Wikipedia talk:WikiProject Biology

Epigenetics

• Epigenetics - main article
  • Epigenetic theory - overlapping content
  • Transgenerational epigenetics - overlapping content
  • Soft inheritance - overlapping content
    • Inheritance of acquired characteristics - negatively characterized as outdated and disproven Soviet dogma that had disastrous administrative consequences
    • Lamarckism - categorized as an obsolete scientific theory, despite contemporary re-analyses within the mainstream scientific community
    • Lysenkoism - depicts Lamarckism, and, specifically, the inheritance of acquired characteristics, as being a textbook example of pseudoscience among Lysenko's many bedlamitic absurdities

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)

Article about Hans Ris

Dear biologists,

as the articles for creation process is severely backlogged, I hope to count on you concerning the review of this article draft :

https://en.wikipedia.org/wiki/Draft:Hans_Ris

Thanks!

"Stargazer"

The naming, usage and primary topic of Stargazer is under discussion, see talk:Stargazer (disambiguation) -- 70.51.200.101 (talk) 06:01, 3 March 2015 (UTC)

AfD Observado.org

The article Observado.org was nominated for deletion at Wikipedia:Articles for deletion/Observado.org. Your feedback is appreciated. – Editør (talk) 17:39, 3 March 2015 (UTC)

TfD: Nomination for deletion of Template:Infraspeciesbox

Template:Infraspeciesbox has been nominated for deletion. Given that these templates are of interest to WikiProject Biology, you are invited to comment on the discussion at the template's entry on the Templates for discussion page. Dirtlawyer1 (talk) 23:16, 15 March 2015 (UTC)

"Homunculus"

The usage and primary topic of " Homunculus " is under discussion, see Talk:Homunculus patagonicus -- 65.94.43.89 (talk) 04:49, 26 March 2015 (UTC)

"Patasola"

The usage and primary topic of Patasola is under discussion, see talk:Patasola magdalenae -- 65.94.43.89 (talk) 04:57, 26 March 2015 (UTC)

Question for posting external links

Hi, I'm an editor for the Embryo Project Encyclopedia and I'm following up on a discussion that you can find here; [1]

I'm looking to connect with the wikimedians who are the main editors of this page, could someone please give me some information on how I could find them? Thank you Page Historian (talk) 21:02, 26 March 2015 (UTC) Page Historian (talk) 21:02, 26 March 2015 (UTC)

A thorough review of the gene article

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. 

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)

Merge Fragile Mental Retardation 2 & AFF2?

Not fluent enough in English to drive the process, I posted here; please have a look. Regards --BonifaceFR (talk) 10:27, 31 March 2015 (UTC)

Odd article that needs some love

I don't really edit much anymore, but just stumbled upon this odd little orphaned article from 2013 that was untagged as part of any project. Really needs a lot of love from a competent editor though: Uracil in DNA. Anyone interested? Acather96 (click here to contact me) 15:12, 6 April 2015 (UTC)

Check needed for Draft:Precambrian Body Plans

This article has been submitted for review through Articles for Creation. I am not familiar enough with the area to tell whether it is just a student paper using mostly primary sources or if this is work from secondary sources and thus a good Wikipedia addition. Can someone take a look at it. Thanks. StarryGrandma (talk) 15:55, 12 April 2015 (UTC)

I haven't looked into copyright issues (there are some comments about that at the top of the page), but content-wise I would have no trouble at all approving this article. It is quite good. Looie496 (talk) 17:08, 12 April 2015 (UTC)

Thank you very much for looking at this. I've approved the article (after looking the changes made to take care of the copyright issues). StarryGrandma (talk) 21:12, 16 April 2015 (UTC)

Capitanian Extinction/Middle Permian Extinction

End-Capitanian extinction event might be profitably turned into an article, since it is about a Big-6 extinction level event, or deleted as a WP:REDLINK; per [2] elevating its status to one of the major extinctions. doi:10.1130/B31216.1 -- 65.94.43.89 (talk) 13:13, 16 April 2015 (UTC)

WikiProject X Newsletter • Issue 3

Greetings! For this month's issue...

We have demos!

After a lengthy research and design process, we decided for WikiProject X to focus on two things:

• A WikiProject workflow that focuses on action items: discussions you can participate in and tasks you can perform to improve the encyclopedia; and
• An automatically updating WikiProject directory that gives you lists of users participating in the WikiProject and editing in that subject area.

We have a live demonstration of the new WikiProject workflow at WikiProject Women in Technology, a brand new WikiProject that was set up as an adjunct to a related edit-a-thon in Washington, DC. The goal is to surface action items for editors, and we intend on doing that through automatically updated working lists. We are looking into using SuggestBot to generate lists of outstanding tasks, and we are looking into additional options for automatic worklist generation. This takes the burden off of WikiProject editors to generate these worklists, though there is also a "requests" section for Wikipedians to make individual requests. (As of writing, these automated lists are not yet live, so you will see a blank space under "edit articles" on the demo WikiProject. Sorry about that!) I invite you to check out the WikiProject and leave feedback on WikiProject X's talk page.

Once the demo is sufficiently developed, we will be working on a limited deployment on our pilot WikiProjects. We have selected five for the first round of testing based on the highest potential for impact and will scale up from there.

While a re-designed WikiProject experience is much needed, that alone isn't enough. A WikiProject isn't any good if people have no way of discovering it. This is why we are also developing an automatically updated WikiProject directory. This directory will surface project-related metrics, including a count of active WikiProject participants and of active editors in that project's subject area. The purpose of these metrics is to highlight how active the WikiProject is at the given point of time, but also to highlight that project's potential for success. The directory is not yet live but there is a demonstration featuring a sampling of WikiProjects.

Each directory entry will link to a WikiProject description page which automatically list the active WikiProject participants and subject-area article editors. This allows Wikipedians to find each other based on the areas they are interested in, and this information can be used to revive a WikiProject, start a new one, or even for some other purpose. These description pages are not online yet, but they will use this template, if you want to get a feel of what they will look like.

We need volunteers!

WikiProject X is a huge undertaking, and we need volunteers to support our efforts, including testers and coders. Check out our volunteer portal and see what you can do to help us!

As an aside...

Wouldn't it be cool if lists of requested articles could not only be integrated directly with WikiProjects, but also shared between WikiProjects? Well, we got the crazy idea of having experimental software feature Flow deployed (on a totally experimental basis) on the new Article Request Workshop, which seeks to be a place where editors can "workshop" article ideas before they get created. It uses Flow because Flow allows, essentially, section-level categorization, and in the future will allow "sections" (known as "topics" within Flow) to be included across different pages. What this means is that you have a recommendation for a new article tagged by multiple WikiProjects, allowing for the recommendation to appear on lists for each WikiProject. This will facilitate inter-WikiProject collaboration and will help to reduce duplicated work. The Article Request Workshop is not entirely ready yet due to some bugs with Flow, but we hope to integrate it into our pilot WikiProjects at some point.

Harej (talk) 01:58, 19 April 2015 (UTC)

Annotated image policy

If anyone has an interest in interactive annotated images, I've made a post on WP:IUP to discuss when wikilinked image annotation is appropriate. T.Shafee(Evo﹠Evo)^talk 02:23, 19 April 2015 (UTC)

New Essay

There is a new essay, "Identifying primary and secondary sources for biology articles", you are invited to comment on.DrChrissy ^(talk) 12:11, 27 April 2015 (UTC)