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WikiProject Biology (Rated Project-class)
WikiProject Biology is part of the WikiProject Biology, an effort to build a comprehensive and detailed guide to biology on Wikipedia.
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EpigeneticsEdit

This interrelated series of articles is one of the most disoriented, contradictory and factually compromised sets that I've encountered on our project in quite some time. Moreover, the overlapping nature of content and lack of adequately unambiguous central navigation is confusing, even for someone who has existing familiarity with the general topic. I'm not certain of how much available manpower WikiProject Biology has to offer at the moment, but I'd like to get the ball rolling on a collaborative effort of some sort.   — C M B J   04:56, 15 November 2011 (UTC)

A thorough review of the gene articleEdit

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:
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  | Maintained) 03:24, 1 April 2015 (UTC)

GlossaryEdit

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  | 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  | 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)

ReferencesEdit

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

Article

Genes[1]:2 are numerous[1]:4 and useful[1]:4.1

References

  1. ^ a b c 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.

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(talkcontribs) 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(talkcontribs) 13:23, 30 June 2015 (UTC)

Third vs. Fourth Generation SequencingEdit

Nanopore sequencing is described as 4th generation Nanopore sequencing and 3rd generation Third-generation sequencing in Wikipedia. Please review and revise. Definitions of third and fourth generation differ amongst sources. Consider adding a page to describe 4th generation. One distinction is that 3rd is all about very long reads whereas 4th is about in situ (single cell) reads.

Facto Post – Issue 2 – 13 July 2017Edit

Facto Post – Issue 2 – 13 July 2017
 

Editorial: Core models and topicsEdit

Wikimedians interest themselves in everything under the sun — and then some. Discussion on "core topics" may, oddly, be a fringe activity, and was popular here a decade ago.

The situation on Wikidata today does resemble the halcyon days of 2006 of the English Wikipedia. The growth is there, and the reliability and stylistic issues are not yet pressing in on the project. Its Berlin conference at the end of October will have five years of achievement to celebrate. Think Wikimania Frankfurt 2005.

Progress must be made, however, on referencing "core facts". This has two parts: replacing "imported from Wikipedia" in referencing by external authorities; and picking out statements, such as dates and family relationships, that must not only be reliable but be seen to be reliable.

In addition, there are many properties on Wikidata lacking a clear data model. An emerging consensus may push to the front key sourcing and biomedical properties as requiring urgent attention. Wikidata's "manual of style" is currently distributed over thousands of discussions. To make it coalesce, work on such a core is needed.

LinksEdit


Editor Charles Matthews. Please leave feedback for him.

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Wikimedia Discord has a Biology Channel!Edit

It has recently come to my attention that not only is there a highly active Wikimedia Discord Server, it also has a #wpbiology channel! See Wikipedia:Discord for more details.

I hope to feature a link to this on the main page after the redesign is complete, but for the time being I wanted to advertise it here. I would love for more people to join, and I hope it will prove a major resource to us going forward as we improve WP:BIOL and it's subprojects. I cannot emphasize how refreshing it can be to talk in real time (or even in voice channels!) rather than in talk pages.

@Evolution and evolvability and Alexmar983: This also should serve us nicely for the user group discussions--they have a #meta channel as well.

Science projectEdit

I just happened across the article Science project, which looks rather unloved. Expansion would be welcome and probably not that difficult. XOR'easter (talk) 01:51, 14 August 2019 (UTC)

Call for portal maintainersEdit

Are there any editors from this WikiProject willing to maintain Portal:Biology and other portals, such as Portal:Biotechnology, that fall within the scope of this WikiProject? The Portals guideline requires that portals be maintained, and as a result numerous portals have been recently been deleted via MfD largely becasue of lack of maintenance. Let me know either way, and thanks, UnitedStatesian (talk) 07:05, 28 August 2019 (UTC)

@UnitedStatesian: you might want to ask about the latter at Wikipedia talk:WikiProject Molecular Biology. --Nessie (talk) 13:37, 28 August 2019 (UTC)

One of your project's articles has been selected for improvement!Edit

Hello,
Please note that Organ (anatomy), which is within this project's scope, has been selected as one of Today's articles for improvement. The article was scheduled to appear on Wikipedia's Community portal in the "Today's articles for improvement" section for one week, beginning today. Everyone is encouraged to collaborate to improve the article. Thanks, and happy editing!
Delivered by MusikBot talk 00:05, 2 September 2019 (UTC) on behalf of the TAFI team

PersecutionEdit

I'm not used to seeing this definition used for human behavior that may threaten animals. However, at least one source (help to evaluate it welcome) uses it.[1] I'm just leaving this note, in case my impression makes sense and an interested editor can improve the related articles. Thanks, —PaleoNeonate – 08:19, 26 September 2019 (UTC)

I assume you mean "persecute" used as a term for harassing animal species? If so, I've heard it several times, and would regard it as standard usage (at least in the UK, I can't speak for other countries). Here are another four sources that use it, and that seem reasonably reliable to me. [2][3][4][5] Anaxial (talk) 19:50, 29 September 2019 (UTC)

WikiProject X Newsletter • Issue 15Edit

Newsletter • September 2019

A final update, for now:


The third grant-funded round of WikiProject X has been completed. Unfortunately, while this round has not resulted in a deployed product, I am not planning to resume working on the project for the foreseeable future. Please see the final report for more information.

Regards,

-— Isarra 19:24, 29 September 2019 (UTC)

Taxonomic boundary paradoxEdit

Taxonomic boundary paradox is a new article, but since it is beyond my expertise I have no idea if this should have its own article on Wikipedia per WP:GNG and so on. I am hoping someone from this project can take a look. This may already be content that we have on Wikipedia. Also, the language is incomprehensible to the general reader and it seems to be written like a scientific paper or journal article. So, I tagged it as needing an expert. Thanks for your help. Regards - Steve Quinn (talk) 09:47, 23 October 2019 (UTC)

I'm no expert, but it reads fine to me. It is certainly a notable topic that is not yet covered in other Wikipedia articles on taxonomy or cladistics. My bigger concern is that it appeared fully formed with no sign of original incremental development. It is possible that it was written off-wiki first, but it was already fully wikified too. Loopy30 (talk) 10:48, 23 October 2019 (UTC)
It is an interesting case. The article is well written and I can believe the interplay of taxonomic assumptions and evolution is notable. But the only person who uses the term "Taxonomic boundary paradox" seems to be Janos Podani. --{{u|Mark viking}} {Talk} 11:10, 23 October 2019 (UTC)
@Steve Quinn and Loopy30: This is an interesting article and is looking at the issues between different methods of nomenclaturally describing the tree of life. As noted above the jargon taxonomic boundary paradox has only been introduced by one author, some 10 years ago, and not overly followed up upon, however the ideas represented by it have been highly discussed in areas of species boundaries and the presentation of PhyloCode and the Linnean system of nomenclature. For our purposes here I think the article should more widely cite other opinions on the matter such as Gould, de Quiroz, Joyce and oters, including responses from the ICZN. It should also be simplified in its terminology and in-line links made where possible to terms, this will include linking the jargon to more regularly known terms that encompass them. Cheers Scott Thomson (Faendalimas) talk 15:33, 23 October 2019 (UTC)
I think it's a keeper but with some flaws, as identified above. It's hard to tell how much synthesis or OR has gone into this - assuming GF, the lede and background material is a summary of Podani, which would make the entire thing somewhat single source-heavy. I've stuck a {{too few opinions}} tag on. Otherwise I believe this is a valid topic and a good basis. --Elmidae (talk · contribs) 15:58, 23 October 2019 (UTC)
Hello to Loopy30, Mark viking, Scott Thomson, and Elmidae. Your feedback here is much appreciated. Sorry it took this long to come back, but the time did allow for a number of responses. I'm glad to see this project's members are now aware of this page. Now, I have another article query for project members, entitled "Transcriptional memory". I will open a section below. ---Steve Quinn (talk) 05:30, 9 November 2019 (UTC)

Request for information on WP1.0 web toolEdit

Hello and greetings from the maintainers of the WP 1.0 Bot! As you may or may not know, we are currently involved in an overhaul of the bot, in order to make it more modern and maintainable. As part of this process, we will be rewriting the web tool that is part of the project. You might have noticed this tool if you click through the links on the project assessment summary tables.

We'd like to collect information on how the current tool is used by....you! How do you yourself and the other maintainers of your project use the web tool? Which of its features do you need? How frequently do you use these features? And what features is the tool missing that would be useful to you? We have collected all of these questions at this Google form where you can leave your response. Walkerma (talk) 04:24, 27 October 2019 (UTC)

Fixing biology typosEdit

At Wikipedia:Correct typos in one click, you can fix typos or tag them for attention in a single click. However, there are a lot of biology terms that we need help with. Can anyone help out with checking whether the typos relating to biology, particularly some obscure species are indeed typos? Thanks! Bellowhead678 (talk) 11:39, 7 November 2019 (UTC)

Fasting statesEdit

Hello, I updated the Intermittent fasting entry, and I need help checking if the infos in Intermittent fasting#Mechanism about the various fasting states transitions are correct, as it's difficult to find a single source that summarizes all fed/fasting states and with enough biological details. If anybody could check if there's not a big mistake written in, even using animal reviews, it would be very helpful (I have already sourced with appropriate reviews on humans, but I want to make sure that the info is correct, as I lack some competence in biology). To be more precise, for the timeframes it's ok, but it's more about what happens in the metabolic sense: when glucagon is released, what does it do, idem for starvation state and ketogenesis, etc. Thank you in advance!   --Signimu (talk) 12:06, 8 November 2019 (UTC)

Transcriptional memoryEdit

Hello again. Transcriptional memory is a relatively new article (since August 2019). However, I am wondering if this topic merits its own article on Wikipedia, per GNG. The page has some wonderful sources, and the text does not seem to be the creator's WP:OR or WP:SNYTHESIS based on these sources. What I mean by this is, you may notice all the references appear to be peer-reviewed biology or microbiology journal articles. The article creator does a good job of simply describing what the sources say. I suppose the only thing to wonder about is if this is already covered in other biology or microbiology. I would appreciate if project members could take a look and make some determinations. Thanks in advance. ---Steve Quinn (talk) 05:39, 9 November 2019 (UTC)

Return to the project page "WikiProject Biology".