Talk:Genetic code

Template:MedportalSA Template:Wikiproject MCB Template:WikiProject Genetics /Archive 1: Oct 2001 - Sep 2006

2 Tables?

It seems rather redundant to have both - I undestand the reasons for setting up the table both ways but I don't think it adds much to the article to include the 2nd table. If there are no objection, I'll remove it. Hichris 18:49, 28 November 2006 (UTC)

And then there's the lack of pretty pictures, but I suppose that isn't really correctable :) Chris Cunningham 18:12, 2 October 2006 (UTC)

It's not really redundant. For me (and hopefully for others) this table is a valuable resource that may be used for designing mutagenesis primers when exchanging amino acids by PCR. May I ask you to put it back, please? This message is encrypted! You'll need a brain to decode it. 14:53, 12 January 2007 (UTC)

While maybe useful to some (I do mutagenesis and haven't found any need for both, but thats me) I don't feel it adds to the article. The information is already there. I'm sure you can find the same sort of table in Text book or elsewhere online, so I'd vote no on putting it back. However if there is a lot of support for putting back then you can do so.

I actually like the circular version of the code, which can be read in both directions (see www.medigenomix.de/pics/molbio/codon_sonne.gif) If someone knows of good image like that, I'd be all for replacing the current table. Hichris 16:39, 12 January 2007 (UTC)

I think the inverse table is relevant and I replaced it. The Dutch version of this artikle (click on the interwiki link 'Nederlands') has a circular table. Maybe someone knows how to copy that table to this page? 132.229.169.132 09:49, 19 January 2007 (UTC)

Here's an alternative presentation, using the IUPAC abbreviations from DNA_sequence:

Alternate inverse table
R=Purine (G or A), Y = Pyrimidine (U or C), N = Any

Ala	GCN	Leu	YUR, CUN
Arg	CGN, AGR (MGR)	Lys	AAR
Asn	AAY	Met	AUG
Asp	GAY	Phe	UUY
Cys	UGY	Pro	CCN
Gln	CAR	Ser	UCN, AGY
Glu	GAR	Thr	ACN
Gly	GGN	Trp	UGG
His	CAY	Tyr	UAY
Ile	AUY, AUA (AUH)	Val	GUN
START	AUG	STOP	UAR, URA

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 (UTC)

Codons

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)

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)

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)

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)

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)

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)

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)

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: [2] Antorjal 01:06, 5 August 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)

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 [3] and in the published USPTO database 7 times [4] 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)

Theories on the origin of the genetic code

Despite the variations that exist, the genetic codes used by all known forms of life on Earth are very similar. Since there are many possible genetic codes that are thought to have similar utility to the one used by Earth life, the theory of evolution suggests that the genetic code was established very early in the history of life and meta-analysis of transfer RNA suggest it was established soon after the formation of earth.

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. For example, C in 2nd position of the codon yields amino acid residues that are small in size and moderate in hydropathy; U in 2nd position encodes average size hydrophobic residues; A in 2nd position encodes average size hydrophilic residues; U in 1st position encodes residues that are not hydrophilic, see Image:Codon_Bias.jpg, adapted from http://www.complexity.org.au/ci/vol01/fullen01/html] and (Yang et al. 1990. In Reaction Centers of Photosynthetic Bacteria. M.-E. Michel-Beyerle. (Ed.) (Springer-Verlag, Germany) 209-218).

There are three themes running through the many theories that seek to explain the evolution of the genetic code (and hence the origin of these patterns). One is illustrated by recent aptamer experiments which show that some amino acids have a selective chemical affinity for the base triplets that code for them. This suggests that the current, complex translation mechanism involving tRNA and associated enzymes may be a later development, and that originally, protein sequences were directly templated on base sequences. Another is that the standard genetic code that we see today grew from a simpler, earlier code through a process of "biosynthetic expansion". Here the idea is that primordial life 'discovered' new amino acids (e.g. as by-products of metabolism) and later back-incorporated some of these into the machinery of genetic coding. Although much circumstantial evidence has been found to suggest that fewer different amino acids were used in the past than today, precise and detailed hypotheses about exactly which amino acids entered the code in exactly what order has proved far more controversial. A third theory is that natural selection has led to codon assignments of the genetic code that minimize the effects of mutations..

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)

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.