Wikipedia:Featured article candidates/Proteasome

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 review. No further edits should be made to this page.

The article was promoted 20:17, 9 January 2007.

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Proteasome

This A-class article was the Molecular and Cellular Biology collaboration from November. The current text was largely written by me, with helpful edits and image contributions from Splette and Willow. It's had an MCB peer review here and a less active main peer review here. Thanks for your comments and suggestions. Opabinia regalis 06:27, 3 January 2007 (UTC)

• Support. The article is comprehensive, well-referenced, and well-written. The editors have greatly improved the article since my comments on the peer review (where I volunteered to help with examples of prose needing improvement, then got caught up in other things and forgot to come back...sorry), especially the removal of an overuse of the passive voice. Even though some of the body of the article is still over my head, it is a complicated subject matter that I don't think could be simplified much more without turning into a whole dissertation on cellular and molecular biology. Instead, the article's lead section introduces the subject matter and conveys the main points in terms that are easily understandable to readers who want the "CliffsNotes" version of things. Nice job. Neil916 (Talk) 07:27, 3 January 2007 (UTC)
• Support. Congratulations to Opabinia et al. :) for taking a complex but very important topic and making it as accessible as it could probably ever be and an interesting read to boot. Fvasconcellos 14:56, 3 January 2007 (UTC)
• Comments

• The first paragraph in the "Unfolding and translocation" section is muddled. Could these steps be put in chronological order?

Tried to clarify. It's hard to be chronological, since it's not known whether deubiquitination (necessarily) precedes substrate unfolding, and there's still debate over which step(s) require ATP hydrolysis vs just binding. Opabinia regalis 03:14, 4 January 2007 (UTC)

• I don't understand this sentence ''The general mechanism for globular protein unfolding itself is not well characterized; however, it is not entirely independent of the amino acid sequence."

Reworded. The unfolding mechanism of the proteasome has to work on any protein that might need degrading, but some substrates are 'better' than others. Opabinia regalis 03:14, 4 January 2007 (UTC)

• Many of the references lack PMIDs

Fixed. Ugh, that's boring. Opabinia regalis 03:14, 4 January 2007 (UTC)

If any refs still lack PMIDs or formatting, I'll gladly help—I love gnome work. Fvasconcellos 21:10, 4 January 2007 (UTC)

Thanks, I think I got them all - I really should start remembering to put them in in the first place. But if you really like this stuff, then you just might be my new favorite editor...no, we need you to keep making nice SVG chemical structures! Opabinia regalis 05:08, 5 January 2007 (UTC)

Yes, you did. Thank you! :) Don't worry, I'll not get sidetracked from my goal of universal vector graphics domination... I've not even joined the Project so as not to get in over my head! Fvasconcellos 15:58, 5 January 2007 (UTC)

However, overall extremely good. TimVickers 00:44, 4 January 2007 (UTC)

Thanks for the suggestions! (Also, excellent prose fixes.) Opabinia regalis 03:14, 4 January 2007 (UTC)

Support. All my concerns have been addressed. A very good article. TimVickers 04:23, 4 January 2007 (UTC)

• Question: what is the general opinion on putting external links above the references? The references section is over a screenful on my very high-res screen; most people must see a wall of text and become rather disinclined to scroll any further. I made this move once on this article and it was un-done not long after; it is that egregious a violation of the WP:MOS? Opabinia regalis 07:39, 4 January 2007 (UTC)
  • My inclination is that external links should *always* be last, since Wikified content is preferable to external content - we don't want to send readers outside of Wiki easily. If there is something really important in an External link, it's good to try to Wikify it. I try to stick to the exact WP:MOS for that reason - See also first, as that is Wikicontent. SandyGeorgia (Talk) 16:12, 4 January 2007 (UTC)
    • That "makes sense" from an editor's perspective, but in terms of usability, the external links are not very visible buried below screenfuls of references that no one in their right mind wants to read through. (Agree about see also above links, but there's no see alsos here.) Opabinia regalis 01:09, 5 January 2007 (UTC)
      • I guess I don't have a problem with External links being buried, as our priority should be to give Wikified content, with External links being a last resort. Just my two cents, SandyGeorgia (Talk) 01:20, 6 January 2007 (UTC)
        • I suppose the link in the TOC is enough. In this case the Nobel interviews are particularly interesting, IMO. Opabinia regalis 02:08, 6 January 2007 (UTC)
• Comment Does anyone think that the lead-in is maybe too long? I'm not used to seeing four long paragraphs of text before the table of contents. --Cyde Weys 17:34, 4 January 2007 (UTC)

Good point. Lead condensed to three paragraphs. TimVickers 17:46, 4 January 2007 (UTC)

Thanks Tim. I added back the definition of protease, since it's a good bet that some readers won't know the term. Opabinia regalis 01:09, 5 January 2007 (UTC)

• Support. Seems to meet all the criteria. Comments: {{Template:Protein topics}}? Years alone shouldn't be linked per WP:DATE, I found quite a few instances where Nobel Prize in Chemistry years were linked. Remove unnecessary bolding from the "Proteasome inhibitors" section, these words should be linked rather than bolded. From the lead: In eukaryotes, they are located in both the nucleus and the cytoplasm. - Remove both, same for many other instances of the word in the article. ...consists of a total of 19 individual proteins - Remove of a total. Add a see also section and link to the Molecular and Cellular Biology portal from it. ...regions,[34] are degraded - No need in a comma here. The Polish interwiki link should probably come earlier in the interwiki list. "Enzyme" is linked twice in the lead. . ..such as infection, heat shock, or oxidative damage, heat shock proteins are expressed - Move the word or. The quotation marks in the second paragraph of the lead make it sound a bit unencyclopedic. Michaelas10 (Talk) 09:44, 5 January 2007 (UTC)
  • Fixed some of these. I don't know what you mean about the protein topics template; could you explain? I added the portal link, but given that the protein topics template is there and most other related articles are linked in the text, I don't think there's much use in a see also section. I think the quotes in the lead are, if not exactly necessary, useful in introducing the terms that used somewhat metaphorically or as an analogy. Opabinia regalis 01:06, 6 January 2007 (UTC)
• Oppose Journal names should not be abbreviated. Abbreviation might be appropriate for a medical journal, but wikipedia is not one (WP:MOS: Do not assume that your reader is familiar with the acronym or abbreviation you are using.), and the non medical students should be able toe easily trace the journal.Circeus 18:39, 5 January 2007 (UTC)
  • Comment Several recent "scientific" FAs (acute myeloid leukemia, Tourette syndrome and cell nucleus to name a few) passed FAC with abbreviated journal names in References. I assume this would be easy enough to fix, but, as this could have significant ramifications (e.g. stipulate the use of full journal names in WP:MEDMOS?) I would, no offense, like to hear other editors' opinions. Fvasconcellos 19:14, 5 January 2007 (UTC)
    • I've found these abbreviated references to be consistently unhelpful, sometimes *actively* so, and systematically change them to longer names when I happen to copyedit medical articles. If it's the task that you find annoying, I can do it myself, and I would have opposed every single of these medical articles on the same ground. I certainly would favor a change in WP:MEDMOS if that is what is needed for this practice to change (I didn't even know such a style guide existed!). It's just another example of the jargonistic tendencies of the medical community to me. Of course, your request for comments is only relevant as far as those commenting are not familiar with the practice of abbreviating journal names.Circeus 19:46, 5 January 2007 (UTC)
      • As I mentioned above, I have no problem whatsoever in doing "grunt" work—it probably wouldn't take more than a few minutes. What I meant by requesting comments was to make sure no one would object to such a change. By the way, WP:MEDMOS is still a proposed guideline, so feel free to comment on its Talk page if you like. Fvasconcellos 20:10, 5 January 2007 (UTC)
    • You can change this if you want, but I don't think this is much of an issue, since authors and title is all you meed to find any article in PubMed and if it has a PMID it is even simpler. It certainly doesn't hurt though and it might help somebody under some circumstances I can't think of. TimVickers 22:53, 5 January 2007 (UTC)
  • I hope I don't sound reactionary in thinking this is an increase in text clutter with little practical benefit? I'm curous to know where/how you're searching if abbreviated journal names are an impediment. Because the abbreviations are standardized and unique, they're actually at least as good if not better than the full title if you just want to find the journal - a search for "chem phys" will get what you want, but "chemical physics" will pick up Chemical Physics, Journal of Chemical Physics, Chemical Physics Letters, etc. And the linked PMIDs largely obviate the need for searching for the citations anyway. Opabinia regalis 01:06, 6 January 2007 (UTC)
    • I disagree with Circeus here for the simple reason that Wiki provides a PMID template which links to the full information on journal-published research - there's no reason to take up space when full bibliographic info and an abstract is one click away, and when standard abbreviations are used. On the other hand, if the trend takes hold, I'll do the grunt work as well (sigh) - but it will certainly take more than a few minutes - it will take me weeks on everything I've written. If this is a strong objection, Circeus might approach Diberri about changing his script to give the full journal name, because doing them by hand will be a b. SandyGeorgia (Talk) 01:18, 6 January 2007 (UTC)
      • Did some more checking, and I don't believe it's possible for Diberri's script to return full journal names, since even PubMed doesn't cite them without clicking on a separate place - so, if we have to do this, it will all be done manually, and will be a lot of work. I also disagree with the argument about laypersons vs. medical jargon - I'm a layperson - all I need to know is how to find PubMed, or Medline if I want to order the full text of the article. I've never known the full names of the journals, or needed them. When I go to a medical library to request the full text of an article, the abbreviations are standard, and there's never been a problem locating the journal I'm asking for. I really don't consider this a valid objection. SandyGeorgia (Talk) 01:47, 6 January 2007 (UTC)
    • It can only be construed as "an increase in text clutter" by people who a) know that some/many journals have "standard" abbreviations. b) are used to seeing them. 90% of our readership don't. Circeus 13:18, 9 January 2007 (UTC)
  • Comment Circeus' suggested formatting of journal titles does not currently have consensus among editors in the sciences. See also followup here and here. Opabinia regalis 05:46, 9 January 2007 (UTC)

If you want to see the reference, click on the link. It is that simple. TimVickers 16:34, 9 January 2007 (UTC)

• Support with a nitpik - book sources need page numbers, pls separate and plug those in, along with an ISBN for the book. (^ a b c d Lodish, H, Berk A, Matsudaira P, Kaiser CA, Krieger M, Scott MP, Zipursky SL, Darnell J. (2004). Molecular Cell Biology', 5th, New York: WH Freeman.) SandyGeorgia (Talk) 01:25, 6 January 2007 (UTC)
  • ISBN added, thanks. Honestly, while I admire your consistent push for better referencing, requiring page numbers on generic textbook references raises my academic heckles. Citations to standard, uncontroversial textbook material are provided for the reader to have a general reference - I never (well, I try not to) cite a textbook for anything that isn't thoroughly well-established material that could be found in any decent text on the subject (I use the Lodish text because that's the one I have on hand, but another one would do just as well). In cases where there are dozens of citations to many disparate portions of the same text, I can see the utility, but here I don't see the point in repeating the same citation four times just to say "p66", "p68", etc. I added the (very short) page range covering the general introduction to proteolysis and the proteasome. What do you think? Opabinia regalis 02:08, 6 January 2007 (UTC)
    • I think that's a fine solution (which I couldn't have known beforehand, since I didn't know the actual pages - sorry to suggest individual page nos when they turn out to be in such a close bracket - but since I wasn't objecting anyway ... ). SandyGeorgia (Talk) 03:30, 6 January 2007 (UTC)
      • Sorry, that was more of a general rant, mostly written before I looked up the page numbers :) I'll get off the soapbox now. Opabinia regalis 03:34, 6 January 2007 (UTC)
        • No need :-) Best, SandyGeorgia (Talk) 03:37, 6 January 2007 (UTC)
• Comments. Not quite there, but nearly. Let's look at the lead.
  • "as well as" (opening sentence) is a marked form of "and". Why is it unexpected that some bacteria should be in the list?
    • See the evolution section - current thinking is that the proteasome proper evolved from hslVU after the divergence of archaea and bacteria, in the archaeal lineage that led to eukaryogenesis. Then lateral gene transfer occurred in those bacteria that possess a proteasome. So it is surprising that bacteria have a 20S proteasome, especially since they don't express ubiquitin itself.
  • "of about 7–8 amino acids long"—better "of seven to eight amino acids long"; but I'm still unsure of the meaning. Should "long" be "length"? Does an acid have length?
    • The lead reorganization lost the wikilink to amino acid, which should answer that question. Wrote the numbers out, but some hedge is needed, since the products' length varies depending on the organism and state of the cell.
  • "Each ring is in turn composed of seven individual proteins"—Is "in turn" necessary?
  • "are made from seven β subunits"—"of", to avoid the sense that only part of the subunits contributes?
  • "was acknowledged in the awarding of the 2004 Nobel Prize"—Remove "ing".

It's very good, but I think you might ask the League of Copy-editors to do a quick once-over when everything else is fixed. Fresh eyes required, and it won't take them long. Tony 11:28, 6 January 2007 (UTC)

Last three minor things fixed, couple of later wording failures fixed; I'll give the copyeditors a ring. Opabinia regalis 03:59, 7 January 2007 (UTC)

The above discussion is preserved as an archive. Please do not modify it. Subsequent comments should be made on the article's talk page or in Wikipedia talk:Featured article review. No further edits should be made to this page.