Wikipedia:Peer review/Eicosanoid/archive1

Eicosanoid
I'd like to get Eicosanoid up to Good Article, or even A standards. David.Throop 23:34, 26 January 2007 (UTC)
 * Is the citation style OK?
 * Does it have too many tables?
 * In particular, should table 2 or 3 be spun off into a List of... article?
 * Does it have enough detail in the Action of prostanoids and Action of leukotrienes sections?
 * Are any parts of it too hard to understand, or too long-winded?
 * Is there anything not covered that should be?

Fvasconcellos
Minor stylistic concerns: I am unfamiliar with the peer review process and don't know if this is frowned upon, but I'd enlist the assistance of an editor experienced with FAC (or at least GA reviewing) to help with copy-editing of the article. I hope some of my comments can be of use, and good luck! Fvasconcellos 14:27, 27 January 2007 (UTC)
 * After a quick read-through: the lead looks good, quite comprehensive, not too long. – Thanks
 * I'm not fond of Harvard referencing at all, but that's not really a valid objection :) I do believe this article could benefit from footnotes as the primary citation style; readability in the "History" section is particularly hampered now with close repetition of researcher names. Formatting of citations is very good. – Thanks, done
 * The "Biosynthesis" section is less readily understandable than the rest of the article. – OK, I've added more material to Action of leukotrienes, so that it matches Biosynthesis.  :-)
 * Table and figure headings, as well as references to them throughout article body, are quite "textbooky"—I imagine this could raise objections in a possible FAC. I don't think tables should be split into separate articles. – Changed
 * In the "Function and pharmacology" section: the "Action of prostanoids" subsection and Table 3 could be rearranged into a subsection such as "Manipulation in medicine" (used in Immune system) or something to that effect.
 * Good use of summary style, leaves room for future expansion if/when necessary. The "Action of prostanoids" section could be fleshed up a little, but this is an "overview"; details should be left to ancillary articles.
 * IMHO, Table 1 could be centered. It's too "skinny" and the right-floating doesn't direct attention to it. – Changed
 * As per MOS:BOLD, italics should be used for emphasis, not boldface. – Changed
 * As per WP:GTL, "See also" templates should immediately follow the section heading. – Changed
 * Inconsistent usage of en dashes and em dashes throughout. – Changed
 * "The first step of eicosanoid biosynthesis occurs when cell is activated by mechanical trauma..."—odd construction.
 * The prose in "Biosynthesis of prostanoids" is somewhat truncated.

Opabinia
These are just a few quick comments, mostly on formatting; this is admittedly not a comprehensive review. I'll try to read the text more thoroughly later. It's great to see articles like this getting some attention.
 * The lead starts with "In human biochemistry" - just humans? Later the article says they're found in other organisms, but do any others use them as signaling molecules? I'd be rather surprised if humans were the only organisms to do so. – Changed
 * "downregulating eicosanoids" - not exactly sure what's being said here. It makes sense to say 'downregulating a gene' or 'downregulating an enzyme' but 'downregulating an organic compound' sounds wrong. Do you mean downregulating eicosanoid synthesis? – Changed
 * Agree that the Harvard referencing is awkward. It's not punctuated properly, which is something I normally wouldn't care about, but in this case it's rather distracting. Examples - the commas between separately parenthesized citations at the end of the lead, and the parenthetical citation of (Cyberlipid Center), which doesn't read as a citation without a date attached. Much as I dislike cite.php, converting to the ref-tag format would help, or failing that, use the Harvard citation templates. – Changed
 * Pathway diagrams are nice but really should be in SVG. Fig. 1 in particular looks too small and pixelated.
 * I'd put table 1 on the left to draw more attention to it, but perhaps reformulating it in a horizontal format would help. – Changed
 * In general, I don't like explicitly referring to tables and figures as table 1, figure 2, etc. in wiki text. We don't have a fig/table labeling system and these are just asking to fall out of sync with later editing. – Changed
 * There are image-crowding issues between table 2 and figure 3. I like table 3 but I'd rather see it wider and centered in its own section rather than inline with the text; it's too fat to sit inline at low resolution. – Changed
 * I'd like to see "eicosanoids in inflammation", since you emphasize that effect in the lead. Starting with the Celsus link is a bit awkward; write his full name and when he documented these signs, and that they are still generally accepted. I think the explanation for redness has been abbreviated too much, because I don't really follow; TXA2 is a vasoconstrictor that promotes the subsequent release of vasodilators?
 * I'm not sure how to fix this easily, but the mechanisms and inflammation sections suffer from TLAO (three-letter acronym overload). Maybe a separate list article would be useful, because it would be tedious and lengthy to show all the acronyms and full names (and ideally, chemical structures) in this article.
 * Also agree with Fvasconcellos that a copyedit by someone familiar with the usual stylistic quibbles of FAC would be useful to clean up punctuation, the occasional awkward sentence, etc. (I don't know much about GA, but my instinct is that technical articles do better with FAC, since GA was the original source of all the cite-after-every-sentence silliness, and is entirely dependent on whether the reviewer actually knows the subject or is just processing the backlog.) Opabinia regalis 03:42, 28 January 2007 (UTC)
 * Thanks for all the comments so far. I will make most of the changes; I've already made some.  Converting from Harvard to ref templates is going to be a head-scratcher, tho.   David.Throop 10:38, 28 January 2007 (UTC)


 * Please see automated peer review suggestions here. Thanks, APR t 15:49, 28 January 2007 (UTC)

István
This topic is especially challenging because real-world research in eicosanoids/prostoglandins is moving quickly, what is accepted now is being continuously overturned. Not long ago, scientists were told that they were metabolic waste products - now we know they are very important regulators. Currently there is a wide (but narrowing) scope of disagreement which should be more clearly noted in the article. IMHO, this article, streamlined, clarified, and tidied up, has a good shot at becoming FA. Some observations: This is a good piece of work and does not lack for detail or scope. It can become FA with some structural streamlining, copyedit and another peer review. István 18:22, 30 January 2007 (UTC)
 * Definition - Choose only one definition, even though there is disagreement. Doing so sets the scope of the article as well, you must also mention competing definitions and explicitly state that the operative definition for this article is xyz.  Everyone can understand that there may be other interpretations, and picking one is necessary to write a concise article. &mdash;Good guidance.   I'm thinking of creating a sub-article with all the bloody detail of which experts use which definitions, and just giving a summary here.
 * Nomenclature section - should be split into "Definition" (see above) and "Etymology" (to explain the greek root of the word, etc.)
 * Lead - the first paragraph should focus precisely what eicosanoids do and not include where they come from, nor why they are called as such - there is plenty of space below. You have a challenge of presenting very technical material so keeping each paragraph within one scope (function, source, etc.) is very helpful to the casual reader.
 * IMHO, the information presentation should be ordered as: Intro (action, definition, source) > Definition (def, alt def, etymology) > Function > Scope of what is known/unknown > summary Biosynthesis > everything else (with "history" being last) &mdash;Would you leave the nomenclature stuff - the explanation of the subscripts and double bonds, the series letters - under etymology?. &mdash;Your call. strictly, its not etymology but rather a key/directory for reference - best to first think what the 20:5n3 adds beyond the wikilink for  EPA  and for whom, and then make a decision.  I suspect its just gilding the lily, and theres already lots of gild.
 * Table 1 - very informative and very ambitious. I think it should be larger to be more legible, and perhaps be presented near the function section. It should also stipulate that this is the n6 branch of the metabolic pathway, that there is a corresponding n3 branch eminating from EPA as well.
 * Biosynthesis - this is very long and complex, and IMHO could be taken out and form its own article, referred to in summary form here (e.g. How to build a wristwatch may be a subarticle of Timepiece) and put more emphasis on action, and dietary/medical control.
 * Mechanisms of n3 action - appears above a chart describing metabolism of both n3 and n6 EFA. The chart should be labelled as such, and the concept more greatly emphasised (which is perhaps the single most important idea of this article) that both metabolic pathways compete for the same enzymes, thus altering the ratio of n3:n6 EFA intake will (we are *almost* sure) alter the relative concentrations of resulting eicosanoids, prostoglandins, leukotrienes, etc. and thus promote a greater or lesser inflammatory response at the cellular level.  The next most important idea are factors which block this metabolism, i.e. alcoholism, trans-fat ;-) intake, diabetes, etc. specifically the Δ6 dehydrogenase which is active at several points of the pathway.
 * The image labeled "Prostacyclin I2" is itself labeled "Prostaglandin I2" on its image page, however is the same structure as is depicted in the Prostacyclin article (print it out, flip the paper over and hold it to the light). I believe the Image page is a misnomer, in any case it must be ironed out before FA(C). &mdash;Prostacyclin is the same thing as Prostaglandin I.  I believe that when they first classified them, prostacyclin was counted as a prostaglandin, but that it was split off as it's own class due to its structural differences (the extra ring).  Unfortuneatly, I haven't seen that spelled out anywhere.  But Prostacyclin is definitely the same as Prostaglandin-I.  I'll put that in the Nomenclature section or a footnote to it.  &mdash;Are the two isomers? Those 5-member rings can be unstable esp with double bonds on either side.  Its something that would definitely be picked up on during FA(C) and easily solved beforehand.
 * the article should briefly describe how the body disposes of these materials
 * the article should mention the scope of this biochemistry - if I am not mistaken I believe that this is shared by all vertebrates, perhaps more specifically mammals or primates? &mdash;I'll say mammals as I can find some authority for that, (tho I doubt anybody's actually looked at the monotremes .)
 * Changing reference format greatly improved the article. It could do with some more streamlining.  &mdash;Thanks.  Besides the twocolumn you've been working, what streamlining are you thinking of? &mdash;Readability - there are lots of Three-letter acronyms, some of which refer to the eicosanoids, some to precursors, etc. many are accompanied by parenthetical explanations of their structure - e.g. EPA(20:5 n3) which could probably be done away with as anyone can click on the link and get an in depth explanation.  Perhaps it *might* work if you put reference to the eicosanoids proper in a different format (color or bolded) to stand out from all the other TLAs.  (but then again it might not).  The infoload is challenging, especially to readability.
 * Once the article is in the structure you want, it should be copyedited for clarity to remove ambiguities. As most of the article is written by one person, it's unavoidable that some passages may be ambiguous.  Its the next step after this peer review (then have another before going FA(C))
 * Finally, I would write this to the audience - I anticipate that many readers come here because they are having health issues (esp. cardiovascular) and look to Wikipedia to start learning about their own condition. They should be treated very sensitively - hence more emphasis on function and control, less on ancilary issues. (and revising the ref format helps them greatly!)  &mdash;This is probably the best advice I've received so far.  It's what got me interested in the topic in the first place, too.  I'll give it a lot of thought.

How are Eicosanoids degraded or disposed of? - they have a short lifetime so there must be a pathway to elimenate them. GB 08:10, 30 January 2007 (UTC)