Wikipedia talk:WikiProject Evolutionary biology

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WikiProject iconEvolutionary biology NA‑class
WikiProject iconThis page is part of WikiProject Evolutionary biology, an attempt at building a useful set of articles on evolutionary biology and its associated subfields such as population genetics, quantitative genetics, molecular evolution, phylogenetics, and evolutionary developmental biology. It is distinct from the WikiProject Tree of Life in that it attempts to cover patterns, process and theory rather than systematics and taxonomy. If you would like to participate, there are some suggestions on this page (see also Wikipedia:Contributing FAQ for more information) or visit WikiProject Evolutionary biology
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A thorough review of the gene article[edit]

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)[reply]

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)[reply]
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)[reply]
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)[reply]

Glossary[edit]

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)[reply]

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)[reply]
...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)[reply]
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)[reply]
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)[reply]
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)[reply]

References[edit]

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)[reply]

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)[reply]
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)[reply]
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)[reply]
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)[reply]
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)[reply]
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)[reply]

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)[reply]

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)[reply]

MBOC references[edit]

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.

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)[reply]

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)[reply]
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)[reply]
@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)[reply]
@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)[reply]
Yep, that works – thanks! Adrian J. Hunter(talkcontribs) 13:23, 30 June 2015 (UTC)[reply]

Needs review: Bias in the introduction of variation (arrival bias)[edit]

I recently submitted a draft article for review on the theory of bias in the introduction of variation (aka "arrival bias") as a cause of orientation or direction in evolution. This is a fundamental theory with substantial empirical support and potentially broad applications in regard to molecular evolution, evo-devo and self-organization.

I would appreciate anyone offering to review this or help identify reviewers. Thanks! Dabs (talk) 21:24, 20 January 2023 (UTC)[reply]

Unreviewed Featured articles year-end summary[edit]

Restoring older Featured articles to standard:
year-end 2022 summary

Unreviewed featured articles/2020 (URFA/2020) is a systematic approach to reviewing older Featured articles (FAs) to ensure they still meet the FA standards. A January 2022 Signpost article called "Forgotten Featured" explored the effort.

Progress is recorded at the monthly stats page. Through 2022, with 4,526 very old (from the 2004–2009 period) and old (2010–2015) FAs initially needing review:

  • 357 FAs were delisted at Featured article review (FAR).
  • 222 FAs were kept at FAR or deemed "satisfactory" by three URFA reviewers, with hundreds more being marked as "satisfactory", but awaiting three reviews.
  • FAs needing review were reduced from 77% of total FAs at the end of 2020 to 64% at the end of 2022.

Of the FAs kept, deemed satisfactory by three reviewers, or delisted, about 60% had prior review between 2004 and 2007; another 20% dated to the period from 2008–2009; and another 20% to 2010–2015. Roughly two-thirds of the old FAs reviewed have retained FA status or been marked "satisfactory", while two-thirds of the very old FAs have been defeatured.

Entering its third year, URFA is working to help maintain FA standards; FAs are being restored not only via FAR, but also via improvements initiated after articles are reviewed and talk pages are noticed. Since the Featured Article Save Award (FASA) was added to the FAR process a year ago, 38 FAs were restored to FA status by editors other than the original FAC nominator. Ten FAs restored to status have been listed at WP:MILLION, recognizing articles with annual readership over a million pageviews, and many have been rerun as Today's featured article, helping increase mainpage diversity.

Examples of 2022 "FAR saves" of very old featured articles
All received a Million Award

But there remain almost 4,000 old and very old FAs to be reviewed. Some topic areas and WikiProjects have been more proactive than others in restoring or maintaining their old FAs. As seen in the chart below, the following have very high ratios of FAs kept to those delisted (ordered from highest ratio):

  • Biology
  • Physics and astronomy
  • Warfare
  • Video gaming

and others have a good ratio of kept to delisted FAs:

  • Literature and theatre
  • Engineering and technology
  • Religion, mysticism and mythology
  • Media
  • Geology and geophysics

... so kudos to those editors who pitched in to help maintain older FAs !

FAs reviewed at URFA/2020 through 2022 by content area
FAs reviewed at URFA/2020 from November 21, 2020 to December 31, 2022 (VO, O)
Topic area Delisted Kept Total
Reviewed
Ratio
Kept to
Delisted
(overall 0.62)
Remaining to review
for
2004–7 promotions
Art, architecture and archaeology 10 6 16 0.60 19
Biology 13 41 54 3.15 67
Business, economics and finance 6 1 7 0.17 2
Chemistry and mineralogy 2 1 3 0.50 7
Computing 4 1 5 0.25 0
Culture and society 9 1 10 0.11 8
Education 22 1 23 0.05 3
Engineering and technology 3 3 6 1.00 5
Food and drink 2 0 2 0.00 3
Geography and places 40 6 46 0.15 22
Geology and geophysics 3 2 5 0.67 1
Health and medicine 8 3 11 0.38 5
Heraldry, honors, and vexillology 11 1 12 0.09 6
History 27 14 41 0.52 38
Language and linguistics 3 0 3 0.00 3
Law 11 1 12 0.09 3
Literature and theatre 13 14 27 1.08 24
Mathematics 1 2 3 2.00 3
Media 14 10 24 0.71 40
Meteorology 15 6 21 0.40 31
Music 27 8 35 0.30 55
Philosophy and psychology 0 1 1 2
Physics and astronomy 3 7 10 2.33 24
Politics and government 19 4 23 0.21 9
Religion, mysticism and mythology 14 14 28 1.00 8
Royalty and nobility 10 6 16 0.60 44
Sport and recreation 32 12 44 0.38 39
Transport 8 2 10 0.25 11
Video gaming 3 5 8 1.67 23
Warfare 26 49 75 1.88 31
Total 359 Note A 222 Note B 581 0.62 536

Noting some minor differences in tallies:

  • A URFA/2020 archives show 357, which does not include those delisted which were featured after 2015; FAR archives show 358, so tally is off by at least one, not worth looking for.
  • B FAR archives show 63 kept at FAR since URFA started at end of Nov 2020. URFA/2020 shows 61 Kept at FAR, meaning two kept were outside of scope of URFA/2020. Total URFA/2020 Keeps (Kept at FAR plus those with three Satisfactory marks) is 150 + 72 = 222.

But looking only at the oldest FAs (from the 2004–2007 period), there are 12 content areas with more than 20 FAs still needing review: Biology, Music, Royalty and nobility, Media, Sport and recreation, History, Warfare, Meteorology, Physics and astronomy, Literature and theatre, Video gaming, and Geography and places. In the coming weeks, URFA/2020 editors will be posting lists to individual WikiProjects with the goal of getting these oldest-of-the-old FAs reviewed during 2023.

Ideas for how you can help are listed below and at the Signpost article.

  • Review a 2004 to 2007 FA. With three "Satisfactory" marks, article can be moved to the FAR not needed section.
  • Review "your" articles: Did you nominate a featured article between 2004 and 2015 that you have continuously maintained? Check these articles, update as needed, and mark them as 'Satisfactory' at URFA/2020. A continuously maintained FA is a good predictor that standards are still met, and with two more "Satisfactory" marks, "your" articles can be listed as "FAR not needed". If they no longer meet the FA standards, please begin the FAR process by posting your concerns on the article's talk page.
  • Review articles that already have one "Satisfactory" mark: more FAs can be indicated as "FAR not needed" if other reviewers will have a look at those already indicated as maintained by the original nominator. If you find issues, you can enter them at the talk page.
  • Fix an existing featured article: Choose an article at URFA/2020 or FAR and bring it back to FA standards. Enlist the help of the original nominator, frequent FA reviewers, WikiProjects listed on the talk page, or editors that have written similar topics. When the article returns to FA standards, please mark it as 'Satisfactory' at URFA/2020 or note your progress in the article's FAR.
  • Review and nominate an article to FAR that has been 'noticed' of a FAR needed but issues raised on talk have not been addressed. Sometimes nominating at FAR draws additional editors to help improve the article that would otherwise not look at it.

More regular URFA and FAR reviewers will help assure that FAs continue to represent examples of Wikipedia's best work. If you have any questions or feedback, please visit Wikipedia talk:Unreviewed featured articles/2020/4Q2022.

FAs last reviewed from 2004 to 2007 of interest to this WikiProject[edit]

If you review an article on this list, please add commentary at the article talk page, with a section heading == [[URFA/2020]] review== and also add either Notes or Noticed to WP:URFA/2020A, per the instructions at WP:URFA/2020. Comments added here may be swept up in archives and lost, and more editors will see comments on article talk. SandyGeorgia (Talk) 19:06, 22 January 2023 (UTC)[reply]

  1. Amanita phalloides
  2. Charles Darwin
  3. DNA
  4. Ediacaran biota
  5. Evolution
  6. Exosome complex
  7. History of biology
  8. Metabolism
  9. Proteasome

There is an ongoing discussion about the Criticism section of Polyvagal Theory. The discussion is here: Talk:Polyvagal theory#Criticism of the criticism. This discussion needs editors who can take the time to read the approximately 10 academic journal articles that have been cited. The issue is whether 95% of the section represents original research on violation of WP:NOR or not. Reading academic articles to confirm the absence of criticism about a topic is a bit challenging, admittedly, which is why I think members of this project might be well-equipped for the task. Ian Oelsner (talk) 22:45, 25 January 2023 (UTC)[reply]

For anyone interested, the discussion is being continued here: Talk:Polyvagal theory#Consolidation of Criticism section to reflect reliable sources and remove original research. Oleasylvestris (talk) 07:35, 8 March 2023 (UTC)[reply]

Project-independent quality assessments[edit]

Quality assessments by Wikipedia editors rate articles in terms of completeness, organization, prose quality, sourcing, etc. Most wikiprojects follow the general guidelines at Wikipedia:Content assessment, but some have specialized assessment guidelines. A recent Village pump proposal was approved and has been implemented to add a |class= parameter to {{WikiProject banner shell}}, which can display a general quality assessment for an article, and to let project banner templates "inherit" this assessment.

No action is required if your wikiproject follows the standard assessment approach. Over time, quality assessments will be migrated up to {{WikiProject banner shell}}, and your project banner will automatically "inherit" any changes to the general assessments for the purpose of assigning categories.

However, if your project has decided to "opt out" and follow a non-standard quality assessment approach, all you have to do is modify your wikiproject banner template to pass {{WPBannerMeta}} a new |QUALITY_CRITERIA=custom parameter. If this is done, changes to the general quality assessment will be ignored, and your project-level assessment will be displayed and used to create categories, as at present. Aymatth2 (talk) 20:02, 10 April 2023 (UTC)[reply]