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Wikipedia:Featured list candidates/DNA codon table/archive1

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The following is an archived discussion of a featured list nomination. Please do not modify it. Subsequent comments should be made on the article's talk page or in Wikipedia talk:Featured list candidates. No further edits should be made to this page.

The list was promoted by PresN via FACBot (talk) 00:25, 30 January 2021 (UTC) [1].[reply]

DNA codon table

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DNA codon table (edit | talk | history | protect | delete | links | watch | logs | views)

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Nominator(s): ~ HAL333 01:37, 1 December 2020 (UTC)[reply]

Here is another attempt at a biological list. If it passes the nomination process, this will be the first featured list covering biochemistry. I find it very interesting that the pageviews for this article peak during working days of a week - I take that to mean that it is used by students. ~ HAL333 01:37, 1 December 2020 (UTC)[reply]

Drive-by comment
  • The table seems to me to be only using colour to denote the Amino-acid biochemical properties of each codon. Using only colour in this way contravenes MOS:ACCESS#Color, so you will need to add some form of symbol as well.......

 Done

@HAL333: you seem to have added the symbols to the keys but not to all the tables......? -- ChrisTheDude (talk) 17:08, 2 December 2020 (UTC)[reply]
Yeah, I haven't gotten to that yet. ~ HAL333 21:18, 2 December 2020 (UTC)[reply]
No worries :-) -- ChrisTheDude (talk) 21:27, 2 December 2020 (UTC)[reply]
Now it's  Done ~ HAL333 03:04, 6 December 2020 (UTC)[reply]
ChrisTheDude Ignoring the 3c question - which you don't have to comment on - does everything else in this list hold up to the featured list criteria? ~ HAL333 18:53, 1 January 2021 (UTC)[reply]
Yes, although I admit reading it fried my brain a bit :-) Are you going to proceed with this nom? I notice below you seem to be leaning towards withdrawal......? -- ChrisTheDude (talk) 19:18, 1 January 2021 (UTC)[reply]
I'll give it a bit more time. If this list is still moribund when I finish the list I am currently working on, I'll withdraw this one. ~ HAL333
Comments

It's been quite the journey watching this page evolve, and it's in a much different place now than it was before when I made my initial comments (see below). With the changes that have been made, this page is now much more comprehensive and stands on its own. I'm happy to change my earlier vote to support. RunningTiger123 (talk) 03:59, 20 January 2021 (UTC)[reply]

Resolved comments from RunningTiger123 (talk) 03:59, 20 January 2021 (UTC)[reply]
Oppose Requesting second opinion – Much of this page seems to be a content fork from the page Genetic code. That page already includes a codon table for RNA, which is essentially the same except for the use of U in place of T. Moreover, many sections of text seem to be lifted from that article. For instance, the page Genetic code states

The three stop codons have names: UAG is amber, UGA is opal (sometimes also called umber), and UAA is ochre. Stop codons are also called "termination" or "nonsense" codons. They signal release of the nascent polypeptide from the ribosome because no cognate tRNA has anticodons complementary to these stop signals, allowing a release factor to bind to the ribosome instead.

while the list's lead states

These three other codons, deemed stop codons, have specific names: UAG is amber, UGA is opal (sometimes also called umber), and UAA is ochre. Also called "termination" or "nonsense" codons, these sequences signal the release of the nascent polypeptide from the ribosome.

Both pages use the same source for these very similar lines. Likewise, the RNA codon table in Genetic code has two footnotes that match the two footnotes for the list, including the sources used. Given these and other similarities, the list fails featured list criteria 3c. In my opinion, the best thing to do would be to move this list into Genetic code so the codon tables are in one place. RunningTiger123 (talk) 19:33, 1 December 2020 (UTC)[reply]

  • RunningTiger123 Could I solve this by adding and changing content, or is this essentially dead in the water? (The two tables are from templates, one of which I modified on this article so that the notes were included at the bottom of the page.) ~ HAL333 20:29, 1 December 2020 (UTC)[reply]
I think the quality of the list is really good; I just don't know that there's enough standalone content to justify a separate page. My biggest issue is that there are two tables with essentially the same information on two different pages; unless that changes, I don't see what purpose this list serves. For this page to have enough unique content, I'd propose the following changes:
  • Move the RNA codon table from Genetic code to this page, or delete it altogether and simply note that the RNA codon table substitutes U for T.
  • Move the tables Human genome codon frequency table and List of alternative codons from Genetic code to this page. Those tables are probably more detailed than general audiences are interested in when reading about the genetic code, so they're a good fit for this page. (Plus, they're hidden already due to their length and detail, so they're easy to remove and replace with "See also" links.) Those tables may need better sources to be included in a FL (as would the standard DNA/RNA codon tables – I'm just realizing that I don't see any sources for them at the moment), but I think that's manageable.
  • Move the page to a more fitting title (such as "DNA and RNA codon tables"). This might require the nomination to be resubmitted – I'm not sure how that works – but it's more optional than the other two, especially if the RNA table is deleted.
My only concern with this is that this essentially leads to the deletion of the section Genetic code#Standard codon tables. I think this would be okay because the specific codons are probably a bit more detailed than the article needs as it tries to give an overview on the topic. Plus, there are several images on the page that already show the various codons, such as File:GeneticCode21-version-2.svg and File:3D Genetic Code.jpg. However, such large changes certainly need more input before moving forward. I've changed my vote from oppose so others can offer their thoughts. RunningTiger123 (talk) 21:13, 1 December 2020 (UTC)[reply]
Quick follow-up: I noticed your comment about the codon tables coming from templates. If that's the case, I'd be a little bit more comfortable having the tables on both this page and the Genetic code article (if the table in this list were to revert to the template) because it would ensure the information stays consistent between the two, which was one of my concerns for having duplicate information. However, I still think my second point is important – moving those two lists would cut out overly detailed information from the article and give this list more of a purpose. RunningTiger123 (talk) 21:20, 1 December 2020 (UTC)[reply]
Thanks! That was really helpful - I'll try to address all of these. ~ HAL333 21:36, 1 December 2020 (UTC)[reply]


Oppose The old version of Genetic code had all of this content and was not so long as to require a split. I'm confused why a separate article is necessary and this needed to be removed from it; it should be merged back. Reywas92Talk 23:33, 13 December 2020 (UTC)[reply]

Actually, it didn't have the DNA codon table. It was more of a CONTENTSPLIT than a SIZESPLIT. And there is a precedent in usage. It is similar to Protein and List of proteins, Carboxylic acid and List of carboxylic acids, etc. ~ HAL333 06:14, 14 December 2020 (UTC)[reply]
They're the exact same thing except T is swapped out for U, I'm not sure you even need both of them in the first place, and the DNA table would still fit back in the main article. This fails criterion 3c, sorry. Reywas92Talk 01:04, 15 December 2020 (UTC)[reply]
A deletion discussion regarding this article reached a consensus to keep. ~ HAL333 20:32, 23 December 2020 (UTC)[reply]
Reading the AfD, it sounds like the page was kept because the content should be included somewhere, but it was not clear if the content should stay on its own page or be merged. (When the AfD discussion was closed, it was noted that whether to merge this into Genetic Code is an editorial decision that deosn't need an admin to enforce.) I personally think that the alternate codon table provides enough content to support a separate page, but I also understand why Reywas92 is concerned about criterion 3c – that's why I requested a second opinion earlier. RunningTiger123 (talk) 21:27, 23 December 2020 (UTC)[reply]
The way I feel about it is that these two articles appeal to two different audiences. A reader of Genetic code is there to understand the fundamental principles and processes and general background. They do not need to know that an RNA sequence of UGG corresponds to Tryptophan. The simple point of the gentic code is that unique sequences of nucleotide triplets are translated into an amino acid. For example, gradeschoolers are only taught the basic fundementals of the genetic code in their classes. They are never compelled to memorize the 64 triplets. This list has a clear utilitarian function that is separate from Genetic code. If a reader of the Genetic code wants to get into the specifics, they may visit the "See also" link to this article. For what it's worth, I have yet to see an IP editor complain about the absence of codon tables on the Genetic code talk page. ~ HAL333 23:57, 23 December 2020 (UTC)[reply]
Formatting help from Dank
  • Comment Could someone help me configure Note B like all of the others? I don't know how to do it if it is at multiple points (if that makes sense...). ~ HAL333 20:28, 24 December 2020 (UTC)[reply]
    • Try this:
{{efn|group=note|name=historical|The historical basis for designating the [[stop codon#Nomenclature|stop codons as amber, ochre and opal]] is described in the autobiography of [[Sydney Brenner]] [refs go here]}}

and then:
Whatever{{efn|group=note|name=historical}}
Whatever{{efn|group=note|name=historical}}
A final defense

Before I scuttle this nomination, I will try to explain why this list conforms to featured list criteria 3c:

  • When I split the "Alternative codons" table from the Genetic code article, it was in an automatically collapsed state. Even though it violated MOS:PRECOLLAPSE, the writers of that article understand that it was too large to be included in full without disrupting the article. If that table, let alone the four others in this list, cannot be reasonably included in the Genetic Code article, than it merits this standalone list.
  • Despite its similarity to the RNA codon tables, the DNA codon tables are not redundant. Before my revisions, around 1,000 visited this list daily just to see the DNA codon tables. Obviously those readers thought that it was relevant. An AfD also reached a consensus that a DNA codon table has a place on Wikipedia.
  • This list, which fills my computer screen around five full times if I scroll, could not be fully merged with genetic code without giving undue weight to codons within the context of that article.

Hopefully this changes your mind. ~ HAL333 19:15, 29 December 2020 (UTC)[reply]

Support from Gerald Waldo Luis

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I love this list, and the format of it! It also meets the criteria, and so I'll support this nomination. I have some comments though.

Resolved comments from GeraldWL 08:39, 19 January 2021 (UTC)[reply]
* Can you add alt texts on the images? I can generally put one, but the image is too complicated for me to textify.
  • "The standard genetic code is traditionally represented as an RNA codon table because, when proteins are made in a cell by ribosomes, it is mRNA that directs protein synthesis." I'd rather have it "The standard genetic code is traditionally represented as an RNA codon table, because when proteins are made in a cell by ribosomes, it is mRNA that directs protein synthesis." Notice the change of the first comma's location.
  • Ref 1, 2, and 3 cited simultaneously. If applicable, I'd favor a breakdown: relocate the citations to where it specifically supports. So in this case, "A codon table can be used to translate a genetic code into an amino acid sequence.[1] The standard genetic code is traditionally represented as an RNA codon table because, when proteins are made in a cell by ribosomes, it is mRNA that directs protein synthesis.[2] The mRNA sequence is determined by the sequence of genomic DNA.[3]"
  • "In this context"-- rather have it "In such context".
  • I think ref 6 is already enough for p. 2 sentence 1.
  • "The first table, the standard table, can be used"-- Would rather change the commas to emdashes.
  • "As multiple codons can code for the same amino-acid"-- why the hyphen?
  • I hope I'm getting lost here, but where is the "translation table"?
  • Lead of section "Alternative codons": do breakdown regarding combi of ref 17 and 18, if applicable.


GeraldWL 09:33, 5 January 2021 (UTC)[reply]

Thanks for the support! The comments were very helpful. ~ HAL333 22:33, 5 January 2021 (UTC)[reply]

Comments Support from Aza24

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Was planning to get to this now but it seems I have too much irl work at the moment. As such, will get here sometime tomorrow. A first comment though

No worries! ;) ~ HAL333 17:44, 11 January 2021 (UTC)[reply]
  • For things like "Similar to translation table 11." it may be worth it to link to the translation table in question like: "Similar to [[#Translation table 11|translation table 11]]" and then putting {{anchor|Translation table 11}} next to the translation table in question Aza24 (talk) 06:57, 11 January 2021 (UTC)[reply]
  • I wonder if the Codon table redirect should be for this article?
  • I think in general you should be linking a lot of the scientific terms in the lead. Even if familiar to you, they seem mostly specialist enough to warrant such linking. E.g. RNA, mRNA, amino acids but probably others too
  • "sometimes also called" – surely just "sometimes called"?
  • the tables are so colorful, I love it!
  • Its not clear what your reference is for the Standard DNA codon table
  • I would assume you meant to put "(*)" next to Termination: stop codon in the key of Alternative codons in other translation tables? I would think the same should be done for this parameter in RNA and DNA Translation tables 1? Not sure if I'm properly explaining here
Good catch. ~ HAL333 00:12, 13 January 2021 (UTC)[reply]
  • Hmm not sure about this, but perhaps copy the key over to above Standard DNA codon table as well? Only because if a reader goes straight to that one they'll have to scroll back up
  • is Genetic code really needed in see also when you already have it in the lead? I would also wonder if List of genetic codes would be better in a the beginning of a certain section as a "further reading" – if you decide to do this you can move the portals to a portal bar below so it doesn't look too odd with just them in the see also
I replaced "Genetic code" with another article and kept the see also section. Is that okay? ~ HAL333 00:12, 13 January 2021 (UTC)[reply]
 Done I appreciate it. ~ HAL333 00:12, 13 January 2021 (UTC)[reply]
Support this is a very well designed list and extremely user friendly. Aza24 (talk) 23:54, 16 January 2021 (UTC)[reply]

Source review – Pass

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Will do soon Aza24 (talk) 20:33, 12 January 2021 (UTC)[reply]

  • All nitpicks, sorry...!
  • "Oregon" in ref 2 seems to be the only location you include, I would recommend removing it
  • You have "National Center for Biotechnology Information: NCBI" in ref 3 but just "National Center for Biotechnology Information" in the others – if you're going to use the abbreviation, I'd put it in parenthesis, not a colon, otherwise it makes them seem like different things.
  • I think "Nature Education" is the publisher for refs 4 and 10
  • Your author names are inconsistent, you got it right in ref 17, but for ones like ref 5, it should be "Shu, JJ" and ref 3 should be "Elzanowski, A; Ostell, J" for example (there are others)
I was trying to use the Vancouver system for the journals but forgot to do a few. I fixed it. Sorry for the confusion. ~ HAL333 15:44, 18 January 2021 (UTC)[reply]
  • there's some really odd formatting with ref 11; I would stick to the cite book template
  • I'm not sure what your retrieval date pattern is here; I thought it was having one for all web sources and not journal articles, but I see you have one for ref 19...?
  • All sources are reliable and appropriate.
  • if you can try and fix the multiple name format issue above in the further reading that would be good too, but I won't hold back a source review pass for that Aza24 (talk) 00:07, 17 January 2021 (UTC)[reply]
 Done Nitpicks appreciated. =) ~ HAL333 15:44, 18 January 2021 (UTC)[reply]
Pass for source review but aren't refs 3 and 19 the same thing? Aza24 (talk) 00:06, 19 January 2021 (UTC)[reply]
How did I miss that? Nice catch. ~ HAL333 01:45, 19 January 2021 (UTC)[reply]

Comment

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There's some oddness around start codons in this list. The lead says that there's 3, usually AUG, while alternative start codons "include" GUG and UUG- so, are there just those 3 or are there more? None of these start codons are mentioned in the tables like the stops are, while the wheel image only has AUG marked. Some clarification would be helpful. --PresN 16:56, 18 January 2021 (UTC)[reply]

Clarified (hopefully). ~ HAL333 19:40, 18 January 2021 (UTC)[reply]

Alright, my issue is sorted, so now promoting. --PresN 04:37, 29 January 2021 (UTC)[reply]

  • Closing note: This candidate has been promoted, but there may be a delay in bot processing of the close. Please see WP:FLC/ar, and leave the {{featured list candidates}} template in place on the talk page until the bot goes through.
The above discussion is preserved as an archive. Please do not modify it. No further edits should be made to this page.
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