I've read the article, kudos to the authors. Excellent article!GetAgrippa 05:46, 21 January 2007 (UTC)

"God did it"

...is being repeatedly added as an "alternative explanation" of how the genetic code came to be, and the explanation of why it should be added is based on editor bias or supression of alternative viewpoints. So let's figure it out:

1. Is the page about a scientific topic, and are the other (non-theistic) explanations within the bounds of mainstream science and well-cited by WP standards? yes
2. Is "God did it" within the bounds of mainstream science? no
3. Is there any extraordinary evidence given to support this fairly extraordinary/non-mainstream-science claim? no
4. Are there any citations being provided that support this alternative viewpoint at all? no
5. Does Gdi it even qualify as a scientific theory? Does not appear so.

Conclusion: does not belong. DMacks 19:57, 30 January 2007 (UTC)

Thanks for the comments DMacks. Your are correct! I have removed it two or three times. I call it vandalism. Well POV pushing for sure, since it is a belief and not a verifiable scientific fact. GetAgrippa 20:23, 30 January 2007 (UTC)

I entirely agree with DMacks. With all my respect, the Bible is not a scientific source. Still there is an option for the supporters of the devine origins of everything. In Cosmology exists something called Anthropic principle. As it says in the dedicated article here in Wikipedia, this is a collective term that attempts to explain the structure of the universe by way of coincidentally balanced features that are necessary and relevant to the existence on Earth of biochemistry, carbon-based life, and eventually human beings to observe such a universe. There is a lot of serious science standing behind it and it is probably the only point at which religion and science get at a shouting distance from each other. I can hardly be more politically balanced.
GGenov 20:34, 30 January 2007 (UTC)

I removed the God did it with references. This is not science as ruled in court cases (contrived dualism argument). This is not NPOV, but POV pushing. I believe there is some scientific credence to the notion of an extraterrestrial origin of life on earth, but this is a horse of a different color. I have noted on this editors Talk that he has a problem with POV pushing and failing to take the rules seriously. GetAgrippa 21:36, 1 February 2007 (UTC)

Frank needs to make a case on the Talk page. His statment is not NPOV, because we would have to include other faiths-God is only the Abrahamic faiths. Further, nowhere in the JudeoChristian bible does it say God (Yahweh, etc.) created the genetic code. The article is about the genetic code. GetAgrippa 22:22, 1 February 2007 (UTC)

No God mention in my last edit, and I retitled the section to say "Scientific theories of the origin of the genetic code". This should be a good compromise. As for vandalism accusations, that violates WP:AGF. NPOV does not equal SPOV, but if you want this to be a science only article then the section heading change is in order. A link to the controversy somewhere should be put in, as it isn't neutral to state only science explanations for the genetic code, but title the section as if it was all inclusive. --Frank Lofaro Jr. 23:50, 1 February 2007 (UTC)

This is a science article. NPOV is per subject not in general. GetAgrippa 00:30, 2 February 2007 (UTC)

The editors on this page might be interested in reading Wikipedia:Requests for arbitration/Pseudoscience. JChap2007 23:38, 8 February 2007 )

I thought whoever made "God Did It" meant it as a joke. 10:21, 3 March 2019 — Preceding unsigned comment added by 2601:341:300:59C0:A143:5208:4032:48D (talk)

Merger proposal

I have written up my issues with Universal genetic code on its talk page. -Madeleine 21:02, 15 April 2007 (UTC)

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)

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 [1] Adam Cuerden ^talk 20:34, 17 April 2007 (UTC)

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)

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)

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)

Scientific theories on the origins?

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)

I think you're right, so I went ahead and changed it. -- Madeleine 22:34, 25 April 2007 (UTC)

See above; it was titled so to keep "God did it" from being added. 142.59.172.187 20:05, 29 May 2007 (UTC)

Codon usage stats in the genetic code image

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)

Freeland et al reference

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)

Image:GeneticCode21-version-2.svg

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)

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)

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)

Why is amino acid residue hydropathy and molar volume encoded in the genetic code prior to translation?

Doug Youvan (talk) 02:04, 25 April 2008 (UTC)

The genetic code is fault tolerant such that point mutations (single base changes) are less likely to cause destabilizing mutations in proteins. Thus, amino acids with similar physical properties are more likely to have similar triplets. From this article: "A practical consequence of redundancy is that some errors in the genetic code only cause a silent mutation or an error that would not affect the protein because the hydrophilicity or hydrophobicity is maintained by equivalent substitution of amino acids; for example, a codon of NUN (where N = any nucleotide) tends to code for hydrophobic amino acids." Madeleine ✉ ✍ 02:52, 25 April 2008 (UTC)

The genetic code is certainly capable of evolving, especially when you don't have a lot of cellular machinery committed to it. As is evident from the article, there are many examples of mitochondrial variations on the genetic code. Tweaking the code isn't impossible - the code, after all, is the product of a specific machinery - tRNA synthetases and tRNA itself, to be exact. It's possible that at a primitive enough point in the history of organismal complexity, this machinery evolved to some semblance of optimality. But this is just my speculation - I'll try and find a few references on the subject. Graft | talk 05:27, 25 April 2008 (UTC)

The source of the figure is here: http://www.complexity.org.au/ci/vol01/fullen01/html/ and that on-line paper's references will show a few interesting things: 1) the structure of a membrane protein can be predicted from the nucleotide sequence (without translation), because the correlation between the structure of the genetic code and the the hydropathy of the amino acids residues is significant, 2) Singular Value Decomposition (SVD) can be used to map amino acid residue hydropathy and molar volume (separately) back onto the triplet codon as a function of the position in the codon and the nucleotide used, and 3) the genetic code as it stands is special as compared to random codes for supporting in vitro directed evolution experiments wherein genetic algorithms (theory and practice) are used to guide the 'doping' of codons in synthetic DNA for combinatorial mutagenesis.

So, my question can be rephrased as follows: Why is the genetic code structured in a manner that predicts (another word might be better ?) the two most important properties of the amino acid residues? I don't believe there is a known feedback mechanism to select for a particular code, nor is the subject discussed much. It would seem that a hypothetical evolutionary selection on the primordial code might have lead to several different codes which we do not see. Any references to this that we can cite?

I should add that there is a related discussion here Talk:Moore-Penrose_pseudoinverse#PseudoInverse_of_Partitioned_Tuples where readers of this discussion should recognize "alphabet = 4" as the four nucleotides, and "word = 3" as the triplet (3) codon. Using that math, the conventional PsuedoInverse (from SVD) is not needed for matrices structured such as the genetic code. It's unclear whether that is a special and / or trivial solution to P=NP. Proper referencing to encyclopedic quality work is needed in that case, too. Doug Youvan (talk) 06:17, 25 April 2008 (UTC)

May I suggest that the "yellow figure" be placed in the article with an explanation of the 20 letter single amino acid code and the use of "N" for any of the four nucleotides in the triplet? Later, some of the more complex discussion (as in above) can be referenced rather than trying to go into this depth. Another editor's help would be appreciated in order to keep this understandable. Doug Youvan (talk) 14:54, 25 April 2008 (UTC)

It's hard to imagine a feedback mechanism these days, but with a much higher error rate in the process of translation redundancy would ensure greater fidelity of the protein. That seems mechanism enough. Graft | talk 15:46, 25 April 2008 (UTC)

So, without any mechanistic explanation, should we just insert the figure as an interesting phenomenon? It's basically the code plus two critical aa residue physicochemical properties in a Venn diagram. The explanation of molar volume is simply size, and the hydropathy scale is basically water solubility. Nothing more needs to be said.Doug Youvan (talk) 16:47, 25 April 2008 (UTC)

No. The diagram is difficult to understand and you're writing a lot of strange OR-ish stuff on this talk page. The observation of this redundancy is not new, try googling [optimization of the genetic code]. If someone else would like to expand the article's coverage of this then that might be nice (although I don't see that it's critical), but I would be uncomfortable with seeing any additions come from you since you seem to be pushing an original research viewpoint that I do not understand. Sorry to be so blunt. Madeleine ✉ ✍ 04:26, 26 April 2008 (UTC)

Is this more understandable? OR-ish does not apply, because this is data already on WP, and I have published in the field.

Doug youvan (talk) 16:43, 30 May 2008 (UTC)

I'll now add this as an external link to the article. The website target has nothing but this figure and the data (referenced) to create the figure. At some point, perhaps the figure can be integrated into the article and we can drop the external link. Doug youvan (talk) 21:47, 30 May 2008 (UTC)

I suggest someone else write the legend for this very simplified, small figure and insert it into the appropriate position in the Article. Doug youvan (talk) 19:42, 31 May 2008 (UTC)

It is clear that Francis Crick could have produced this diagram decades ago. He is often referenced for looking into structuring within the genetic code, but then he apparently reversed his position. This was not understandable to me until, just today, I searched "Thomas Jukes" (and) "Francis Crick" on Google and found this statement from Crick:

"The lectures will be concerned with the impact of biological ideas, both present and future, on our concept of the world. They will not be militantly anti-Christian, but nevertheless will be directed against the sort of ideas at present held by many religious people." - Referenced as 14 December 1965 from http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=546341 - having many internal links that an historian should now study in reference to Intelligent Design. Doug youvan (talk) 00:29, 1 June 2008 (UTC)

In thinking that someone might have actively opposed Crick's statement (only 20 years after WWII), and given the politics of big science, it seemed like a Crick opponent would suffer damage. Given the glaring hole at the Karolinska for the structure of tRNA, I just went to Alex Rich's website at MIT and found this letter: http://profiles.nlm.nih.gov/SC/B/B/X/W/_/scbbxw.pdf Doug youvan (talk) 01:13, 1 June 2008 (UTC)

Sorry - This out of sequence, but I now see Holley goes to Salk with Crick in 1968. Historical. Doug youvan (talk) 02:39, 3 June 2008 (UTC)

No one seems to be watching this page, so I made ~ 10 posts on the Talk pages of ~ the last 10 editors on this article. That is a request to review [[Image:Codon_Bias.jpg]] before it is inserted. Doug youvan (talk) 05:08, 1 June 2008 (UTC)

Wikipedia:ARCHIVE Please do not archive this section at this time: "There are two main methods for archiving a talk page, detailed below. Regardless of the method you choose, you should leave current, ongoing discussions on the existing talk page." Doug youvan (talk) 10:17, 1 June 2008 (UTC)

None of these diagrams above mean much to me on their own. Please draft a paragraph outlining what you wish to insert and citing the references that make the points that are also made in the text. Please note that references cannot be used to provide data that is then interpreted in a novel way on Wikipedia - that is original research. The ideas and arguments cannot be novel, you must simply report what others have said in publications on the topic beforehand. Tim Vickers (talk) 18:31, 1 June 2008 (UTC)

Tim - Please click on the black-and-white figure, above, and it will take you Commons where the key is given in the description. You will see see links to two published papers. One is on-line. This figure is a re-draw and simplification of the published figure. In particular, I redrew so that the black and white version shown here survives reduction in physical size. The "yellow" published figure which you see above on this discussion page is the same as the one referenced through Commons, and it does not survive physical reduction in size. I still think I should avoid writing the legend myself so as to double check any possible typos. A typo in the genetic code will propagate rapidly from this article. The pattern is referenced in the issued USPTO database as a program from MIT (Cyberdope) 19 times [2] and in the published USPTO database 7 times [3] Thanks. Doug youvan (talk) 20:17, 1 June 2008 (UTC)

Sorry, I mean please provide a draft of the text that you wish to insert, I've started a section below. Tim Vickers (talk) 20:33, 1 June 2008 (UTC)

Draft

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)

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)

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) oops Doug youvan (talk) 16:43, 2 June 2008 (UTC)

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)

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)

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)

Alternate representations of the genetic code

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)

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)

Is there the possibility to delete this particular talk section (Alternate representations of the genetic code)? The Journal of Theoretical Biology accepted my article and I have calmed down considerably after my initial shock at the results of playing sudoku with the genetic code. Apologies again for not following proper procedures. I don't know if I'm entitled to delete the section but I give my full consent to anyone who wishes and is entitled to do so. Agabirhei (talk) 19:36, 4 July 2008 (UTC)

The forbidden combinations of gentic codes and amino acids

The following codon and the corresponding amino acid combinations do not occur in nature.

1. TGGTGTATG corresponding to the amino acid combination WCM
2. TGGATGTGT corresponding to the amino acid combination WMC
3. TGTATGTGG corresponding to the amino acid combination CMW
4. TGTTGGATG corresponding to the amino acid combination CWM
5. ATGTGTTGG corresponding to the amino acid combination MCW
6. ATGTGGTGT corresponding to the amino acid combination MCW

These combinations are found only in certain genetically modified clones and hypothetical proteins. To verify this (this won't take not more than a miniute):

1. Run blastp at http://blast.ncbi.nlm.nih.gov/Blast.cgi for wcmwmccmwcwmmcwmwc and check the output, check for the proteins, find whether they are hypothetical or biochemically characterized.
2. Run blastn at http://blast.ncbi.nlm.nih.gov/Blast.cgi for TGGTGTATGAAAAAAAAAAA, TGGATGTGTAAAAAAAAAAA, TGTATGTGGAAAAAAAAAAA, TGTTGGATGAAAAAAAAAAA, ATGTGTTGGAAAAAAAAAAA, ATGTGGTGTAAAAAAAAAAA, and check each output. One would find similar sequences only, no exact match (except some clones). —Preceding unsigned comment added by Jeyamalini (talk • contribs)

Are they forbidden (they would have some alternative effect or lead to an impossible/incompatible situation), or are they just base-sequences that nothing happens to use? Are they really not found in nature, or are they only not found in the subset of nature that has been gene-sequenced? "Hypothetical" and "biochemically characterized" excludes all the things that exist or have existed but that have not been studied yet. If there is really something special about these sequences that they can't occur or have been proven not to occur in general (not just blast datasets), then someone will have certainly published about it and we need a source supporting that strong claim. If it's just a novel thing something someone stumbled upon, it's WP:OR, and Wikipedia isn't for publishing of original results--publish it in a good journal and Wikipedia (a collection of non-experts) will trust the editorial judgement of experts (journal staff). DMacks (talk) 05:40, 22 September 2009 (UTC)

If you BLAST experiment is correct, these sequences do not occur in the non-redundant set of sequenced genomes. This is different from them being "forbidden" There are probably many combinations of nucleotides that either do occur but have not been seqenced yet, or do not occur in any living organism. This is to be expected. Tim Vickers (talk) 17:06, 22 September 2009 (UTC)

If every genome can be sequenced, then the genetic code itself may be disproved. As of now, there is no such combination of genetic codes which occur in nature. If there are not found in nature, it is not wrong to assume that they are forbidden.

Actually it is completely wrong to assume they are forbidden! You are assuming there is a cause (rather than coincidence) and you are not even ruling out experimental design flaws (extrapolating from a known incomplete dataset without knowing the existing data is a representative sample). "There are no students named Jake in my class, therefore my university does not allow anyone named Jake to take any classes?" DMacks (talk) 02:50, 23 September 2009 (UTC)

Amino acids are not used with equal frequencies. The least frequently used one in humans is W, while the most frequent L is used eight times as often. In addition, particular amino acid orderings are favored or disfavored because they lead to structural instability or are targets for other enzymes which recognize certain amino acid sequences and modify the protein based on them.

Your analysis is flawed and demonstrates your lack of experience in the field. You can't use BLAST like this, it's a seed based method meant to extend to significantly long patterns with various point scores given for extensions. You never use it to look for matches so short.

Actually getting the data and doing a vaguely reasonable analysis is not difficult. Download the human genome protein sequences from ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/protein/ then write a perl program to iterate through every three letter combination of amino acids. Count how many proteins have a given combination. Here are the the fifteen rarest, in order of increasing frequency: MWW (43), WCM (54), MWC (59), WWC (69), CMW (72), WMW (73), CWW (75), WHW (76), WWM (76), YWW (76), HWW (84), WWW (84), MMW (85), MWM (87), HMW (87). There is no sharp drop-off in frequency that would support your immodest proposal of some not-yet-discovered deep biological rule regarding the letters W, C, and M.

Is it an immodest proposal? Are they biochemically characterized proteins?

In fact, this is what we'd expect given which amino acids are the rarest: W, M, C, Y, and H (in order of increasing frequency). All these trinucleotides have W in them, although WWW is probably less rare due to some instances of repetitive sequences (cf. trinucleotide repeat disorders).

Most days I wouldn't bother to do any analysis in response to someone being so rude. I guess I was bored. Your persistent editing of the main page was totally out of line. If you want to do bioinformatics, go to grad school and learn how to do it there. Then publish it in a journal. Not here. -- Madeleine ✉ ✍ 03:52, 23 September 2009 (UTC)

Removed computer science detail from "Transfer of information via the genetic code"

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)

Prokaryotic v eukaryotic

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? ^Bongo_matic 06:21, 8 October 2009 (UTC) Talk:Genetic code/Archive 1/GA1

Merge proposal

Resolved

 – Redirected here. Adrian J. Hunter^{(talk•contribs)} 18:08, 9 June 2010 (UTC)

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)

Internal section link

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)

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) (ps. New topics go down the bottom) (pps. Good copy edits!).

MCB Collaboration of the month

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:

1. 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)

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)

Just to add to the work list to remember (also for myself):

2. Section Genetic code#Sequence reading frame: Add the term Open reading frame = ORF. I will check some references since this article in WP is not well referenced as well. --Firefly's luciferase (talk) 03:14, 9 March 2010 (UTC) 3. Two details to be added: wobble base (for the base that is not necessary to determinate a particular amino acid. And, more details on Selenocysteine and Pyrrolysine, I think. --Firefly's luciferase (talk) 03:19, 9 March 2010 (UTC)

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)

Codon Table

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)

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)

Hmm... It appears you are right. For some reason, I was under the impression that DNA codons have always been used but I could've confused this page with some other sites. You are right again in that a lot of biochem and genetics textbooks use an RNA codon table instead of a DNA codon table because that reflects the biochemistry of the process.

I made the change from the standpoint that RNA codons should be of less interest than DNA codons in practice. Unless a genome biologist is working exclusively with mRNA, he'd likely be much more interested in DNA codons than RNA codons. That stems partly from the fact that much of genes that are annotated are now stored as DNA sequences rather than RNA sequences.

If the consensus is that a RNA codon table is more appropriate, then I'd concede. However, I'd prefer to have a DNA codon table in this wiki so that people who are actually working with codons will be able to refer to those tables. Although of course... it's really just a matter of changing an U to a T, but that can be tedious depending on what one's using it for. —Preceding unsigned comment added by Bobthefish2 (talk • contribs) 17:34, 10 September 2010 (UTC)

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)

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)

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)

Textbooks I checked

Snustad, D. Peter; Simmons, Michael J. (2003). Principles of genetics. New York, NY: John Wiley Sons. p. 325. ISBN 978-0-471-44180-9. Campbell, Neil; Reece, Jane (2005). Biology. San Francisco: Pearson, Benjamin Cummings. p. 314. ISBN 978-0-8053-7171-0. Tobin, Allan J.; Morel, Richard E. (1997). Asking about cells. Fort Worth, Tx: Saunders College Publishing. p. 362. ISBN 978-0-03-098018-3. Ladiges, Pauline Y.; Evans, Barbara; Saint, Robert (2010). Biology: An Australian Focus. Australia: McGraw Hill. p. 239. ISBN 978-007027440-2. McMurry, John; McMurry, Susan (2000). Organic chemistry. Pacific Grove, CA: Brooks/Cole. p. 1174. ISBN 0-534-36274-5. Elliott, William Rowcliffe; Elliott, Daphne C. (2001). Biochemistry and molecular biology. Oxford: Oxford University Press. p. 382. ISBN 0-19-870045-8. Adrian J. Hunter(talk•contribs) 05:08, 11 September 2010 (UTC)

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)

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)

Quotes for some of the challenged statements

My recent edit here came up for discussion at Wikipedia talk:No original research: what you wrote 'the code is determined by' just doesn't make sense that I can see. And you have gone and stuck it in again. The code 'just is', it is interpreted to produce things, it is not determined by the proteins or enzymes it produces. Do you mean determines? by user:Dmcq

No, the code isn't "just is". The DNA sequence just is, but "the code" in this context isn't the DNA sequence. The genetic code is the correspondence by which three-letter codons in nucleic acid sequences yield amino acids in proteins.

When I say that it's determined by stuff coded for in the DNA, I mean that the aminoacyl-tRNA synthetases are ordinary proteins: they're produced from genes using the genetic code, same as any other protein. And that the tRNAs are, like any other RNA, produced by transcription from DNA (followed by processing, although I didn't mention that). It's hard to find a quote for the former. In most contexts, it would never occur to anyone to doubt that the synthetases are coded for in DNA just like any other protein. If you know enough to be talking about them in the first place, you don't need to be told that. The best I can find at the moment is a search listing lots of genes for aminoacyl tRNA synthetases: [4] Each entry tells what chromosome the gene is on, but it doesn't belabor the fact that it's DNA.

The fact that tRNAs are coded in DNA is much easier. Here's a quote for the it: "Transfer RNA molecules, like mRNA and other types of RNA, are transcribed from DNA templates." p 325, Biology, Neil A. Campbell ISBN 0-8053-1880-1 And for the fact that tRNAs are processed rather than having the original transcript be the final form: "tRNAs are covalently modified before they exit the nucleus", p 338 Molecular Biology of the Cell, Bruce Alberts et al., ISBN 0-8153-3218-1.

But to avoid running afoul of SYNTH, I would have to find those two statements together in the same source, making their implications at least as explicit as I did. Hard plus easy isn't somewhere in between, in this type of case. Hard plus easy is well-nigh impossible, so the article never gets improved in ways that are hard plus easy. I hate SYNTH. Suppose I took this "original research" to a journal that publishes original research. Would they vet it for correctness and then publish my article? No, they would assign an intern (if they felt sorry for me enough to waste the time) to explain to me that my supposed discovery was already obvious to everyone back in 1959. Here in WP, though, it's unverifiable original research. Did I mention that I hate SYNTH? (If anyone feels the need to answer that question, please do so at Wikipedia talk:No original research#I hate SYNTH.)

The problem in the article that got me to make the edit was that it said mRNA is produced directly by transcription, i.e. that there are no introns. I wrote, "In eucaryotes, the result of transcription is not mRNA itself, but pre-mRNA." Here's the corresponding statement in Campbell: "In bacteria, mRNAs are ready for translation as soon as they peel away from their DNA templates. In contrast, the RNA products of transcription in eukaryotes are processed before they leave the nucleus as mRNA." Campbell p 325 --Dan Wylie-Sears 2 (talk) 05:21, 23 May 2011 (UTC)

The discussion here and at Wikipedia talk:No original research#I hate SYNTH is complicated by the fact there were two parts to your edit. Addressing both of them:

(1) The article previously stated "Each protein-coding gene is transcribed into a template molecule of the related polymer RNA, known as messenger RNA or mRNA." You noted that this implies there are no introns, and I agree that that sentence was potentially misleading. Your edit fixed that problem but also introduced some confusing wording. I've edited that paragraph myself to provide what I hope is clearer, simpler wording. I agree that whole section could use more work.

(2) You added a new paragraph that stated that the genetic code is determined by the tRNAs and the aminoacyl tRNA synthetases. You are 100% correct. I don't think this is obvious—it's actually counter-intuitive that the genetic code is determined by the genome via the genetic code—but the fact is self-evidently true to someone who understands these concepts and takes the time to think them through. But... I don't think that statement belongs in the "Transfer of information via the genetic code" section. It's far too confusing to someone who's still learning the basics of molecular biology, which presumably includes most of this article's readership. For the same reason, I doubt you'll find that statement in a general biology textbook like Campbell. The section where that statement belongs is the "Origin" section, and you may find a supporting citation in one of the papers already cited there. I do think the statement needs to be cited, because (a) it would show a reader that this initially surprising fact is not something we've made up ourselves, and (b) it would allow an interested reader to follow-up with a more detailed, professionally written source.

Adrian J. Hunter^{(talk•contribs)} 12:13, 23 May 2011 (UTC)

I agree that the edit makes it clearer, and that "Transfer of information via the genetic code" isn't a satisfactory spot for the statement. I had been planning to make a new section for it, but then I saw that much of the content would duplicate what was already in the "Transfer ..." section. Counter-intuitive but self-evident is a good description. The most reasonable interpretation of current policy is that it needs to be cited. And even if not required, a citation would be good to have. But I think self-evident should be enough that a citation wouldn't be necessary, provided there are citations of everything needed for it to be self-evident. If we were polishing an already-stellar article, it might be a priority, but at the current level I think time is better spent improving the text of the article than digging for such a citation. --Dan Wylie-Sears 2 (talk) 17:52, 23 May 2011 (UTC)

I had a misunderstanding of what you were trying to say. However it seems that a mountain is being made of a molehill. The genetic code as defined is not a complete description of the whole process of generating proteins or other products, it is simply confined to the correspondence between codons and amino acids with a bit extra about things like stop and start codons. That eukaryotes chop bits out is interesting but not very relevant. The bit you were saying about determines can simply be summarized as that the DNA is part of a system with its environment in the cell, The genetic code is a description of part of how the environment interprets the DNA to form products and in turn those products help form the environment. I'm pretty certain there is some elementary introduction around that would say something straightforward like that if you feel it needs to be said. It would theoretically be possible to have two completely different organisms using the same DNA starting with different environments but using different genetic codes but I see no point in underlining this. Dmcq (talk) 12:55, 23 May 2011 (UTC)

Mea culpa for the mountain. As I mentioned on the SYNTH talk page, I'm once-burned from a SYNTH dispute some years back. I don't remember any details, only that the word SYNTH elicits a visceral reaction (which I already toned down about 30 decibels before I clicked submit on any of this).

I like the idea of two completely different organisms with the same DNA sequence. It could be easier than it sounds, and might even be workable in a science-fiction story, for a sufficiently nerdy audience. --Dan Wylie-Sears 2 (talk) 18:01, 23 May 2011 (UTC)

Re. Reversals of edits on "Genetic Code" page: Nucleic Acid Analogs

(Copied from my user page where it shouldn't have been) Dmcq (talk) 10:56, 24 July 2011 (UTC)

The problem here is that not all the new synthetic bases are analogs. For example, several synthetic bases are not analogs of A, C, G, T and U. For another example, Watson-Crick complements require A/T or A/U and C/G pairings; however, another synthetic base is X/X. X is its own Watson-Crick complement. None of the standard DNA or RNA bases are self-complementary. Thus, X is not an analog of anything previously discussed. Thus, adding the material as you require to Nucleic Acid Analogs would be incompatible with the actual research. While this refers to the research of Eric T. Kool (one such article appearing as xDNA in Wikipedia), Kool and other researchers have several more non-analog bases. I think it would be wrong to put factually-incorrect information under Nucleic Acid Analogs.

Typical codons are based on the standard DNA bases A, C, G and T, but if synthetic bases are used (such as X, which is not a nucleic acid analog) then the corresponding synthetic codons are entirely different. For example, a codon such as iso-C/X/G could hardly be included under a discussion of Nucleic Acid Analogs since once again X is not a nucleic acid analog. Just to be clear here, an analog usually is understood to mean a derivative of a standard base. X and other synthetic bases are not derivatives of A, C, G or T. This becomes even clearer when dealing with synthetic codons based on 4-bases. Thus the research based on "the 65th codon" certainly cannot come under standard codons of analogs of nucleic acids.

Synthetic mRNA anti-codons must be treated similarly. Furthermore, synthetic tRNA also should not be treated under analogs of nucleic acids. Indeed, analogs of nucleic acids really should be treated entirely separately from codons, anti-codons, mRNA, tRNA and synthetic amino acids. The idea of putting all these things together under Nucleic Acids sounds very strange. No acceptable book in standard biochemistry has ever done this. Shadow600 (talk) 05:44, 24 July 2011 (UTC)

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)

Expanded Genetic code

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)

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)

Which DNA strand

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)

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)

Specifically address genetic-code/genome confusion?

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)

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)

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

The misuse continues: [6]. 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)

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)

Coming at this from a background of linguistics, I have a problem with using "code" to describe the subject matter of the article, as well as describing the codon as "transmitting information." The problem is that the codon describes the relatively circumscribed behavior of a limited series of chemical compounds, and the only "information" conveyed is the actual configuration of those chemical compounds. I recognize that a linguistic metaphor is useful, and possibly deemed essential by biologists in order to understand the workings of the codon and communicate it to others, but there should be a clear and unambiguous statement somewhere in the article that this is a heuristic device, and that the codon is not identical to a linguistic code.Digthepast (talk) 15:19, 26 September 2011 (UTC)

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)

Suggestion for Figure 4

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)

Redundancy and Origin

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)

Figure 4 Error

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)