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Wikipedia:Peer review/LSm/archive1

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LSm edit

This is my first Wikipedia article, so any reasonable comment is welcome. My vision is that various protein families/folds would have a Wikipedia article, and I used Myosin, Histone and Globin fold as examples. My intention was to produce a LSm protein review article within the Wikipedia world, with value to the full spectrum of readers from the lay person to the professional molecular biologist, and everyone in between. Bob Plaag 20:25, 27 January 2007 (UTC)[reply]

Thanks. I took a quick look, and will review each suggestion over the next couple of days, as time permits. Bob Plaag 20:45, 28 January 2007 (UTC)[reply]
There is a lot to review in the automated review. My plan is to cut and paste these automated comments into my talk page, and indicate my action for each one, creating a documentation trail. Bob Plaag 03:38, 9 February 2007 (UTC)[reply]

Here are the comments that APR generated for me. Bob Plaag 04:01, 9 February 2007 (UTC)[reply]

LSm edit

The following suggestions were generated by a semi-automatic javascript program, and might not be applicable for the article in question.

  • Please expand the lead to conform with guidelines at Wikipedia:Lead. The article should have an appropriate number of paragraphs as is shown on WP:LEAD, and should adequately summarize the article.[?]
EDIT: The lead was expanded to three paragraphs to conform with Wikipedia guidelines. The first paragraph is a basic introduction, the second briefly describes the origin and history, and the third paragraph is a brief description of structure and function, roughly paralleling the remainder of the article. Bob Plaag 03:20, 15 February 2007 (UTC)[reply]
EDIT: I added a short 4th paragraph for a sentence that didn't really fit into the previous three Lead paragraphs. Bob Plaag 20:12, 16 February 2007 (UTC)[reply]
I searched for an applicable infobox, and concluded that there are none. Bob Plaag 01:07, 14 February 2007 (UTC)[reply]
  • Per Wikipedia:Manual of Style (numbers), there should be a non-breaking space - &nbsp; between a number and the unit of measurement. For example, instead of 2nm, use 2 nm, which when you are editing the page, should look like: 2&nbsp;nm.[?]
EDIT: Included non-breaking space between number and its unit, to comply with Wikipedia style. Bob Plaag 04:07, 10 February 2007 (UTC)[reply]
  • Per Wikipedia:Manual of Style (numbers), please spell out source units of measurements in text; for example, the Moon is 380,000 kilometres (240,000 mi) from Earth.[?] Specifically, an example is 7 nm.
EDIT: Changed unit measurement to comply with Wikipedia style. Bob Plaag 04:07, 10 February 2007 (UTC)[reply]
  • Per Wikipedia:Manual of Style (headings), headings generally do not start with articles ('the', 'a(n)'). For example, if there was a section called ==The Biography==, it should be changed to ==Biography==.[?]
EDIT: Removed "The" from lead of 3 headings. Also headings that were worded as a sentences were converted to noun phrases (such as The Smith antigen is discovered to Discovery of the Smith antigen) to comply with Wikipedia Manual of Style. Bob Plaag 04:07, 10 February 2007 (UTC)[reply]
EDIT: Removed links from headings. Each instance was already linked in the paragraph associated with the heading. Bob Plaag 04:07, 10 February 2007 (UTC)[reply]
EDIT: I also moved a reference from a heading "Biogenesis of snRNPs" into body text. I had to create a one-sentence paragraph just below the section title in order for this to make sense. Bob Plaag 20:12, 16 February 2007 (UTC)[reply]
EDIT: I removed "LSm" from several headings, and I agree that this was an improvement.
  • However, I kept "LSm" in several headings. Specifically: "Discovery of the LSm fold", LSm is an integral part of the expression. I tried replacing it, but other constructions were longer, awkward, and less clear, such as "Discovery of shared structure" or "Discovery of a new protein structure".
  • Within "Functions", LSm is an integral part of specific protein names, such as "Lsm2-8 ring", and I could not think of an alternative.
  • Within "Evolution and phylogeny" the titles "Homomeric LSm rings in bacteria and archaea" and "Heteromeric LSm rings in eukaryotes" also seemed essential. "Homomeric rings in bacteria and archaea" seemed to be too non-specific, and simply "Bacteria and archaea" definitely did not capture the essential difference of the LSm rings in these groups. Bob Plaag 20:12, 16 February 2007 (UTC)[reply]
EDIT Checked headings. Capitalized words were proper nouns ("Smith"), abbreviations of proper nouns ("Sm"), or acronyms that are generally capitalized ("RNA", not rna, "SMN", "LSm", "snRNPs") in the professional literature. "Spinal Muscular Atrophy" and "Gemin7" appear in the literature more often than "Spinal muscular atrophy" and "gemin7", but changed to "Spinal muscular atrophy" as used in its Wikipedia article. "Archaea", "Bacteria", "Eukaryotes" treated as common nouns. "External Links" changed to "External links". Bob Plaag 04:07, 10 February 2007 (UTC)[reply]
  • Per WP:WIAFA, this article's table of contents (ToC) may be too long- consider shrinking it down by merging short sections or using a proper system of daughter pages as per Wikipedia:Summary style.[?]
  • I looked over the Table of Contents with a critical eye. There are 7 top level sections, including "References" and "Notes". The only one that stood out was "Biogenesis of snRNPs". This could arguably be transfered to the Wikipedia article snRNP which has a short paragraph on snRNP Biogenesis. Arguing against this move is that this section in LSm is more focused on the assembly of the Sm proteins onto the small RNA, rather than on the overall process of snRNP biogenesis. Also, much of the early research about LSm (specifically the Sm) proteins centered on how this assembly took place. So I decided to keep this section within this article. However, if another Wikipedian has a very strong opinion to cut this section out and paste it into the snRNP article, I will not start a edit/reversion war. Bob Plaag 20:12, 16 February 2007 (UTC)[reply]
  • Then there is the matter of the second level headings. I feel that each paragraph should have a central theme, which becomes its heading (except for the paragraphs within the Lead). Scientific articles tend to be rather dense, so I feel that giving a heading to every paragraph greatly assists the reader in understanding the purpose of a paragraph, and why it is there. Possibly, the TOC could be shortened by keeping paragraph headings with the body, but keeping them out of the TOC. Maybe someone else could voice their opinion on this. Bob Plaag 20:12, 16 February 2007 (UTC)[reply]
  • GB had a comment on the value of a table. This could effectively replace the paragraph-level headings in the "Functions" section. And maybe a table and keeping these heading in the TOC would be best. Does anyone want to voice an opinion on this? Please see my response to his request for a table. Bob Plaag 20:12, 16 February 2007 (UTC)[reply]
  • There are a few occurrences of weasel words in this article- please observe WP:AWT. Certain phrases should specify exactly who supports, considers, believes, etc., such a view.
    • it has been
This occurs under Biogenesis of snRNPs, and properly indicates that this is a hypothesis. This hypothesis is made in the reference [24] for this paragraph. Bob Plaag 04:56, 21 February 2007 (UTC)[reply]
    • apparently
I apparently overuse this word. I deleted all uses of it, and the text reads better for it. Bob Plaag 04:56, 21 February 2007 (UTC)[reply]
    • might be weasel words, and should be provided with proper citations (if they already do, or are not weasel terms, please strike this comment).[?]
  • As done in WP:FOOTNOTE, footnotes usually are located right after a punctuation mark (as recommended by the CMS, but not mandatory), such that there is no space in between. For example, the sun is larger than the moon [2]. is usually written as the sun is larger than the moon.[2][?]
EDIT Moved reference 4 to end of sentence. Bob Plaag 20:12, 16 February 2007 (UTC)[reply]

You may wish to browse through User:AndyZ/Suggestions for further ideas. Thanks, APR t 15:46, 28 January 2007 (UTC)[reply]

END OF AUTOMATED REVIEW COMMENTS BY APR. Bob Plaag 04:01, 9 February 2007 (UTC)[reply]

  • I would like to read a definition of LSm in the opening paragraph. All I see is that it is historically connected to Sm. Is the definition a protein that binds to U6? Should SmD be in bold?
Thank you for this suggestion about including a definition of LSm in the opening paragraph. I have been busy recently, but will critically review my work with your comment in mind. Like most illogical things, the reason behind Sm and LSm are historical. Basically, the Sm proteins were the first to be discovered. Later, similar proteins were discovered that were 'like Sm' proteins, abbreviated LSm. Sm proteins are a subset of the LSm proteins. Obviously, I need to edit this for clarity. The connection to U6 is just that the first LSm proteins identified (that weren't Sm proteins) bind to U6. Later, other LSm proteins were discovered that have nothing to do with U6. The basic definition of a LSm protein is the 'protein fold', as described under Characteristics. I did not bold SmD, because SmD is not a single protein, but a mixture of 3 Sm proteins that were not initially distinguished. I had hoped that the second sentence following would clarify this. I'll look at this again. Bob Plaag 03:38, 9 February 2007 (UTC)[reply]
I expanded the lead to three paragraphs as suggested by Wikipedia guidelines. The last sentence in the first paragraph is essentially the definition as LSm proteins are defined by structural similarity to each other. Giving a detailed description of this structure occurs later in the article. Does the following sentence suffice as a definition? "All LSm proteins have similar three dimensional structures and assemble into rings of six or seven individual LSm protein molecules." Bob Plaag 03:20, 15 February 2007 (UTC)[reply]
I did some more thinking, and changed the above sentence into an explicit definition (among other wordsmithing of the Lead). "LSm proteins are defined by a characteristic three dimensional structure and their assembly into rings of six or seven individual LSm protein molecules." Thanks for forcing me to put a lot more effort into the Lead, which is after all, the most important part of a Wikipedia article. Bob Plaag 05:44, 16 February 2007 (UTC)[reply]

The The LSm fold (tertiary structure) section seems to be talking about secondary structure - but I am no expert in this area! I find it hard to follow this paragraph. -- The article looks quite attractive to me with good explanations of the history, fabrication, and use of the proteins. GB 10:57, 29 January 2007 (UTC)[reply]

Thanks for pointing this out. I will critically review this paragraph, and try to improve the clarity. I guess that in the tradeoff between brevity and clarity, I was too brief. Briefly, the secondary structure is simply a five (or eight) strand beta sheet. The tertiary structure concerns how this beta sheet is folded into a 3-dimensional structure. I agree that the distinction is a bit subtle. Bob Plaag 03:38, 9 February 2007 (UTC)[reply]
I have started a major edit of the LSm/Characteristics section, which needs improvement. Unfortunately, I am leaving it as a 'work in progress' before I leave on my trip, but the present state is no worse than what I started with. Please be patient with me. Bob Plaag 23:40, 20 February 2007 (UTC)[reply]
I had some time to 'finish' the section about the LSm structure. Please let me know if you think this was an improvement, and/or offer some other suggestions or criticisms. Bob Plaag 04:45, 21 February 2007 (UTC)[reply]

Tables edit

Apart from an Infobox there could be some tables to summarise and compare. There could be a table listing all the different kinds of LSm, along with some of their properies -eg Oligomer size, discoverer, MW, organisms... Another table possiblitity is of the components found in LSm. Just a suggestion. GB 01:27, 14 February 2007 (UTC)[reply]

I am working my way down this list. I promise that I will get to yours. One problem that I am running into is length as I am already at 36 kilobytes. Bob Plaag 03:24, 15 February 2007 (UTC)[reply]
So far, counting all of the known LSm homologs, in all species that have a LSm protein sequence in the NCBI database, numbers over 1,000, which would be beyond the scope of a Wikipedia article. But, all is not lost. The last External link listed brings you to a database of LSm sequences. The version, as of today, is a few years old, but I assure you that a far more extensive list is in the works. I know this because I created it, and my colleague is in the process of getting his website (where this database is located) updated. But maybe a short table would be helpful. Let me ponder this idea for awhile. Bob Plaag 19:41, 15 February 2007 (UTC)[reply]
Yes Bob I was only thinking of a couple of small tables, that could summarise wht the text says. Tables and pictures do not really count in the size limit - as long as you can edit it with out a problem! My suggestions are to try to get the article to A rating. Certainly it will not be worth the effort to document 1000 species variations, but the ones found in humans would be good to have. You are the most responsive peer review canditate editor I have seen so far! GB 23:08, 15 February 2007 (UTC)[reply]
Thank you for the compliment. I do try. (As a note, I will be travelling for almost a month, and won't be able to respond and work on this article during this time. Please be patient during this hiatus, as I promise to get back to answering these reviews.) I did some thinking, and think that the appropriate place for a small table would be within the "Functions" section. This section basically lists the types of LSm proteins with their functions as much as is known. It is on my 'To Do' list for this article. Bob Plaag 20:12, 16 February 2007 (UTC)[reply]
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