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)

Mutation rate

I don’t think we need to discuss mutation rate in this article since it is covered elsewhere. But if we include it, we should at least get it right.

The overall DNA error rate per replication is about 10^-10 - it includes the DNA replication error rate of 10^-8 and the fact that 99% of these errors are repaired. That gives 0.3 mutations per haploid genome per replication.

The mutation rate per generation in humans is not the same as the mutation rate per replication. The two papers that are referenced refer to the per generation mutation rate (10^-8). Thus every newborn baby has about 60 (2 X 30) new mutations according to this mutation rate - the latest data is closer to 100 mutations per human generation. Genome42 (talk) 02:07, 5 December 2023 (UTC)

I strongly recommend that we delete the section on "Molecular evolution" since it doesn't belong here and the material is covered elsewhere. The material in the subsection on "Mutation," for example, is covered in Mutation rates where the mutation rate in humans is said to be 50-90 mutations per generation. This conflicts with the value of 30 that was just added to this article. (The Mutation article is closer to being correct and the value stated here is wrong. The actual value is probably closer to 100 but we'll deal with that in the Mutation article.)

This example illustrates the problem with redundancy. When the main article is updated and corrected, the other entries become wrong and this helps spread misinformation and confusion. Genome42 (talk) 21:14, 10 December 2023 (UTC)

Book "How Life Works" (2023) worth considering?

A review by scientist Denis Noble of a new book entitled "How Life Works: A User’s Guide to the New Biology" (2023) by Philip Ball (editor of the journal Nature) may be worth considering? - iac - Stay Safe and Healthy !! - Drbogdan (talk) 04:51, 6 February 2024 (UTC)

Nonsense. Denis Noble is not a credible authority on genes and neither is Philip Ball. I haven't got my copy of Phil's book yet but I'm familiar with his earlier writings. This is very controversial and bound to get us into bitter edit wars. Genome42 (talk) 18:25, 7 February 2024 (UTC)

References

Drbogdan (talk) 04:51, 6 February 2024 (UTC)

More about definitions

The following quote (emphasis added) is from the chapter on meiosis in the textbook Biology: The Unity and Diversity of Life, by Starr, Taggart, Evars & Starr (15th edition, Cengage Learning, 2023), p. 188:

“Your body cells are diploid (2n), which means they contain pairs of homologous chromosomes. THE TWO CHROMOSOMES OF EACH PAIR HAVE THE SAME GENES, but their DNA sequence is not identical. This is because you inherited your chromosomes from two parents who differ genetically … Members of a species have the same traits because THEY HAVE THE SAME GENES.”

Correct me if I’m wrong, but the authors are here using “gene” in a different sense from any of the definitions that are currently listed in the wiki article. Roughly speaking, they are using “gene” to mean “locus along a DNA strand”, and *not* to mean the particular sequence of nucleotides that is present at that locus.

This textbook has the subtitle “AP Edition Update” so it is intended to be an authoritative source for students studying for the AP exam.

I am not a biologist. Could a biologist please comment on whether the discussion of gene definitions in this article should be broadened to include the definition given in the textbook? NB such a definition must be consistent with the statement that “all individuals in a species have the same genes”. LyleHoward (talk) 17:11, 8 October 2024 (UTC)

I don't think the high school textbook is using the word "gene" in a way that differs from the definition used in this article. Genome42 (talk) 21:33, 9 October 2024 (UTC)