Talk:Gene

Suggesting 2015 GA Review

Transcluded from Talk:Gene/Review

To WP:MCB, WP:GEN, WP:BIOL and WP:EB

The gene article gets 50,000 views per month but has been de-listed as a featured article since 2006. Given the success of the recent blitz on the enzyme article, I thought I'd suggest spending a couple of weeks seeing if we can get it up to a higher standard. I'm going to start with updating some of the images. If you'd like to help out on the article, it'd be great to see you there. T.Shafee(Evo﹠Evo)^talk 09:49, 31 March 2015 (UTC)

It appears the main reason gene was delisted as a GA was sourcing (see Talk:Gene/GA1). The following free textbook is probably sufficient to document most basic facts about genes:

• Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002). Molecular Biology of the Cell (Fourth ed.). New York: Garland Science. ISBN 978-0-8153-3218-3.

a second one is even more relevant, but unfortunately not freely accessed:

• Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick R (2013). Molecular Biology of the Gene (7th ed.). Benjamin Cummings. ISBN 978-0-321-90537-6.

I will start working on this as I find time. Boghog (talk) 17:58, 31 March 2015 (UTC)

Thanks for the prompt on this! I see I did do some work here back in the day, but not enough. Looks like a typical large-but-untended wiki article - bloated up with random factoids with no attention to the flow of the article. I'm pretty busy for this week and out of town next week, but I'll try to give it some attention. Opabinia regalis (talk) 19:19, 31 March 2015 (UTC)

I'll probably go through and make all the necessary MOS tweaks for FA status to the article within the next week. Too preoccupied with other articles at the moment to make any substantive content/reference changes though. Seppi333 (Insert 2¢ | Maintained) 03:24, 1 April 2015 (UTC)

Glossary

Snooping around I encountered Template:Genetics glossary, I don't know it's backstory, but it is a rather cleaver idea for a template in my opinion. I partially reckon it might go well under the first image in place or the second image depicting DNA, which conceptually is a tangent. I am not sure, hence my asking. --Squidonius (talk) 21:47, 1 April 2015 (UTC)

Including a glossary could be useful, but I think it should be concise and tailored specifically for this article. Currently {{Genetics glossary}} contains 22 entries and some of the definitions are quite lengthy. A shorter glossary, closer to the size of {{Transcription factor glossary}} or {{Restriction enzyme glossary}}, IMHO would be more effective. Another option is to transclude the {{Genetics sidebar}} which in turn links to {{Genetics glossary}}. Boghog (talk) 06:38, 2 April 2015 (UTC)

...could also just transclude a collapsed version - provides the full set of terms and takes up little space. If people need a glossary, they can expand it. Glossaries probably shouldn't be expanded by default unless there's a lot of free space along the right side of the page between level 2 sections (i.e., horizontal line breaks), since images and tables should take precedence. Seppi333 (Insert 2¢ | Maintained) 07:25, 2 April 2015 (UTC)

Collapsed or not collapsed, {{Genetics glossary}} is still way too long. Glossaries should be restricted to key terms with short definitions that can quickly be scanned while reading the rest of the article. IMHO, a long glossary defeats its purpose. Furthermore an uncollapsed glossary is more likely be read and if kept short, no need to collapse. Boghog (talk) 08:30, 2 April 2015 (UTC)

Fair enough. Might as well make a new one since it's not referenced anyway; imo, glossaries should cite sources, preferably another glossary, because it's article content. Seppi333 (Insert 2¢ | Maintained) 08:39, 2 April 2015 (UTC)

Hmm, apparently I added a bunch of stuff to that template awhile back, but don't remember it at all. It appears to be a subset of the article genetics glossary. (I'm not really sure we need both.) I agree that the template is way too long, and as constructed is hard to ctrl-F for a term.

I suggest just linking to the MBC glossary as a "reference". I would consider this kind of thing as a summary analogous to the lead paragraphs; no need for a clutter of little blue numbers. Opabinia regalis (talk) 21:47, 2 April 2015 (UTC)

References

I'm planning on adding some more Molecular Biology of the Cell references to the article using {{rp}} to specify chapter sections. I went to the MBOC 4th ed. online page but I can find no way of searching by page number, chapter, section or anything else. Any ideas on how to specify specific sections as is possible for Biochemistry 5th ed. online? Alternatively, maybe there's a more easily refernced online textbook for general citations. T.Shafee(Evo﹠Evo)^talk 11:30, 20 April 2015 (UTC)

I had the same train of thought here on the regular talk page. How about something like this? Uses {{sfn}} to include links to individual sections as notes. Of course, now they're separate from the rest of the references, but maybe it's not a bad idea to distinguish 'basic stuff you can find in a textbook' from 'specific results you need to consult the literature for'. Opabinia regalis (talk) 06:09, 21 April 2015 (UTC)

You're right, I missed that. I agree that it's actually a good way to format it. Having a separate list that indicates the significance of the references is useful. T.Shafee(Evo﹠Evo)^talk 08:06, 21 April 2015 (UTC)

I am not a big fan of {{sfn}} templates. They are more complicated and harder to maintain. Plus they don't directly address the problem of searching Molecular Biology of the Cell. What seems to work is to search for the chapter or subchapter titles in quotes. For example search for "DNA and Chromosomes" provides a link to the introduction of chapter 4. Then one can reference the chapter or subchapter number with {{rp}}. I am busy this week but should have more time this weekend to work on this. Boghog (talk) 12:21, 21 April 2015 (UTC)

I mis-described my own suggestion; it's actually {{efn}} (not that that's better). I like your method better from an aesthetic and maintenance point of view, but the problem is that giving a reader a reference to "chapter 4" is less useful if there's no obvious way to get to chapter 4 from the book's table of contents page. I don't see a way to provide separate links for each chapter/section without splitting up the references in the reference list. We could use {{rp}} like this, but I think the links police won't like that. Opabinia regalis (talk) 18:03, 21 April 2015 (UTC)

OK, I now see what you mean. The choice is between {{efn}} and in-line external links and {{efn}} is the lesser of two evils. One other possibility is to append the chapter external links to the citation:

• Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002). Molecular Biology of the Cell (Fourth ed.). New York: Garland Science. ISBN 978-0-8153-3218-3. Chapter 4: DNA and Chromosomes; Chapter 7: Control of Gene Expression; Chapter 7.1: An Overview of Gene Control; Chapter 7.2: DNA-Binding Motifs in Gene Regulatory Proteins; Chapter 7.3: How Genetic Switches Work

or have separate citations for each chapter where only the |chapter= and |chapterurl= parameters differ:

• Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002). "Chapter 7: Control of Gene Expression". Molecular Biology of the Cell (Fourth ed.). New York: Garland Science. ISBN 978-0-8153-3218-3. {{cite book}}: External link in |chapterurl= (help); Unknown parameter |chapterurl= ignored (|chapter-url= suggested) (help)

Boghog (talk) 18:47, 21 April 2015 (UTC)

My first reaction to your 'appended links' idea was that we shouldn't create our own linked pseudo-TOC given the publisher's apparent desire not to have a linked TOC hosted by the organization they actually licensed the content to. But all the other ideas do essentially the same thing, so that's a bit silly. I think I like that idea in combination with {{rp}} chapter labels best, as it's least intrusive in the text, makes clear how many citations go to a general reference, and doesn't require a separate list or potentially fragile formatting. Opabinia regalis (talk) 20:49, 21 April 2015 (UTC)

I've not done much non-standard reference citation so I'll wait until you've done a couple so that I can see the format in context before doing any more. The ones I added yesterday shouldn't be too difficult to reformat. T.Shafee(Evo﹠Evo)^talk 12:24, 22 April 2015 (UTC)

You're the one currently doing the work, so I think that means you get to decide :) Opabinia regalis (talk) 19:01, 22 April 2015 (UTC)

MBOC references

Article

Genes are numerous and useful

References

Glossary

Ch 2: Cell Chemistry and Biosynthesis

2.1: The Chemical Components of a Cell

Ch 4: DNA and Chromosomes

4.1: The Structure and Function of DNA

4.2: Chromosomal DNA and Its Packaging in the Chromatin Fiber

Ch 6: How Cells Read the Genome: From DNA to Protein

6.1: DNA to RNA

6.2: RNA to Protein

Ch 7: Control of Gene Expression

So {{rp}} labels the chapter number but does not provide any easy link to the actual information. Therefore it's combined with a list of chapter links. the benefit is that the {{rp}} template is relatively easy to maintain and the list of chapter links doesn't require maintainance and places all the MBOC links together. As stated above, there's basically no way to avoid linking individually to chapters if we want to cite MBOC. I'll finish building the chapter list over the next couple of days. T.Shafee(Evo﹠Evo)^talk 01:29, 27 April 2015 (UTC)

I've finished adding MBOC references up to section 3 (gene expression). Also, whoever originally wrote the gene expression section of the article really liked semicolons! T.Shafee(Evo﹠Evo)^talk 10:51, 27 April 2015 (UTC)

Looks great, I like the collapsible box! I can't find it at the moment, though - IIRC there is somewhere an agreement not to use collapsed boxes for references for accessibility reasons. I don't see it in WP:ACCESSIBILITY so I could be misremembering, and since the box contains links and not the reference note itself, it's probably fine. Just wanted to mention it in case someone recognized the issue. Opabinia regalis (talk) 07:50, 28 April 2015 (UTC)

@Opabinia regalis and Evolution and evolvability: The guideline is MOS:COLLAPSE, which states "...boxes that toggle text display between hide and show, should not conceal article content, including reference lists ... When scrolling lists or collapsible content are used, take care that the content will still be accessible on devices that do not support JavaScript or CSS." I checked this article on my phone, a mid-2011 model, and that entire box just doesn't appear at all using the default mobile view. I tried setting the template parameter expand=true so the box is expanded by default but that made no difference. Maybe better to change to a bulleted or indented list? Adrian J. Hunter^{(talk•contribs)} 10:50, 30 June 2015 (UTC)

@Adrian J. Hunter: Well spotted - It's really irritating when templates don't work properly on mobiles! I've changed the MBOC list to be wrapped in {{Hidden begin}} + {{Hidden end}}, which renders properly on phones (default expanded). T.Shafee(Evo﹠Evo)^talk 12:31, 30 June 2015 (UTC)

Yep, that works – thanks! Adrian J. Hunter^{(talk•contribs)} 13:23, 30 June 2015 (UTC)

Definitions

Notified: WP:MCB, WP:GEN, WP:MED

The definition of gene is probably one of the most important parts of this article. At the risk of opening Pandora's box on, it might be worth checking that we're using the best available definitions. Currently we list three definitions:

1. Gene#Lead - A gene is the molecular unit of heredity of a living organism.

   Clear and simple, but lacks any mention of function.

2. Gene#Lead - Therefore, a modern working definition is "a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions, and/or other functional sequence regions".

   The only definition that we are directly quoting from a reference and seems verbose to me.

   The use of "associated with " feels unnecessarily confusing.

   Also, close to tautology: "genomic sequence... which is associated with... other functional sequence regions".

3. Gene#Functional definitions - A broad operational definition is sometimes used to encompass the complexity of these diverse phenomena, where a gene is defined as a union of genomic sequences encoding a coherent set of potentially overlapping functional products.

   It think this is fine but omits heredity. Does it need to? What phenomena fit this definition but are not heritable?

   Exclusion of regulatory sequence doesn't seem hugely necessary.

Overall I think that we do need a simple layman's definition as well as a more nuanced, broader, technical definition. Both probably need to encompass:

• Molecular / sequence / locus / encoding
• Heritable
• Functional / expressed

T.Shafee(Evo﹠Evo)^talk 01:10, 14 June 2015 (UTC)

[1] perhaps?..--Ozzie10aaaa (talk) 01:22, 14 June 2015 (UTC)

You'd think that developing a really good single-sentence definition would be really important, but... I just can't get myself too worked up about it. It's a fuzzy concept; people use slightly different definitions for different purposes; the question of 'what do we annotate as a gene' is subtly but significantly different; etc. etc. I looked around a little specifically in the education literature and found this hilarious "simplified" model: DOI 10.1007/s11191-008-9161-7. (This thesis studying representations of genes in textbooks is pretty interesting: [2] Not so useful for our purposes, though.) Opabinia regalis (talk) 05:38, 16 June 2015 (UTC)

You're probably right. I might still have a crack at polishing the currently existing sentences over the next few days, but we do a pretty decent job of describing the key elements in the functional structure section. Also, one of the papers that comprises the thesis you mentioned was actually a pretty good history of the definition. T.Shafee(Evo﹠Evo)^talk 12:08, 19 June 2015 (UTC)

I've now updated the definitions in the article:

1. a region of DNA that controls a discrete, hereditary trait in an organism

   based on the the definition from the MBOC glossary since I think this more clearly includes the key elements

2. any discrete region of heritable, genomic sequence which affect an organism's traits by being expressed as a functional product or by regulating expression

   still based on the same references, but reworded to simplify the language and sentence structure whilst still being thorough.

3. a union of genomic sequences encoding a coherent set of potentially overlapping functional products

   left alone with only a minor change to the sentence before it.

I think that these should suffice as a simple summary for a brief visitor, as well as a more detailed definition for anyone more interested. T.Shafee(Evo﹠Evo)^talk 12:16, 25 June 2015 (UTC)

so, is gene a material, address, or information? If material, it should be DNA (or RNA for minor cases), which is very clear, but remains some unexplainable attribute. If address, even more unexplainability, which seems current definition. If information, I find no problem when I consider genetic materials are just media of genetic information, but it's just my impression. What is the formal, gold standard consensus of current definition? Current lede seems tautological, or pretty much redundant at least, and does not seem to provide clear idea.

• A gene is a locus (or region) of blah blah blha defines a gene is an address.
• Genes can acquire mutations in their sequence, leading to different variants, known as alleles defines a gene contains sequence a part of which is mutable in their address. It also defines the mutated variant is called allele. The question is that, if an allele is also defined as sequence, can it be a gene when sequence is contained in the address (gene). Also if a gene is defined as sequence, can it point an address when many experiments had suggested that genes can function regardless of, even out of, the chromosomal location.
• Therefore, a broad, modern working definition of a gene is any discrete locus of heritable, genomic sequence. might represent best, but it still states that a gene is a locus. Uh, could be tautology. Well, polygenes?

--Wordmasterexpress (talk) 09:55, 5 October 2016 (UTC)

Dear @Wordmasterexpress, Evolution and evolvability, Ozzie10aaaa, and Opabinia regalis: I appreciate your efforts to come up with a definition. When writing an intro paragraph, I think it is allowed to use a heuristic, where short and efficient may take the overhand over "complete". For the latter, one may expect the user to read the article. The first paragraph is what people see on other pages where the word is used and linked so that when readers hoover over the word, they get a pop-up of the first paragraph to remind them what the word is about or give a heuristic that makes them understand what it is about. Right? It's quite popular to refer to things as "the smallest unit of" e.g. a genetic codification of a protein that will eventually result in a trait. Isn't that good enough for most popular readings or when you come across the word in a wikipedia article? Look e.g. at how "engram" - the unit of cognitive information inside the brain - is defined, or atom, or molecule. Sincerely, SvenAERTS (talk) 03:45, 24 January 2020 (UTC)

refs

References

Not only proteins

The first sentence says that a gene codes for a protein. The last paragraph says that this is under discussion, that a gene also can code for functional non-coding RNAs. But that discussion was concluded long ago. I checked several of my rather oldish biology books. For example, the glossary in Hartwell, Hood, Goldberg, Reynolds, Silver, Veres; Genetics, from Genes to Genomes; 2004: ... segment of DNA in a discrete region of a chromosome that serves as a unit of function by encoding a particular RNA or Protein. --Ettrig (talk) 09:18, 28 October 2017 (UTC)

Different versions of the article have mentioned RNA genes in the lead e.g.

• "A gene is a locus (or region) of DNA that encodes a functional RNA or protein product" Special:Permalink/702868373
• "The word is used extensively by the scientific community for stretches of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) that code for a polypeptide or for an RNA chain that has a function in the organism." Special:Permalink/666720556

There is the later section on RNA genes too. After browsing through the history, it seems that mentions of RNA genes in the lead are frequently removed to "improve clarity". Personally I think these not mentioning them introduces inaccuracy. It may be best to involve other editors of the article in this discussion to prevent any rapid reversions e.g. @Evolution and evolvability: & @Headbomb: who mention RNAs in their edits. --Paul (talk) 08:59, 29 October 2017 (UTC)

@Ettrig: That's a great improvement, I'm not sure about this sentence "A gene is a subsequence of DNA which codes for a molecule that has a function". What about RNA viruses? Maybe add a "usually" in there somewhere. --Paul (talk) 21:52, 29 October 2017 (UTC)

Agree, RNA should be included. This is an omission of the same kind as the one I fixed. I will add or RNA. This is a bit crude. But my feeling is that nucleotides is less well known. --Ettrig (talk) 07:15, 30 October 2017 (UTC)

Added RNA, with some difficulty. The current text does not cover the retrovirus case. I now empathize with the clarity argument. We want the first sentences to be correct and also very succinct and accessible. --Ettrig (talk) 07:22, 30 October 2017 (UTC)

Hello all. Sorry to be late to the thread! Great work so far. You're correct that it was high time for the lead to be brought into line with the rest of the article. My main outstanding issue is the term "subsequence" in the first sentence. I think that "sequence" would suffice and I don't think extra useful specificity is added to the definition by using "subsequence". Indeed it's the only time the term is used in the article. T.Shafee(Evo&Evo)^talk 00:36, 31 October 2017 (UTC)

Yes, indeed. And thanks to @Chiswick Chap:. --Ettrig (talk) 12:43, 31 October 2017 (UTC)

Requested Edit: Structure and Function / Structure chapter referencing own research

I request a volunteer to review a proposed reference to own research. Details below.

At the end of this paragraph:

The transcribed pre-mRNA contains untranslated regions at both ends which contain a ribosome binding site, terminator, and start and stop codons.[42] In addition, most eukaryotic open reading frames contain untranslated introns, which are removed and exons, which are connected together in a process known as RNA splicing. Finally, the ends of gene transcripts are defined by CPA sites, where newly produced pre-mRNA gets cleaved and a string of ~200 adenosine monophosphates is added at 3′ end. PolyA tail protects mature mRNA from degradation and has other functions, affecting translation, localization, and transport of the transcript from the nucleus. Splicing, followed by CPA generate the final mature mRNA which encodes the protein or RNA product.[43] Although the general mechanisms defining locations of human genes are known, identification of the exact factors regulating these cellular processes is an area of active research. For example, known sequence features in 3′-UTR can only explain half of all human gene ends. [CITATION PROPOSED HERE]

I am requesting a reference to a recent paper from our lab - https://pubmed.ncbi.nlm.nih.gov/34104882/

Wikipedia guidelines suggest citing review papers first, however, this is the first study that assesses whether known sequence elements are sufficient to predict human gene ends. Strikingly, we found that known elements can only explain half of all human gene ends. This project was aimed at answering fundamental questions of human gene definition. The results are significant and highlight the magnitude of missing information in the current understanding of processes human cells utilize to locate their genes. Therefore, this study is the most relevant and most recent source on the subject.

To justify expert knowledge - this paper comes from Hughes lab at the University of Toronto. Dr. Timothy R Hughes is a John W. Billes Chair of Medical Research and Canada Research Chair in Decoding Gene Regulation, one of the most cited Canadian researchers.

Y Done with minor edits (missing articles, punctuation). Heartmusic678 (talk) 15:06, 22 July 2021 (UTC)

Difference between gene and chromosome

How does the gene differ from a chromosome? 41.116.8.55 (talk) 16:08, 13 January 2022 (UTC)