Talk:Genetic code/Archive 2

This is an archive of past discussions about Genetic code. Do not edit the contents of this page. If you wish to start a new discussion or revive an old one, please do so on the current talk page.

Archive 1

Archive 2

There has been a lot of back and forth on Duons. We should come to con consensus before it goes into the main article.

My take on the whole this is summed up quite nicely in this article^[1] basically the "duon" functionality is already well know and already has defined names like Regulatory DNA sequences, promoters, enhancers, termination sequences. These terms are already used in the Article and I don't think we should be using a term that basically boils down to a PR buzz word. it should not be in the introduction of the article, if at all. Ryftstarr (talk) 14:29, 16 December 2013 (UTC)

This whole Duon stuff is obviously PR buzz and trying to make the fact that epigenetic modifications occur within protein sequences a novel finding AND a distinct phrase is quite laughable. Also, the even larger claim that non-coding selection on protein regions being unknown is even more unbelievable. For transcription factor binding sites within proteins check back to at LEAST 2001, http://nar.oxfordjournals.org/content/29/19/4070.long . This concept is not at all controversial for people in the specific field of epigenetics (modifications to DNA that do not change the underlying genetic code). Also ideas about optimal codons have been expressed since at least 1987 (http://nar.oxfordjournals.org/content/15/3/1281).

Neglecting this background makes the recent insertion both shortsighted and also suspect in seeming to increase the tout of its scientific claims.

REGARDLESS, none of this discussion belongs in an introduction to the genetic code. At best it should be a distant footnote at the end linked to the more extensive discussion on codon usage. Were the editors not aware of this 30+ year research topic (http://en.wikipedia.org/wiki/Codon_usage_bias)?

To be more specific, the last paragraph of the introduction is distracting to a general introduction of the genetic code, which is specifically about the translation of mRNA into a protein sequence. Trying to shoe-horn into some talk about how organisms are more than protein (I happen to agree with things being more than proteins) is obviously out of place and seems like proselytizing. Again, if you really want it to be there, mention it in the context of the main body, not 1/3 of the introduction.

99.174.80.45 (talk) 04:45, 17 December 2013 (UTC)Thomas

I'd support a single sentence noting that the base-sequence has more functions than just encoding proteins, specifically noting non-coding regions (general idea) and regulatory domains in particular. It helps define the scope of the article to the coding regions rather than the whole sequence. It's a pretty important point that not all the DNA is coding, and from what I see it's a pretty common misconception even among science students.DMacks (talk) 05:01, 17 December 2013 (UTC)

I agree with both of those points DMacks. My main dispute was 1) overemphasis to a secondary point in the intro and 2) ignoring the rest of the extensive research on non-coding regions. I agree that the idea of DNA sequence=deterministic is misleading and worth mentioning, but as currently stated it seems to undercut the whole premise rather than the reality being more nuanced. A single sentence linking out to regulatory sequences and possibly codon usage seems like a good idea.

Though, I have to mention the overall misconception about the role most of these regulatory processes play. Most epigenetic modifications, be they transcription factors, DNA methylation, or histone modification, largely relate to changes in how MUCH of a given protein is produced, rather than WHAT protein is produced. There are some recent studies showing that histone/methylation can affect whether introns/exons are included/excluded thereby changing the protein sequence, but that does not (currently) seem to be a primary function. So again, the actual research is much less clear than is currently purported. As it stands, the last paragraph of the intro speaks more about the relevance of protein abundance evolution vs protein sequence evolution. I'm forgetting the more eloquent description of this debate, but it is a long-going discussion in the evolution literature. 99.174.80.45 (talk) 05:15, 17 December 2013 (UTC) Thomas

• I agree with the above, specifically that the term "duon" should not appear in this article and that a sentence on non-coding functionality is warranted (but the current paragraph should be removed) benmoore 09:40, 17 December 2013 (UTC)

Here is a rough draft of a replacement sentence: "While the genetic code determines the protein sequence for a given coding region, other genomic regions can influence when and where these proteins are produced" This sentence could be expanded to talk about further impact towards phenotype, but then in my opinion it starts to get bogged down in specifics that are tangential to the main article.99.174.80.45 (talk) 05:04, 18 December 2013 (UTC) Thomas

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

Robertmacl (talk) 12:45, 13 May 2014 (UTC)

Descriptions of the genetic code have improved in the past ten years, but even a simple definition is still lacking. The old definition is no longer explicitly given - the genetic code is a transfer of linear information from DNA to protein - but it is still strongly implied in everything being said here. The net effect is that there is no working definition for molecular information, and molecular information is the purpose of genetic translations.

I think there is a simple, logical foundation for the genetic code. I think that the genetic code, if it is properly understood, is central to all processes in life. I think there is a phenomenal amount of molecular information stored in and translated by the genetic code, not just codons and amino acids.

I seem to be the only person on the planet that feels this way about it, and that's okay. But I'm a little bit surprised that after ten years these valid ideas are not even mentioned on a page like this. I think for the sake of debate, you should point them out if only to refute them, or tell people why they should reject them.

If anybody cares to understand this, they can start here: http://www.codefun.com/

Many sources use the term "genetic code" to mean "genome", and it sounds like you're arguing for a similarly inclusive or broad definition. I think this article should narrowly define "genetic code" to mean essentially what a codon table shows, as it currently does. Otherwise the scope of this article becomes ill-defined, and would overlap with related articles. Adrian J. Hunter^{(talk•contribs)} 05:33, 22 July 2014 (UTC)

I absolutely do not mean "genome." If you want to define the genetic code to be "essentially what a codon table shows" then I think that should be included as the first line in the page. Then I think you should explain exactly what a codon table is and exactly what it shows, because other than being defined that way, that is not what the genetic code is.

The basic problem is that "everybody knows" that the genetic code is something that translates "molecular information." Unfortunately, this represents nothing but a tautology in that molecular information is defined as that thing translated by the genetic code, and the genetic code is defined as essentially what a codon table shows.

My basic point is that a codon table is a very small part of what the genetic code actually is, and I am limiting this here specifically to the molecular information translated from nucleotide sequences to protein sequences. The genetic code at that level is still so many things that I think it is incumbent on any explanation like this to clearly define what it is explaining. Short of that, it does more to confuse people than actually clear things up.

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

I would say that tRNA is the molecule that does the translation from codon to amino acid. It is like a dictionary or something. You are correct, it is only because of the tRNA that AAA means Lysine. The translation from AAA to lysine has nothing to do with ribosomes. It is the tRNA and only the tRNA that translates codon to amino acid. "All" that the ribosome does is to get the correct tRNA to match the mRNA and then join the amino acids into a polypeptide. Note that the tRNA also provides the energy for the ribosome to move the mRNA by 3 bases as the mRNA is read. This probably should be clarified -- Lehasa (talk) 13:51, 22 February 2015 (UTC)

Trying to use this data, I found it confusing. It's clearly not percent, since it sums to more than 100. I looked at the column heading, but was not familiar with the percent-like symbol. I hovered over the symbol, and it said "per mille", so I though it was per thousand, but was not sure in what language (I don't know Latin).

I went to the original reference cited in the section, which said "per thousand", which made sense. So I looked up per mille and found that I was not alone is not being familiar with this:

The term occurs so rarely in English that major dictionaries do not agree on the spelling or pronunciation even within a single dialect of English[10] and some major dictionaries such as Macmillan[11] and Longman[12] do not even contain an entry.

So I changed it, so now when you hover over the symbol it says "per thousand", which will be more helpful to the reader, I think. Other opinions are welcome. LouScheffer (talk) 12:29, 17 October 2016 (UTC)

The hover-text sounds like a good reason, even though it is only a redirect to our article that uses "per mille" as its actual name. DMacks (talk) 12:38, 17 October 2016 (UTC)

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

I was wondering whether there has been any research in Decipherment of the DNA. For instance, there are various types of mutations of the same gene in the human population, which express themselves as differences in real life between the humans.^[1]

Logically, each of these mutations is a code for a different message that conveys details on how to do something in the human body. My guess is that each of the 64 codons is a base building block in that code (so comparable to a letter in our own alphabet). Each gene (or hence sequence of codons) will (I think) convey a message to what type of tissue needs to be build (i.e. fat, bone, flesh, ...) and how long this strand of tissue needs to be, and its shape, and to what tissue it should connect). The thickness of the tissue is probably not specified directly, but rather specified by a seperate gene, perhaps via the "codon for specifying length". The latter, I assume because a disease like Talk:Sclerosteosis also exists.

The reason why this is useful to know is because, at present, for treating genetic diseases, we can only just use the genetic code of humans without that disease to overwrite the faulty gene in a person with the disease. However, as Stephen Friend from The Resilience Project found out, there are many versions of "good genetic code", and not all version will work on that person. We don't know why this is, and so every gene therapy that would be undertaken becomes a puzzle, and each gene therapy may need to be repeated several times. If we understand what message is in the gene, we might avoid all this.

KVDP (talk) 09:13, 27 June 2017 (UTC)

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

Currently, in section "RNA codon table", the header on the "Inverse table for the standard genetic code" table refers to "DNA codons", which should be "RNA codons". It looks like the same template is being used for both DNA and RNA codons, and the substitution T->U is made. However, the column name should be specific. Probably having separate tables would simplify things :) DeepCurl (talk) 16:42, 24 March 2019 (UTC)

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

Take a look at the new 3-D image and consider what is said in the article: "The reason may be that charge reversal (from a positive to a negative charge or vice versa) can only occur upon mutations in the first position, but never upon changes in the second position of a codon." Consider positive {R,K} <-> negative {D,E}. This statement is misleading. Please check me. Charles Juvon (talk) 22:41, 9 September 2020 (UTC)

— Preceding unsigned comment added by Charles Juvon (talk • contribs) 23:23, 9 September 2020 (UTC)

@Charles Juvon: That could certainly be removed as uncited, but I don't actually see the problem. All the negative amino acids are GAN. A charge reversal by mutation in the second position would be to or from G[C/G/U]N, but all G[C/G/U]N codons encode uncharged amino acids.

First position charge reversal is possible as AA[A/G] encode lysine and GA[A/G] encode glutamate.

By the way, I'd been thinking earlier that it would be great if your image conveyed which groups the amino acids belong to, and now you're half-way there. Would you consider distinguishing non-polar and uncharged polar amino acids by colour? Adrian J. Hunter^{(talk•contribs)} 00:24, 10 September 2020 (UTC)

@Adrian J. Hunter: Yes, I do see the first position change for E<->K. However, the first position does nothing for D and R. (I doubt the first position / charge change will survive a statistical test, but that is WP:OR.) So, let's leave the sentence as it is for now. Highlighted 3-D codes would help, and yes, I can make some more in PowerPoint. Notice that U1 encodes the aromatics. Charles Juvon (talk) 02:01, 10 September 2020 (UTC)

@Charles Juvon: I've tweaked the wording to indicate that it's only possible for certain codons, and also to indicate that the sentence is supported by the citation at the end of the previous sentence. Adrian J. Hunter^{(talk•contribs)} 02:15, 10 September 2020 (UTC)

@Adrian J. Hunter: That looks good. Would you like to pick the sets of amino acids to color in a future 3-D image?Charles Juvon (talk) 10:31, 10 September 2020 (UTC)

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

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)

This article should contain a reference to what ACGTU stand for. There's no obvious way to find the definitions of the symbols if you don't already know the basics. — Preceding unsigned comment added by 71.182.155.221 (talk) 18:18, 9 February 2021 (UTC)

May I suggest that this image would be useful for our readers: [[1]]

Charles Juvon (talk) 22:21, 27 August 2020 (UTC)

It looks like this figure can't be inserted where I want to: https://en.wikipedia.org/wiki/Wikipedia:Teahouse#Image_next_to_a_Table? Charles Juvon (talk) 18:28, 28 August 2020 (UTC)

Thanks Charles Juvon – this is great! I suggested 10 years ago (above) that a cubic codon table would be handy, but this is the first time I've ever seen one. I've shared this with my second-year genetics students.

I don't think to the right of the big table is the best place for this, as stacking large entities horizontally is inconvenient for people viewing from a mobile device, which is half of Wikipedia's viewers. So I've put it in the Degeneracy section. This isn't perfect as it creates whitespace at the bottom of the following section when viewed on a wide screen, but it's the least bad option I can find. Adrian J. Hunter^{(talk•contribs)} 08:54, 29 August 2020 (UTC)

Adrian, Thank you for your help. Perhaps as people write, some future reformatting can eliminate white space. Charles Juvon (talk) 18:52, 29 August 2020 (UTC)

Hello Charles. You are the only person on the planet I know of having pulled that visualization off. Congrats for a brilliant mind. I made an identical cube 21 years ago and put it on the Internet. I have prepared a new page with a complete explanation of my thoughts here: 3D RNA Codons Be kind, I am not a scientist.

H2mex (talk) 03:03, 27 June 2021 (UTC)

Given the current last sentence of the Article and references 99 and 100, we might want to use this material from https://arxiv.org/ftp/arxiv/papers/1303/1303.6739.pdf : "Recent biotech achievements make it possible to employ genomic DNA as data storage more durable than any media currently used (Bancroft et al., 2001; Yachie et al., 2008; Ailenberg & Rotstein, 2009). Perhaps the most direct application for that was proposed even before the advent of synthetic biology. Considering alternative informational channels for SETI, Marx (1979) noted that genomes of living cells may provide a good instance for that. He also noted that even more durable is the genetic code. Exposed to strong negative selection, the code stays unchanged for billions of years, except for rare cases of minor variations (Knight et al., 2001) and context-dependent expansions (Yuan et al., 2010)." ----Charles Juvon (talk) 20:18, 5 November 2020 (UTC)

That's from arXiv pre-print server. Was it published elsewhere in a peer-reviewed scholarly journal article? In the past few years, I have read about the use of genomes of living cells as a novel form of data storage that might even be feasible to implement, although I don't recall details of scope, quantity, cost, or anything else. I'd be okay with a sourced sentence or two about it.--FeralOink (talk) 00:12, 4 July 2021 (UTC)

Unless someone has a better idea, we need to go back to the March 15, 2021 version. The top figure is an embarrassment. That editor is now in red letters. Charles Juvon (talk) 01:45, 17 June 2021 (UTC)

Thank you, Charles Juvon. I agree. For anyone who questions my decision to remove the diagram added by this edit, please note: An IP editor with a history of merely SIX edits and no talk page added a diagram at the very top of an "All Wikipedia Level-4 vital" and "All Wikipedia GA-Class vital" article without providing any explanation here, nor in in the edit. Someone with expertise should assess whether the source in the first paragraph (about 64 parts) is appropriate for this article's lead. It has been there for months and seems to be associated with the diagram I just removed.--FeralOink (talk) 15:28, 27 June 2021 (UTC)

I found something else, need Charles Juvon or Adrian to confirm. Back on 13 October 2017, IP editor 155.69.125.199 added a source to the last sentence of the very first paragraph of the article. The sentence ends with the number 64. I am referring to this edit, i.e. the addition of the following BioSystems journal source to this sentence:

The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries.<ref>{{cite journal | title = A new integrated symmetrical table for genetic codes | journal = BioSystems | date = 2017 | first = Jian-Jun | last = Shu | volume = 151 | pages = 21–26 | doi = 10.1016/j.biosystems.2016.11.004 | pmid = 27887904 | arxiv = 1703.03787 | bibcode = 2017arXiv170303787S | s2cid = 1121152 }}</ref>

Much later, on 21 May 2021, the similar but not identical IP user 155.69.183.58 altered the article as follows:

The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries.<ref name="Shuintegratedcodes">{{cite journal | title = A new integrated symmetrical table for genetic codes | journal = BioSystems | date = 2017 | first = Jian-Jun | last = Shu | volume = 151 | pages = 21–26 | doi = 10.1016/j.biosystems.2016.11.004 | pmid = 27887904 | arxiv = 1703.03787 | bibcode = 2017arXiv170303787S | s2cid = 1121152 }}</ref>

[[Image:Other genetic codes by Jian-Jun SHU.jpg|thumb|300px|Integrated symmetrical table for genetic codes from Shu, 2017.<ref name="Shuintegratedcodes"/>]]

The Jian-Jun SHU.jpeg image is the "embarrassing" figure we excised. I was curious, and checked the journal article. The entire point of the article seems to be the creation of the table. It appeared as an arXiv pre-print and in BioSystems in November 2016.

This is the implausible abstract, referring to the embarrassing figure (via Elsevier) "A new integrated symmetrical table for genetic codes" https://www.sciencedirect.com/science/article/abs/pii/S0303264716302854?via%3Dihub emphasis mine

"Degeneracy is a salient feature of genetic codes, because there are more codons than amino acids. The conventional table for genetic codes suffers from an inability of illustrating a symmetrical nature among genetic base codes. In fact, because the conventional wisdom avoids the question, there is little agreement as to whether the symmetrical nature actually even exists. A better understanding of symmetry and an appreciation for its essential role in the genetic code formation can improve our understanding of nature’s coding processes. Thus, it is worth formulating a new integrated symmetrical table for genetic codes, which is presented in this paper. It could be very useful to understand the Nobel laureate Crick’s wobble hypothesis — how one transfer ribonucleic acid can recognize two or more synonymous codons, which is an unsolved fundamental question in biological science."

The only citations it has received are in Wikipedia articles! All appearing on May 25, 2021 or May 27, 2021. See here for the Wiki article names. Oh joy it is in Pubmed...

The same IP editor(s) 155.69.180.58 and 155.69.183.58 are sticking the embarrassing figure in other articles, e.g. see this change for DNA and RNA codon tables. Fortunately, editor HAL3000 caught them and removed them with the edit summary, "Hideous". I agree.

The IP editors stuck it in Codon degeneracy too.

There is NO WAY that chart "could be very useful to understand the Nobel laureate Crick’s wobble hypothesis". Am I right? I am sad that Elsevier publishes crud like this, which only serves to clog up Wikipedia. I will warn the IP addresses to stay away from further insertions of that diagram.--FeralOink (talk) 06:41, 3 July 2021 (UTC)

Agreed and sentence deleted. Charles Juvon (talk) 14:58, 28 June 2021 (UTC)

Ah, I figured it out! See this image from Commons! https://commons.wikimedia.org/wiki/File:Genetic_code_by_Jian-Jun_SHU.jpg Image description: Date 1 January 2017; Source Own work; Author Jian-Jun SHU. He's putting his own work in Wikipedia, and has a sockpuppet on Commons, Cuhs. Sorry for the mess. I know what to do now.--FeralOink (talk) 06:52, 3 July 2021 (UTC)

This is copied from my Talk page: "They stand out regardless as one of the most distinct pieces when U and G are at the ends. May I show you my thoughts with this page I created RNA Codons

H2mex (talk) 19:25, 3 July 2021 (UTC)" Charles Juvon (talk) 13:44, 12 July 2021 (UTC)

I have just captioned the figure on Commons: "Trivial nonsense used to vandalize our genetic code article". Charles Juvon (talk) 13:53, 12 July 2021 (UTC)

I nuked the images from commons as license-violations. Jian-Jun Shu is also adding their own ideas and self-cites to various WP articles. I removed some, am uncertain about others, and don't have time to finish even a first pass. If anyone has a moment, please look at the science/math articles in [2]. DMacks (talk) 14:37, 12 July 2021 (UTC)

Oh, and there is on-wiki technical evidence that:

• H2mex (talk⁺ · tag · contribs · deleted contribs · logs · filter log · block user · block log · CA · CheckUser(log) · investigate · cuwiki · SI)
• Cuhs (talk⁺ · tag · contribs · deleted contribs · logs · filter log · block user · block log · CA · CheckUser(log) · investigate · cuwiki · SI)

are the same person as each other. I've indefed H2mex (the newer of the two) on both enwiki and commons for abusing multiple accounts. DMacks (talk) 14:47, 12 July 2021 (UTC)

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

Please consider this CC4.0 and use as you wish.

https://www.youtube.com/watch?v=eHZxMAZTFcY Doug youvan (talk) 17:13, 9 September 2023 (UTC)

It does not appear to have an open-license on the YouTube site. DMacks (talk) 18:56, 9 September 2023 (UTC)

Thanks for finding that. I see only two choices: Standard YT and License Creative Commons - Attribution. I would set it to CC4.0, but there are no further options, so I just set it to the latter. Doug youvan (talk) 22:02, 26 September 2023 (UTC)

If another editor feels this would work in the article, please use it. Graph Construction: In our graph, vertices represent the 20 amino acids and the "Stop" signal. An edge connects two vertices if the amino acids they represent can be interchanged through a single point mutation in their corresponding codons. This graph is not just a visualization but an analytical tool, spotlighting the possible amino acid replacements due to minor genetic variations. Highlighting Mechanism: Using the computational capabilities of Mathematica, and with the expertise provided by Centaur Intelligence, each amino acid (and the Stop signal) is successively emphasized. When highlighted, all directly reachable amino acids through a single point mutation are illuminated, thus displaying the mutation landscape for each amino acid. Results: The resultant graph unravels the dense web of interconnections among amino acids based on single point mutations. As we animate through each amino acid, patterns emerge, revealing which amino acids can easily mutate into others and which remain more isolated.

https://www.researchgate.net/publication/374262107_Visualizing_the_Effects_of_Single_Point_Mutations_on_RNA_Codons_Using_Graph_Theory

https://www.youtube.com/watch?v=WsGw5w6tiyE

Doug youvan (talk) 01:58, 29 September 2023 (UTC)

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

https://www.researchgate.net/publication/374973672_Codon_Cluster_Analysis_With_Hydropathy_Written_by_GPT-4_in_Python Doug youvan (talk) 19:38, 25 October 2023 (UTC)

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