Wikipedia:Featured article candidates/Major urinary proteins/archive1

The following is an archived discussion of a featured article nomination. Please do not modify it. Subsequent comments should be made on the article's talk page or in Wikipedia talk:Featured article candidates. No further edits should be made to this page.

The article was promoted by SandyGeorgia 22:23, 19 June 2010 [1].

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Major urinary proteins

Major urinary proteins (edit | talk | history | protect | delete | links | watch | logs | views)

• Featured article candidates/Major urinary proteins/archive1

Nominator(s): Rockpocket 13:41, 10 June 2010 (UTC)

I am nominating this for featured article because FAs on proteins are extremely under-represented (in fact I think Exosome complex may be the only other one). I am the sole significant contributor, and wrote and researched the article from scratch for this purpose. As far as I am aware it meets all current FA criteria and I think (hope!) that it is sufficiently well written to be accessible to a layperson. I look forward to your constructive criticism. Thanks for your consideration. Rockpocket 13:41, 10 June 2010 (UTC)

• No dab links or broken external links. Esuzu (talk • contribs) 18:18, 10 June 2010 (UTC)

Sources: All sources look good, immaculately presented. Brianboulton (talk) 21:15, 10 June 2010 (UTC)

Is there a reason why the publication date for reference 17 is not in parentheses, while the dates for all the other references are in parentheses? Generally it is best to have the sources be as consistent as possible. Other than that, article looks great. Stonemason89 (talk) 22:43, 10 June 2010 (UTC)

Its a consequence of a quick of the template. If the news citation has an author, then the date placed in parentheses before the title. If there is no author, then the date gets placed after the title, but without parentheses. Unfortunately, BBC News does not give authors on their website. In an attempt to maintain consistency, I have now added parentheses manually. Rockpocket 08:47, 11 June 2010 (UTC)

Comment Support: This article is an interesting read and seems quite comprehensive. As you note, articles on proteins (and, unfortunately in the past year or two, molecular and cellular biology generally) rarely appear at FAC. Kudos for bringing this article so far! A few comments:

• Per guideline, the number of references in the lead should be pared down to few or none.
• The first paragraph of the lead is slightly too technical -- I can imagine the layperson quickly bouncing because of intimidating terms and dense jargony phrases. An appositive near gene cluster would help. The last sentence of the lead should be shifted down a gear for the layperson.
• More broadly, I feel like the article would be a bit too laborious for the layperson to read through. Finding the best balance between thoroughness and accessibility is difficult, but after reading this article I think greater weight should be given to accessibility. Although I don't think we necessarily need to aim for a 9th-grade Flesch-Kincaid reading level on article with this granular specificity, I do think that technically dense sentences should be filled in more liberally with appositives and other ways of diluting jargon. Here are some specific examples that could be addressed:
  • "Since they were named, the proteins have been found to be differentially expressed in other exocrine tissues, including lachrimal, parotid, submaxillary, sublingual, preputial and mammary glands."
  • "these duplications occurred very recently in mouse evolution and may still be occurring through recombination of endogenous retrovirus elements."
  • "Rat Mups also bind limonene-1,2-epoxide, resulting in a hyaline droplet nephropathy that progresses to renal cancer."
• References should appear only after punctuation.
• The article mentions there are several dozen known major urinary proteins. Scanning through, I see only one, Fel d 1, with an article on it. Are none of the others notable enough to warrant their own articles?
• I'm of the opinion that captions of images of proteins should contain some identifier of the protein, e.g. its PDB or HUGO (or in this case, perhaps MGI?) ID.
• Captions that are complete sentences should end with periods; those which aren't shouldn't.
• Should "The Mups in C57BL/6J mouse urine by gel electrophoresis" read something more like "The Mups in C57BL/6J mouse urine analyzed by gel electrophoresis"?

I'll add any additional concerns as they come to me. Emw (talk) 03:40, 11 June 2010 (UTC)

I think these are all very helpful criticisms, thank you. I'll do my best to address them throughout the day. Rockpocket 07:33, 11 June 2010 (UTC)

I hope I have been able to address these concerns:

• I have removed all the references from the lead and ensured all content is sourced (and linked) at the appropriate place in the main text.
• I have tried to systematically replace all technical language in the lead with simpler terms. Where technical terms are still present, I have employed appositives. I agree about the final sentence - I've softened and simplified it considerably.
• I have gone through the article section by section and tried to remove unnecessary jargon. I feel the main text should be a little more detailed, which makes some technical terms difficult to avoid, but I can see it was certainly excessive before (particularly in the examples you highlighted).
• All references should now be after punctuation only.
• I'd given this a bit of thought myself. My original intention was to write content on each Mup individually. However, when reasearching it it became obvious this was going to be very challenging. The main reason is because until very recently the genetic basis of Mup coding was not known. Therefore, while there is a lot of literature on Mups stretching back ~50 years, its difficult to pin down which Mup the authors are referring to (indeed, for a long time the singlular "MUP" was used to refer to any and all of them). It is possible now to go back and deduce which is which based on sequence analysis but that involves a significant amount of WP:OR, and even then it isn't always clear because they are so similar to each other (in some cases they differ only at a single base pair!). Also, for the same reason, the nomeclature of Mups is all over the place in the literature and database. MUP1, Mup1 and MUPI all actually refer to different proteins. You'll notice, if you read the article carefully, I've tried to keep anway from naming rodent Mups as much as possible. Its for these reasons that I decided the best way to document them is to do so collectively. As more literature becomes available and one nomenclature becomes standard, I think it is possible that individual Mups will be sufficiently notable to have their own articles (Darcin seems the most obvious candidate, but at the moment it is unclear whether that name will be accepted by the community). The exception to this is perhaps Fel d 4 - mainly because it has a fair amount of information about its allergenic properties available, and it is a single Mup in that species. I've currently redirected that to this article, but when I have a spare moment, I'll write a specific article and make sure it is appropriately linked.
• I've included PDB identifiers. MGI would be better, ideally, but that would require significant amount of OR to map the structure (which was resolved before the genes were identified) to the correct gene.
• I think I have resolved the punctuation of captions, let me know if I've misunderstood your concern.
• Yes, I've replaced that caption with your suggestion.

Thanks for reading it so thoroughly, Emw. Your suggestions have been most helpful. Rockpocket 12:45, 11 June 2010 (UTC)

Your fixes have addressed my concerns. I think the article is now much more accessible, yet still deep enough in coverage for someone with background in molecular biology to come away informed. Very well done, and please keep up the great work! Emw (talk) 16:34, 12 June 2010 (UTC)

• Support—I believe this article satisfies the FA criteria. All but one of my concerns have been addressed, and I'm sure that will be rectified at some point.

  Comment—It is a good article and I enjoyed the read, but I think it has a few problems. I've tried to correct them where I could, but several remain:

  • The lead does not summarize the Discovery section.
  • The article left me with a pair of unanswered questions that I would like it to explain, if possible:
    • Why have only humans (among plancental mammals) evolved not to encode for these proteins? Is it because of our poor olfactory sense?
    • Why have these proteins become allergens to humans? It doesn't seem like a useful trait.
  • There is some unnecessary vagueness:
    • "Humans in good health excrete urine that is largely free of protein, therefore physicians and scientists have long been interested in proteinuria, the excess of protein in human urine, as an indicator of kidney disease." How long has this been known and studied?
    • "Soon after their discovery in rodents..." How soon? Should we go by the date on the earliest cited paper: 1979?
    • The last section begins, "While the detection of excreted Mups by other individuals...". The remainder of the section talks about mice, but those have already been discussed. What is meant by "other individuals"?
  • Please fix the reference genome red link so the reader has a place to look it up.
  • Please wikilink the term "sequential duplications" to an explanation.
  • There are a pair of grammar issues in the sentences that begin "One unusual Mup..." and "Other Mups were tested...". Please address them.
  • Minor point of style: the article switches between spaced em-dashes and spaced en-dashes. This is covered in the MoS. Please make them consistent. Em-dashes should not be spaced, per the MoS.

  Thank you.—RJH (talk) 17:08, 13 June 2010 (UTC)

Hello RJHall. Thanks for your edits and comments. I hope I have addressed them to your satisfaction

• I have now added a sentence to the lead about their discovery.
• Yes, those are interesting questions. Unfortunately, in the case of your first question, the answer is simply not known. The human pseudogene was only characterized relatively recently and since then its function (or lack thereof) has not even been speculated on in the literature. So it is difficult to add hypotheses to the article without engaging in OR. From my own research, I would propose that it is likely that they were lost in humans because we lack a functioning organ to detect them. It appears that the loss of lots of pheromone detection genes in humans co-incided with the evolution of trichomatic color vision. If that is the case, it makes one wonder what the endogenous function is. I'm beginning to think there is no endogenous function and the whole point of them is that they serve as signals. With regards to your second question, I have cited the one published paper that speculates on this. The suggestion is that molecular mimicry is at play.

  That works for me, thank you.—RJH (talk)

• I have addressed the first two with specific dates. The latter was ambiguous and I've clarified what I meant.
• I have written a stub on reference genomes, I'll expand that when I have some time.
• I have linked it to a section on evolution by duplication.
• Grammar fixed, hopefully.
• Amazing. I've been editing WP for almost five years and only now do I learn that there are different dashes!? Thanks for letting me know, I've replaced them all with em-dashes, no space.

  Unfortunately the {{mdash}} template does introduce spaces. You can see the nbsp and the extra space in the template source. The em-dash policy is given at MOS:EMDASH, if you would like to check it.

I should have paid more attention to the template. As far as I can tell, the nbsp seems to leave a trailing space too. I think I have resolved it by using the em-dash in the symbol bar, sans spaces, but I could be wrong. Rockpocket 10:08, 15 June 2010 (UTC)

Rockpocket 15:28, 14 June 2010 (UTC)

Thank you for addressing my concerns.—RJH (talk) 22:46, 14 June 2010 (UTC)

• Support - A well-written, comprehensive article on a specialized topic. Obviously very well-researched. An excellent article. ceranthor 02:20, 15 June 2010 (UTC)
• Comment: The first paragraph of the lead states: "Mup proteins form a characteristic baseball glove shape". However I didn't see a reference in the article for this description of the shape. Axl ¤ [Talk] 18:13, 15 June 2010 (UTC)

Hello. Yes, you are correct. I have a source that describes a lipocalin as "baseball-glove" shaped (thought not a Mup specifically), but most simply use the term "glove" (probably because they are not North American!) I'll use the less specific term in the lead, and add the correct source in the text, by "Consequently, they form a characteristic glove shape, encompassing a cup-like pocket that binds small organic chemicals with high affinity" Rockpocket 09:45, 16 June 2010 (UTC)

Thanks for clarifying that. Axl ¤ [Talk] 10:43, 16 June 2010 (UTC)

• Support. This article is excellent. Rockpocket has done particularly well to make the highly technical information as accessible as possible. Axl ¤ [Talk] 10:44, 16 June 2010 (UTC)
• Support - Engaging, comprehensive, beautifully written and illustrated, the article satisfies all the criteria IMHO. Graham Colm (talk) 17:00, 16 June 2010 (UTC)

• Images; have images been reviewed? SandyGeorgia (Talk) 18:54, 19 June 2010 (UTC)

• Image review - Sandy, all the scientific images have appropriate licences and attribution. The ones from Genome Biology are free to use under Creative Commons (Attribution 2.0 Generic). The old (1895) cartoon is in the public domain because first publication occurred before January 1, 1923. Graham Colm (talk) 19:10, 19 June 2010 (UTC)
  • Thanks, Graham! SandyGeorgia (Talk) 19:36, 19 June 2010 (UTC)

The above discussion is preserved as an archive. Please do not modify it. No further edits should be made to this page.