Wikipedia:Featured article review/Enzyme/archive1

Enzyme

Enzyme (edit | talk | history | protect | delete | links | watch | logs | views)

• Featured article candidates/Enzyme
• Featured article candidates/Enzyme/Archive 1
• Featured article candidates/Enzyme archive 1
• Featured article candidates/Enzyme inhibitor
• Featured article candidates/Enzyme kinetics

• Featured article review/Enzyme/archive1

Notified: TimVickers, Vital articles/Expanded, Vital articles, WikiProject Molecular and Cellular Biology, WikiProject Genetics

I am nominating this featured article for review because, I think this article doesn't fit the criteria anymore. There's a lot sections or sentence need additional footnotes, "Uncompetitive inhibition", "Non-competitive inhibition", "Mixed inhibition", "Uses of inhibitors", "Control of activity" said there's five main ways that enzyme activity is controlled in the cell, but two sections without any footnotes, consider this article are already been featured for more than 8 years, I think is time to have a good review here.--Jarodalien (talk) 06:50, 13 February 2015 (UTC)

• Also, I had nominated the article translated from this article (version 2007) for FAR at Chinese Wikipedia, and there's a huge objections against to me personally, apparently a lot wikipedians there feel this is such an "important", "vital" article, so doesn't need to strictly follow the criteria, or least should had a "different" criteria, or pointed out there's only 3 footnotes at German version, 29 footnotes at Japanese version, but they're all featured articles... The thing that make this even more pathetic is, there's nobody, I mean nobody done anything to improve it, I could only hope nothing similiar will happen at here.--Jarodalien (talk) 07:17, 13 February 2015 (UTC)

See the WP:FAR instructions; you were supposed to give two weeks notice. Eight days is cutting it close: [1]. I suggest that an email to Tim Vickers would resolve the issues; he is no longer active, but he is still around. I will email him now. SandyGeorgia (Talk) 13:37, 13 February 2015 (UTC)

Tim is notified. @FAR coordinators: coordinators will decide if this FAR should remain listed, since the requisite two to three weeks notification was not given (marginal at eight days). SandyGeorgia (Talk) 14:09, 13 February 2015 (UTC)

The article isn't really up to standards any more. Knotty and technical lead, random little factoids that have crept into the text, and not enough references. Tim Vickers (talk) 15:28, 13 February 2015 (UTC)

Thanks, Tim ... so I recommend this article remain listed, even though FAR instructions were not followed. Good to "see you" again! SandyGeorgia (Talk) 15:32, 13 February 2015 (UTC)

I want to apologize for the inconvenient that I caused, I have no intention to do anything harm the procedural fairness. Mostly I'm only active at Chinese wikipedia, translate articles from here to there, so I'm not quite familiar with the procedure here, and as everybody here could notice that my English are very poorly. The last article I nominated for reivew is Paul Kane, almost one year ago, down there is FAR coordinator Nikkimaria's reply, "If in a week or two there has been no action, feel free to re-raise this FAR." So I thought one week is just fine. Again, I apologize for this, feel free to do anything that fit the procedure.--Jarodalien (talk) 06:30, 17 February 2015 (UTC)

It's like a 2006 reunion in here. I wandered back a few weeks ago and this popped up on my watchlist, so I cleaned out some of the creeping cruft. A couple of quick comments before I forget:

• References: I see at least eight textbooks in the ref list - Stryer 2002, Voet & Voet 2011, Moran 2012, Cornish-Bowden 2004, Blackstock 1989, Price 2000, Skett 2001, and Suzuki 2015. Cornish-Bowden and Suzuki look a little more specialized, but the rest are general biochemistry textbooks cited for very basic general claims. It'd be nice to either consolidate on one offline text (recent edition of Stryer or Voet & Voet presumably) or replace/supplement with links to relevant sections of the Stryer edition supplied by NCBI Bookshelf here.
• Lead image: I hate to object to one of Willow's images, but I don't love this one. The rotation is fast enough to be distracting on a small screen where it dominates the text, and there's not enough depth cuing - am I the only one who gets the spinning dancer effect here? My brain can't seem to make up its mind on which way the protein is spinning. Opabinia regalis (talk) 22:20, 21 February 2015 (UTC)

I agree with O. regalis on the rotating lead image problems (at time of writing, boghog has replaced it with as static version). The fast spinning is a bit distracting (compare to slower version). Perspective in protein ribbon diagrams is often difficult but rendering outlines helps by resolving which loop is in front of which.

I'd love to render a new lead image if others are happy - Are we set on glyoxalase? I think it'd be better to use a structure with bound substrate to show the active site. Any suggestions? T.Shafee(Evo﹠Evo)^talk 23:11, 22 February 2015 (UTC)

Great, thanks! No particular attachment to glyoxalase from me. How about lysozyme? Opabinia regalis (talk) 03:38, 23 February 2015 (UTC)

Lysozyme has the advantage of being a relatively small enzyme that is easy to view in a small figure (see example). I also agree that it would be good to show a bound substrate (or product). PDB: 148L​ might be appropriate (catalytically inactive mutant lysozyme with substrate). I used PyMol to create the graphic and I agree that the default cartoon is harder to visual in a small figure. Using the setting cartoon_fancy_helices, 1 produces a more distinct outline. Boghog (talk) 08:07, 23 February 2015 (UTC)

Good suggestion on consolidating the book citations. I will work on this (using the online Stryer NCBI Bookshelf as much as possible) as I find time. Boghog (talk) 09:40, 23 February 2015 (UTC)

That looks like a good choice for the lysozyme structure. Thanks for working on Stryer - I think it's a good idea to have an accessible online reference for the kind of basic information these textbook cites are mostly attached to. Opabinia regalis (talk) 06:21, 24 February 2015 (UTC)

There are incomplete citations everywhere, and some of the new citations breach WP:CITEVAR (Tim used the Diberri format). SandyGeorgia (Talk) 14:22, 23 February 2015 (UTC)

Consistent journal citations are now used throughout (note: {{vcite2 journal}} templated citations render identically to Diberri format: Vancouver system for authors and CS1 style for everything else). Citations with PMIDs should be complete. A few journal citations that are not stored in PubMed as well as book citations may be incomplete. I will try to locate and add the missing citation data. Boghog (talk) 15:38, 23 February 2015 (UTC)

Thanks so much! What I'm seeing now is numerous websites that have no publisher listed, and no accessdate. If no one else gets to those, I can eventually do them. The journals are consistent now, but it's the websites that have incomplete citation info. SandyGeorgia (Talk) 20:14, 23 February 2015 (UTC)

Oops, looks like I cargo-culted the {{vcite2 journal}} template without fixing the author parameters. Thanks for fixing that and the web citations, Boghog. (BTW, what tool are you using to fix the template parameters and retrieve the DOIs? The auto-PMID-filler doesn't seem to capture DOIs.) Opabinia regalis (talk) 06:21, 24 February 2015 (UTC)

And thank you Opabinia regalis for the extensive work that you have put in getting this article back to FA standard. In answer to your question, I am using Wikipedia template filling which is essentially Diberri's tool with one minor change ({{cite journal|author}} → {{vcite2 journal|vauthors}}). This tool obtains its data from PubMed. PubMed doesn't always have the DOIs either, so sometimes I manually fill these in. Boghog (talk) 06:49, 25 February 2015 (UTC)

Thanks! So I guess you have a script that runs that tool for all the malformatted PMID-containing templates in an article? Either that or you have a hell of a lot more patience than I do ;) Opabinia regalis (talk) 07:44, 25 February 2015 (UTC)

Citations look good now (thanks, everyone!), except that I'm not sure that introducing inline page numbers isn't a change in style that introduces inconsistency-- not fussed about it, but not thrilled with it either.

On the other hand, there are MOS issues everywhere. Image captions are overly long to the point that the text in them should be cited, image layout is creating problems with text, there is incorrect use of italics and bolding throughout (I got some of it, but by no means all), etc ... a thorough MOS review will be needed once text is settled. And this is a glaring WP:MSH issue:

• 5 Cofactors and coenzymes
  • 5.1 Cofactors
  • 5.2 Coenzymes

This is another MSH issue:

• 8 Inhibition
  • 8.1 Types of inhibition
  • 8.2 Functions of inhibitors

The text in the lead is bouncing all over the place, with no clear flow (the lead in the featured version did not have that problem ... returning to some of Tim's original wording might help).

Repetitive prose: half (three out of six) of the paragraphs in "Etymology and history" begin with "In <date>" ... prose needs to be varied.

Do we really need that bolding in the chart in "Industrial applications"?

Further reading and External links need some serious pruning. SandyGeorgia (Talk) 14:43, 24 February 2015 (UTC)

Thanks for the good suggestions Sandy. I nuked the external links section since it didn't seem to contain any links of great value. Concerning inline page numbers, I am not sure what the best solution is. Different pages of the same textbook are being cited to support different statements and it is important to specify the specific page that is being cited. The options are (1) repeat the full citation, changing only the page number, (2) use {{rp}} as is done now, or (3) switch to {{sfn}} templates. Option #1 is redundant, #2 is the simplest, but is a bit messy looking and as you say inconsistent, and #3 is more complicated and harder to maintain. IMHO, as long as {{rp}} is not used too often, solution #2 is the most practical. Thoughts? Boghog (talk) 07:14, 25 February 2015 (UTC)

• Lead: back to something very similar to Tim's version.
• History section: tweaked prose a little.
• External links removed (thanks Boghog!) and further reading trimmed.
• Italics/bold sorted out, I think.

• Page numbers: this problem gets a 'meh' from me. I think it's a case of false precision to be pointing at specific pages in specific editions of specific printed textbooks for basic material that can be found in most college-level textbooks on the subject, not to mention that the internet is full of mostly futile attempts to explain enzyme kinetics to premeds. These must all be in the same chapter/section of the book; maybe just cite "chapter 3" or whatever it is.

• Industrial applications table: if this hadn't been in the featured version I would've suggested moving it to its own page. It's ugly and bulky. I think the bold text does help highlight the applications in the table, since the rows are all different sizes and they don't all have a picture.

• Images: I'm a little lost on the image-crowding issue you mentioned in your edit summaries, Sandy. I'm looking at it on a very small screen (macbook air) and I don't see problems. I put File:Competitive_inhibition.svg back to the larger size because it's unreadable as a thumbnail (but maybe a simpler image would be better). File:Methotrexate_and_folic_acid_compared.png should probably be replaced in any case with a 2D SVG version with the compounds stacked rather than mirrored; much easier to see the differences that way. Opabinia regalis (talk) 07:44, 25 February 2015 (UTC)

I'm not fussed about the page numbers, and agree with Boghog's analysis of the options (prefer those to dreaded sfn). On the images, I can live with it if others disagree-- I will look at the article on other computers and browsers once we're "almost there". Thanks everyone for rescuing Tim's work !!!

Can someone who speaks biology address the MSH issues I mentioned above, by perhaps renaming the overall sections so that the sub-sections aren't repeats? SandyGeorgia (Talk) 13:35, 25 February 2015 (UTC)

Forgot about the headers. Fixed the cofactors (turns out the two subarticles got merged at some point anyway). Call me unimaginative but I'm not coming up with a good solution for inhibition; making the subheads 'types' and 'functions' is unsatisfying. Enzyme inhibitor has a lot of TOC repetition too, for the same reason. Opabinia regalis (talk) 06:33, 26 February 2015 (UTC)

I'm planning on going through the images this weekend and updating several of them to be at least in a consistent style, and better labelled. Additionally, I agree that the table is horribly formatted - can we reformat it somewhat (e.g. WP:MST) with either shading, or altering the orientation of the cells? Ps, sorry if I'm indenting wrong, I struggle with wikimarkup formatting in longer conversation threads! T.Shafee(Evo﹠Evo)^talk 11:43, 25 February 2015 (UTC)

Removing the images from the chart would be a good step. SandyGeorgia (Talk) 16:55, 25 February 2015 (UTC)

That's great on the images, thanks! I did think those black backgrounds were looking a little dated.

I tried removing the images from the table and tweaking the cell alignment; it looks a little less sloppy now. Also trimmed some cruft and fixed some links. The idea of decorative images here isn't bad, but they're hard to format and even if we make them all consistent sizes, cruft will creep back in. Opabinia regalis (talk) 06:33, 26 February 2015 (UTC)

Jarodalien, if you have any remaining concerns about the article, could you please list them? SandyGeorgia (Talk) 02:50, 28 February 2015 (UTC)

Based from the version I can see now, feels:

1. lead section, too many paragraph;
2. five types of inhibition, four main ways to control enzyme activity, their names should not be boldface;
3. More footnotes: "Structure" (second & third paragraph), "Thermodynamics", "Involvement in disease", "Naming conventions", "Kinetics" (second paragraph), "Functions of inhibitors" (first paragraph, and "A common example of an irreversible inhibitor that is used as a drug is aspirin, which inhibits the COX-1 and COX-2 enzymes that produce the inflammation messenger prostaglandin, thus suppressing pain and inflammation."), examples at "Industrial applications" should all have footnotes, just feel featured articles should not require readers go to another article try to locate a source.

That's all, thanks.--Jarodalien (talk) 06:57, 28 February 2015 (UTC)

Thanks, Jarodalien. From this version reviewed, I see the issues on 1 and 3. On number 2 (the issue of bold in the lists), at the time this article was written, WP:MOSBOLD called for bolding of items in a bullet-point list. It no longer does, as far as I can tell. I don't know when that change was made, but it does appear that what was once correct per MOS is no longer called for, and that bolding should be removed. Perhaps Maralia has kept up with that MOS issue, or one of the other FAC or FAR coordinators ... @FAC coordinators: , @FAR coordinators: ... and can inform us on current guideline. SandyGeorgia (Talk) 14:23, 28 February 2015 (UTC)

Boghog, per WP:ITALICS, I'm not sure that changing the bolded list to italics is correct;[2] see my explanation above for why the list was bolded (it was called for in older versions of MOS). And to whomever has dealt with this, thank you !!!! Overuse of however; (I thought I had checked Tim's version for too much however, henceforth, furthermore, and subsequently ... ) SandyGeorgia (Talk) 14:29, 28 February 2015 (UTC)

SandyGeorgia I don't have any really strong feels about this and I will not oppose changing it back if that is the consensus. I wanted to note however that the guidelines on the use of italics and bolding in these situations is not so clear. These bolded/italicized phrases beginning each bullet point are functionally equivalent to section headings. Per MOS:BOLD, one use of bolding is [t]o identify terms ... at the beginning of a section of an article, which are the targets of redirects to the article or section. However in this case, there are already separate articles devoted to each these terms. According to WP:HEAD, Headings should normally not contain links, especially where only part of a heading is linked. Also IMHO, the look of bolded wiki links is somewhat jarring. One possible solution is to move the links out of the bolded phrases entirely. Finally per MOS:EMPHASIS, Italics may be used to draw attention to an important word or phrase within a sentence. Boghog (talk) 15:20, 28 February 2015 (UTC)

SandyGeorgia These bulleted lists can be considered an embedded lists and in particular definition lists. I have formatted the list using H:DL markup (<semicolon> "term" <colon> "definition"). Does this look any better? Boghog (talk) 18:22, 28 February 2015 (UTC)

I now also moved the wiki links from the bolded term headings to the prose in this edit. Does this look OK? Boghog (talk) 19:48, 28 February 2015 (UTC)

Much better, thanks Boghog! SandyGeorgia (Talk) 22:48, 28 February 2015 (UTC)

• Two weeks in, and the article is still a long way from standard-- mostly uncited text at this point. SandyGeorgia (Talk) 03:20, 1 March 2015 (UTC)

Long discussion with subheads moved to the talk page in this edit per comments below. Opabinia regalis (talk) 06:41, 2 March 2015 (UTC)

Um, someone made a wreck of the Table of Contents at WP:FAR by adding sub-heads here ... please review FAR instructions ("... and should avoid segmenting review pages ..."), and we can use article talk for lengthy commentary (please do). SandyGeorgia (Talk) 14:21, 1 March 2015 (UTC)

Sorry, I forgot that this page is transcluded into WP:FAR. The length of this review is getting pretty long and is become difficult to navigate and edit. Perhaps it would be best to move the last two sections of this review to the enzyme talk page. Boghog (talk) 19:30, 1 March 2015 (UTC)

Done, see above. Opabinia regalis (talk) 06:41, 2 March 2015 (UTC)

Are there any other outstanding source concerns here? I am out of time this week for writing that isn't work, but digging up niggling references is doable. Opabinia regalis (talk) 07:27, 3 March 2015 (UTC)

Lots of good work, but uncited text still. Jarodalien, perhaps you could add cn tags on any text that you believe still needs citation? SandyGeorgia (Talk) 14:47, 3 March 2015 (UTC)

@Jarodalien:. SandyGeorgia (Talk) 14:58, 4 March 2015 (UTC)

I already did that, looks fine to me now. I just hope someone else could review those sources.--Jarodalien (talk) 15:13, 4 March 2015 (UTC)

Jarodalien, what sources are you concerned about? All of the editors working on this article are experienced Wikipedians ... SandyGeorgia (Talk) 15:27, 4 March 2015 (UTC)

I'm fine with this article now. I didn't mean to question any sources, only seens each FAC will had a source review (and image review) by another editor. So how's this work next, should I withdraw the nomination?--Jarodalien (talk) 00:54, 5 March 2015 (UTC)

If you are concerned about images, we can ask Nikkimaria to have a look. If all of your concerns as the nominator are satisfied, you can suggest the FAR be closed now (without moving to the FARC phase), or you can suggest (with reasons why) that it be moved to the FARC phase for others to opine whether the FA should be delisted or kept. Regards, SandyGeorgia (Talk) 03:19, 5 March 2015 (UTC)

All my concern has been addressed, I suggest close this FAR if no one else rise anything other issue within one week, thanks for the good work and patient from everybody.--Jarodalien (talk) 08:15, 5 March 2015 (UTC)

I found a good amount of uncited sentences and paragraphs in the article. I tagged them with the citation needed tag. This review should probably not end until after these missing citations are added. PointsofNoReturn (talk) 04:12, 6 March 2015 (UTC)

Our remarkably patient Boghog has provided additional citations. PointsofNoReturn, it appears that you simply tagged the last sentence of every paragraph if it did not already end in a citation, even for trivial statements and near-tautologies (e.g. penicillin and aspirin are common drugs; the enzyme-product complex releases products; quantities of enzymes can be changed by degrading them). Thanks for your review, but it would be more helpful in future reviews to be a bit more discriminate. Opabinia regalis (talk) 09:22, 6 March 2015 (UTC)

• Ping WT:MED. SandyGeorgia (Talk) 15:15, 6 March 2015 (UTC)

As this looks to be in keep territory and there are editors active in maintaining the article, I am going to close this. If you feel the close was premature, please do raise any issues on the article talk page or improve the article yourself! DrKiernan (talk) 15:17, 7 March 2015 (UTC)

• Closing note: This removal candidate has been kept, but there may be a delay in bot processing of the close. Please leave the {{featured article review}} template in place on the talk page until the bot goes through. DrKiernan (talk) 15:17, 7 March 2015 (UTC)