User talk:Eryk (Wiki Ed)/sandbox/genes and proteins

Miscellaneous thoughts from Opabinia

Disclaimer: I'm not at all involved in any education-related projects here and therefore have no experience with what works or not with students.

• At WT:MCB you described this as focused exclusively on writing these kinds of articles, but the whole "Editing Wikipedia articles on genes and proteins" appears to be general advice, of the type I'd expect to appear in material not specifically targeted at this audience. Maybe repetition is a feature though.
• "Close paraphrasing" is sometimes a bit complicated with technical articles. Non-specialist Wikipedians sometimes overreact when they see long technical phrases repeated, especially when they know they're dealing with students. Emphasizing this too much, especially when the writer is new to the topic, has a tendency to cause "rephrasings" that distort the meaning of the text. I'd suggest recommending that people always read multiple sources fully before trying to write, which naturally tends to reduce the temptation to copy phrases.
• People who are writing about basic research in the life sciences have a tendency to play up the possible clinical correlations/disease associations/medical uses/etc. as a way of making something seemingly boring and abstruse appear important and relevant. Academics teaching science writing tend to pass on this pattern, and students do it with even less awareness of the context. Writing badly about medicine as a student is a really good way to get a lot of complaints on your talk page around here. Instead of just punting to MEDRS, I'd add a sentence of caution about this type of writing. We just want to know what's known about the gene/protein, not what applications the research might have in the future or what fluff someone padded their discussion section with.
• Say something like "use caution when citing the primary literature"; the current definition of "primary source" is the usual wikipedia-idiosyncratic wikibabble. Yeah, a research paper does sorta-kinda report "firsthand experience", but it's not at all a useful way to describe it to students. In practice, articles about genes and proteins almost always cite extensively from the primary literature anyway.
• Maybe have a link to Beall's list, or another resource for identifying poor journals?
• For proteins, we might also want to know if there are notable small molecules that bind to/inhibit/activate/etc. the protein of interest. (Another reason to be cautious about the medical stuff; many of these will be drugs or candidates.)
• Not sure if this is available in other materials, but a sentence about how to find things on Commons might be useful. There are not-beautiful-but-acceptable auto-rendered protein images for a large chunk of the PDB (circa 2009, IIRC) available by searching the PDB ID.
• Suggest putting the infobox code vertically formatted in a collapsed box, so when they copy and paste it's easy to fill out.
• Does Citoid do ISBNs now? It didn't work when I just tried it.
• Tell them about how to give references a name and refer to the same reference multiple times. Maybe even tell them about the evil {{rp}} template. Newbie articles often repeat full citations and it's annoying to clean up.
• Since this is the material specifically about genes and proteins, I suggest pointing to a wikiproject talk page rather than the Teahouse, which is really mostly useful for general advice.

Opabinia regalis (talk) 20:30, 16 December 2015 (UTC)

Thanks so much, Opabinia regalis! Eryk (Wiki Ed) (talk) 18:36, 21 December 2015 (UTC)

Some suggestions to consider

• For the section on: Structuring your genes or proteins article: The HeartBD2K team has already edited 300+ heart-related gene/protein articles in Wikipedia and includes the following sections in all the pages they've done: Structure, Function, Clinical Significance, Interactions. Since 3 of the 4 are already in your list of suggested things to include, may as well include structure. History/Discovery also appear frequently in Wikipedia articles on genes/proteins (eg- CASS4) and could also serve as a potential section.
• For the infoboxes: The protein infobox template you mention is good for articles about protein families like F-box_protein, but articles about a specific gene/protein would be better served by the PBB template which contains both gene and protein info and can be maintained by the Protein Bot box. The info box is kept on a separate template page that is named based on its Entrez gene id, and then referenced in the actual article, so a student might have to generate the template if it doesn't already exist ( list of existing PBB templates. An example of this is CDK2
• Mirroring Opabinia regalis's suggestion, the Gene Wiki or Molecular and Cell Biology Project portals might be a good place to point.

--Gtsulab (talk) 19:04, 17 December 2015 (UTC)

Thanks Gtsulab, this is helpful! Eryk (Wiki Ed) (talk) 18:37, 21 December 2015 (UTC)

---Forgot to mention, it looks great so far! And it looks like someone's already added the history/discovery potential section. Gtsulab (talk) 19:58, 17 December 2015 (UTC)

And just to add to Gtsulab's comment, you can autopopulate a {{GNF_Protein_box}} using the tool at http://biogps.org/GeneWikiGenerator/. Search for the gene of interest. If the wikipedia page already exists, it will show you where that lives (to prevent duplicates that need to be merged later). If the gene page does not yet exist, that tool will guide the user through creating the template and a stub page. There is no reason why individuals should be filling out those templates by hand! And newly added templates will be kept up to date by User:ProteinBoxBot. Good luck with your initiative. I'd also be very interested to know how you intend to "market" this to students and teachers. Through our NIH grant for the "Gene Wiki", we would gladly contribute to this effort! Best, Andrew Su (talk) 16:44, 18 December 2015 (UTC)

This is interesting, thanks for bringing it to my attention, Andrew Su. Eryk (Wiki Ed) (talk) 18:37, 21 December 2015 (UTC)

Specifically discouraging some common undergraduate writing behaviors

Sorry for the late suggestion -- I've been traveling and only just saw this. I think it might be helpful to add a specific caution in Section 1 against editorializing (although I'm going to do it right now). Many undergraduates are trying to unlearn many years of poor writing instruction, and need as many reminders as possible to not use language like "Interestingly," "In my opinion," etc. Also, thanks for creating this handbook! It is a terrific resource and I am planning to use it this spring for an adopt-a-stub project I'm doing with my Advanced Cell Physiology class. -- Katbartlow (talk) 19:26, 2 January 2016 (UTC)

Hi Katbartlow! That's great to know. If you want to learn about our other tools and resources for teaching with Wikipedia (and we can also send you free print copies of this handbook for your students when we get them printed!) drop us an e-mail: contact@wikiedu.org. Eryk (Wiki Ed) (talk) 19:16, 5 January 2016 (UTC)

Writers should write for Lay Persons in Plain English/Plain language

Please quote from and refer writers to any of these:

• Plain English
• Plain language
• the essay: Wikipedia:Use_plain_English

I think it should be #1 in your list (unless it is covered in the material that precedes this special set of pages). If you would like me to add a section to the draft manual, I will.

As an example of what NOT to do, see my comment at [1] about a problem with an article that is way too technical for the lay person. --David Tornheim (talk) 02:20, 14 February 2016 (UTC)