Wikipedia:Featured article candidates/Polyclonal B cell response/archive1

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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 not promoted by User:SandyGeorgia 19:49, 30 June 2008 [1].

Polyclonal B cell response[edit]

Self-Nominator(s): —KetanPanchaltaLK


I'm nominating this article for featured article because...the article covers an important concept in immunology, and it has recently been promoted to the GA-status. Also, in my judgment, the article satisfies all the criteria for FA-class, and if certain deficiencies are pointed out, they can be improved upon, in turn improving the overall quality of the article. KC Panchal (talk · contribs)19:43, 22 June 2008 (UTC)[reply]

  • Some comments for the time being. This is an accurate, comprehensive and fairly well-written article. A complex, highly technical subject has been described in relatively plain English and congratulations are in order. I noticed a few problems during my first reading.
  • Botulism is not an infection, it is caused by poisoning. The bacterium does not cause infection but its neurotoxin is lethal. The toxin is produced in food that has been under-cooked and subsequently stored under anaerobic conditions.
  • When describing the innate immune system, elements is a poor choice of word; mechanisms would be better.
  • Stomach juice - this is gastric fluid.
  • What language is Klon?
  • Each such group is not idiomatic language.
  • Parent would be better than mother when describing primary cells. Life is too short to argue about this :-)
  • The diagrams are too big; readers who require a closer inspection only need to click on them.
  • The first, (excellent and fun to see), image should be relegated to the end of the article.

I can see that many hours of work have gone into this, so please take these comments in good spirit. I will have more to say about this interesting contribution during its candidature. GrahamColmTalk 20:44, 22 June 2008 (UTC)[reply]

Reply

  • Botulism is not an infection, it is caused by poisoning. The bacterium does not cause infection but its neurotoxin is lethal. The toxin is produced in food that has been under-cooked and subsequently stored under anaerobic conditions.
    • Yes, you're right there. Actually, I'd included that as I wanted to cite an example of disease caused by toxin. Well, now I've changed the example to diphtheria, which satisfies both the criteria—it's an infection, its symptoms are somewhat related to a toxin (and, a third subconscious criterion that it's well known. I changed "contagious"--->"infectious" not out of stubbornness, but contagious diseases are more like subset of infectious disease. And, the concepts being dealt with in the article would still apply even irrespective of whether the disease spreads through direct contact or through a vehicle. The way I have opened the section "from one organism to another" I wanted to make it apparent that the two organisms could be of different species altogether. I'm now not sure if the idea has got conveyed sufficiently well. But, would also believe that even that subtlety does not come in way of understanding the concept KC Panchal (talk · contribs) 21:39, 22 June 2008 (UTC)[reply]
  • When describing the innate immune system, elements is a poor choice of word; mechanisms would be better.
  • Stomach juice - this is gastric fluid.
    • Even I wasn't sure which of the two usages is better. So, had used "stomach" thinking of it as less technical. I'll make the change if you/some one else make the same suggestion again. KC Panchal (talk · contribs)
  • What language is Klon?
  • ''Each such group is not idiomatic language.
  • Parent would be better than mother when describing primary cells.
    • Well, I have encountered this (mother cell) usage quite often. The progeny would be called daughter cells. KC Panchal (talk · contribs)
  • The diagrams are too big; readers who require a closer inspection only need to click on them.
  • The first, (excellent and fun to see), image should be relegated to the end of the article.
    • I agree, but am not able to think of a context (for that image) at the end of the article. But, I think you'd also agree that the image provides one of the best explanations of the whole concept. Well, I have shifted the image, and put another one in its place. KC Panchal (talk · contribs)
Thanks for the encouraging remarks. Yes, it's true that a lot of hard work has gone into it. I'm sorry if you thought my changing "contagious" to "infectious" back as somewhat rude, but I did provide an explanation for it in the edit summary. In fact, I'm getting scared. I'm suspecting you're being very euphemistic with your criticism. And of course, this is the first time I've been so intimately associated with an article. So, have no idea of the FA procedure. Your and other reviewers' guidance would be of utmost importance. KC Panchal (talk · contribs) 21:39, 22 June 2008 (UTC)[reply]
  • Parent would be better than mother when describing primary cells.
    • See this as an example:

      "During DNA replication, all the information in the mother cell must be transmitted to the daughter cells."

      KC Panchal (talk · contribs) 22:24, 22 June 2008 (UTC)[reply]
It's the juice I don't like—would you drink it? :-) GrahamColmTalk 22:34, 22 June 2008 (UTC)[reply]
  • Opposing for now. The article is accurate and comprehensive but it's not ready for featured status yet. The prose, on the whole is of a high standard, but there are lapses. Take this section for example:
Engulfing the pathogen (along with the antigens on it, i.e., phagocytosis) because of specific (by B cells) or nonspecific (by macrophages) recognition, and antigen processing. This activates the B cell only partially.

is very problematic. And this:

The epitopes that compose the proteins that serve as antigens..

will stop many readers dead in their tracks. The section on antigen presentation is similarly difficult to follow. There are other lesser problems such as the use of likewise and somewhat, but my fundamental issue is that the article is not written in summary style. I know it is difficult to strike the right balance between comprehensiveness and summary style but a better attempt should be made. Here's my attempt at an explanation of B cell selection:

Only a few lymphocytes bind to any particular antigen. These lymphocytes are said to be “selected”. They bind to the antigen because they have the corresponding antibodies on their surfaces. Once selected, the lymphocytes reproduce and form a clone of identical cells. The cloned cells then produce many more corresponding antibodies. Later they become plasma cells and produce copious amounts of antibodies, first IgM and then IgG.
Well, there's a subtlety here. The first (naive) cell that would have responded and all the daughter cells would also be known as a single clone. Likewise, if another naive cell with the very same specificity (same antibody receptor) would get selected and proliferate, all the progeny (memory as well as Plasma cells) of the both the naive cells would be considered to be one clone. In spite of how clone has been explained in the article, criterion for what constitutes a clone is epitope-specificity rather than which cells is derived from which one. KC Panchal (talk · contribs) 20:20, 24 June 2008 (UTC)[reply]
Yes, I know, but a subtlety that nicely illustrates my point, quod erat demonstrandum. GrahamColmTalk 20:57, 24 June 2008 (UTC)[reply]

Clearly, far from perfect, but I fear that unless an attempt is made to make the article more accessible to the Wikipedia general readers, the article will not achieve FA status. Please don't shoot the messenger. GrahamColmTalk 18:50, 23 June 2008 (UTC)[reply]

Following your pointing out, I have identified an underlying cause for the article not appearing in summary style; that being trying to be explain those concepts that don't form the core of this article in greater details than required. I'm trying to correct that. Could I have a few days (say 3-4 from today) to try to rectify that? In the meantime, I'll greatly appreciate if you could cite specific instances of language, content or layout that are not in keeping with the requirements of FA. KC Panchal (talk · contribs) 20:20, 24 June 2008 (UTC)[reply]
Comments from other reviewers will no doubt follow, SandyGeorgia decides how long candidatures run, not me. But the article and this page is on my watchlist and I will help where I can. GrahamColmTalk 20:57, 24 June 2008 (UTC)[reply]
Graham, I've made some changes in almost all sections, mostly, trying to uncomplicate the sentences. Also, I have removed some relatively unrequired info from the earlier paragraphs. Please do see if these changes have on the whole improved the article in the desired way. KC Panchal (talk · contribs) 07:06, 26 June 2008 (UTC)[reply]
  • Comment There are some short sections and paragraphs, like the one in "History". Could those be expanded? Gary King (talk) 01:09, 23 June 2008 (UTC)[reply]
    • I have significantly expanded the "history" section. Some of the sections that seem short are actually just subsections, which of course can be expanded, but that'd make them too detailed. If that is alright, I'll expand them. But, personally I felt that the level of details that the article, and the various sections in it have maintained are most optimum for "stress-free" reading. Another short section is the one titled "Infection", which cannot be expanded without getting irrelevant in the process. I'd a doubt with the "History" section, though: several scientists mentioned have received Nobel Prize—does that require mention? KC Panchal (talk · contribs) 10:27, 23 June 2008 (UTC)[reply]

Comments

Otherwise sources look good, links checked out with the link checker tool. Ealdgyth - Talk 12:33, 23 June 2008 (UTC)[reply]
I think I have satisfactorily resolved the issues you pointed out above. KC Panchal (talk · contribs)17:00, 23 June 2008 (UTC)[reply]

Comments by delldot talk 07:12, 28 June 2008 (UTC)[reply]

  • Multiple multiples in the second sentence
  • Do you have to use immunological in the first sentence, or could you get away with immune? (This is shorter and more familiar, maybe less intimidating)
    • Very right. It was "immunologic"; some one must have changed it to "immunological", which I did notice, but didn't really mind, then.
  • B cell linked twice in the lead
  • The opposite of polyclonal are monoclonal antibodies, which are all react only against a single antigen, and are not usually produced in a natural immune response, but only in diseased states like multiple myeloma, or through specialized laboratory techniques. -- A long, confusing sentence. Is "The opposite of polyclonal are" ok wording?
  • The next sentence is This is because polyclonality of response reduces the specificity of antibodies produced. What is because of that? The use of this is often ambiguous.
  • You might want to crop Image:Burnet in 1945.jpg, I don't know if you need all that background and it would allow a better closeup of his face.
  • Such substances are known as soluble antibodies and perform important functions in countering them. It's not clear how this sentence fits with the ones before it, or what them refers to. On rereading, actually it is clear delldot talk 07:04, 28 June 2008 (UTC)[reply]
  • Very picky point: some punctuation comes before the ref tags, some after. Sometimes the note tags come before the ref tags, sometimes vice versa.
    • That's not picky at all. I'd tried to maintain a pattern:notes and references (in that order) follow any punctuation without intervening SPACE. Well, I did find about four to five instances of lapses. May be they crept in because of different preferences by different users. Corrected them. KC Panchal (talk · contribs) 13:09, 28 June 2008 (UTC)[reply]
  • Perhaps FAC regulars can clear this up, but I think boldface is being overused. For example, opsonin is bolded in the notes, it looks like it's just because it's being defined. I believe italics is used for that purpose.
  • It looks like a lot of copy editing could be done. Perhaps you know a copy editor who owes you a favor?
    • None so far. I'd appreciate your pointing out the errors. Copy edit for grammar or spellings? KC Panchal (talk · contribs) 13:09, 28 June 2008 (UTC)[reply]
      • Grammar mainly, and awkward wording. Maybe you can look through old FACs and find people that have done copy editing for others, and as them. I can continue pointing out individual problems, but they are extensive and I would prefer to come back after the whole article has had a copy edit. I believe it's customary for an outside editor to copy edit the page. delldot talk 13:29, 28 June 2008 (UTC)[reply]
  • In response to the above question about whether to include Nobel Prizes in the history section, I would say yes, include them.

I'm going to bed now, I'll be back with more comments later. delldot talk 07:00, 28 June 2008 (UTC) A few more:[reply]

  • Both cell-mediated and humoral responses are very specific, and tend to improve with repeat exposures to the same pathogen and constitute the adaptive immune response. I would leave the second half of this sentence for another paragraph, since the rest of the paragraph discusses just specificity.
    • I have split the two concepts into two sentences. Though, didn't split the matter into two paragraphs as that would have made the individual paragraphs too short, and the new info required to expand them would have been irrelevant. KC Panchal (talk · contribs) 13:09, 28 June 2008 (UTC)[reply]
      • I still don't understand why these concepts are linked enough to belong in the same paragraph. It looks like you may be able to combine this paragraph and the one below it, to better contrast innate and adaptive, and to keep the discussion of specificity together.

delldot talk 14:38, 28 June 2008 (UTC)[reply]

        • The concepts are not necessarily related, but as I pointed out they're not significant in the article's context to have respective paragraphs for themselves. KC Panchal (talk · contribs) 10:54, 29 June 2008 (UTC)[reply]
  • The innate immune system provides relatively nonspecific protection (e.g., acidity of stomach secretions). I would expand this sentence a bit to explain a bit more.
    • Expanded the innate immune system part.
      • Good, but now stomach acidity is brought up twice in close proximity. delldot talk 14:38, 28 June 2008 (UTC)[reply]
        • Isn't that alright? Considering we're talking of innate immunes system, and that'd be the simplest example to consider. KC Panchal (talk · contribs) 10:54, 29 June 2008 (UTC)[reply]
  • The captions are awfully long and wordy, I bet they could be cut down. delldot talk 07:12, 28 June 2008 (UTC)[reply]
    • Some of the images have been taken "as is" from their context without modification. It'd be helpful if you could point out which of the captions you found particularly verbose? KC Panchal (talk · contribs) 13:09, 28 June 2008 (UTC)[reply]
      • I've seen somewhere people saying that no caption should be longer than four lines.
        • I think I've reduced the caption size for most of the images, except for one explaining the steps in B cell stimulation, which obviously would be long, unless of course, I remove the steps from the caption. Do you suggest that I remove the steps.
Thanks Delldot a lot for your review. That was most useful. KC Panchal (talk · contribs) 13:09, 28 June 2008 (UTC)[reply]

More comments from delldot talk

  • Monoclonal antibodies are more specific, and hence are preferred over the polyclonal antibodies in some applications. -- The idea of specific hasn't been introduced, maybe just explain instead of using the word. Also, the idea of applications hasn't been introduced. What applications? Again, maybe just explain. delldot talk 14:38, 28 June 2008 (UTC)[reply]
    • I've modified the concerned paragraph in light of your suggestions. KC Panchal (talk · contribs) 10:54, 29 June 2008 (UTC)[reply]
      • Very nice work. I agree with JFW below that this may be too much detail for the lead (sorry, I know it's my fault you added the detail in the first place!). What do you think of the tweak I did (moving the detail on monoclonal down, leaving one sentence in the lead)? Feel free to rv me if you don't think it's an improvement. delldot talk 17:15, 29 June 2008 (UTC)[reply]
  • Question: under Specific recognition of epitope by B cells, is e.g. used right here? for the situation being discussed here (e.g. the antigen recognition by the B cell) -- e.g. means for example and i.e. means that is.
  • Going through the article, I'm seeing a lot of opportunities to reduce redundancy (e.g. "longer in length", "also show a similar enhancement"). I'm working on some of them, but I still recommend finding an experienced copy editor to help out. Have you checked out User:Tony1/How to satisfy Criterion 1a#Eliminating redundancy? delldot talk 18:37, 29 June 2008 (UTC)[reply]
  • In spite of the fact that there are so many diverse pathogens, many of which constantly keep on mutating, it is a great surprise that a majority of individuals remain infection-free. -- I'm not following, why's that a surprise? Also, about the redundancy, would it change the meaning to change In spite of the fact that to although? But I think the sentence would make more sense if it was Since there are so many diverse pathogens, many of which constantly keep on mutating, it is a great surprise -- the more pathogens, the more surprising not being infected is, right? Also, I think it's infection free here, not infection-free because it's after the word it's modifying (individuals). This is my reading of hyphen, correct me if I'm wrong. Lastly, constantly keep on is also redundant.
    • I've rephrased the entire paragraph. As far as I know, may be the Oxford dictionary people have done away with hyphen totally in one of their dictionaries. Don't know if every one is to follow suit. But, may be usage of hyphen is independent of whether the combined qualifier (adjective) is used before before the subject or after it. But, of course, I can't say that with much confidence. KC Panchal (talk · contribs) —KetanPanchaltaLK 16:48, 30 June 2008 (UTC)[reply]
      • The logical problem is still there: Although there are many diverse pathogens, many of which keep on mutating, it is a surprise that a majority of individuals remain free of infections. Seems like it's a surprise since there are so many pathogens, right? (or Given that, maybe). The more pathogens, the likelier disease is? If I'm misunderstanding this, maybe it could be clarified in the article.
      • Actually, I think you're right about the hyphen thing, after another reading of WP:HYPHEN; infection-free is closer to the "well-behaved" example than the "well polished" thing because it's a single modifier. But I'm not sure if this just applies to well. If you find out from a more seasoned copy editor, let me know, won't you? delldot talk 17:05, 30 June 2008 (UTC)[reply]
  • This maintenance of disease-free state requires the body to recognize as many pathogens (antigens they present or produce) as known to exist. -- known to? What does them being known have to do with it?
  • Such an altered epitope binds less weakly with the antibodies specific to the unaltered epitope that would have stimulated the immune system. -- unclear. Is it really less weakly?
  • The phenomenon of autoimmunity can be simply explained in terms of the immune system making a mistake by wrongly recognizing certain native molecules in the body as foreign, and in turn mounting an immune response against them. -- This is awkward and hard to follow. I think part of my trouble understanding this article has to do with the long sentences.

Gotta go again, I'll have more comments in a while. delldot talk 20:44, 29 June 2008 (UTC)[reply]

  • Oppose for the time being. The article pitches in the right tone and takes a good general look at an important phenomenon in mammalian immunology. Given my limited technical experience in the field it would be immensely helpful if some editors with expertise in immunology (Ciar or DO11.10) could offer their comments and perhaps assist in making further improvements. At the moment my specific criticisms: (1) Do we really need a general introduction into the field of immunology? Is there any hope of making it more concise with fewer level 2 headers. (2) The images are generally lifted from free sources but would benefit from being redrawn on scale with a different background. (3) I'm sure the distinction with monoclonal proteins can be safely left out of the introduction. (4) The etymology of "polyclonal" belongs in the lead, not halfway down. (5) If there are multiple footnotes referencing to the same source, why is that source in "further reading" and does it otherwise appear in the footnotes in various formats? (6) Why are some facts referenced to unreliable web sources, such as undergraduate teaching material? (7) What is the point in the one external link, which appears to be someone's personal web page? (*) In short, I think much work is needed before this gets to FA standards, and I strongly suggest involving two immunology editors mentioned earlier. JFW | T@lk 11:57, 29 June 2008 (UTC)[reply]
Response to comments by JFW:
    • "Do we really need a general introduction into the field of immunology? Is there any hope of making it more concise with fewer level 2 headers."
      • I have clubbed this section with the preceding one dealing with "Infection". I'd kept it the way it was as that would introduce an uninitiated reader gradually to the topic. To impress the importance of antibodies in immune response upon the readers' mind would be very important. But, have significantly shortened the section now. KC Panchal (talk · contribs) 15:20, 29 June 2008 (UTC)[reply]
    • "The images are generally lifted from free sources but would benefit from being redrawn on scale with a different background."
      • Well, not all the images are taken from the public domain. I've myself created the four images (the least attractive-looking ones) mostly using PowerPoint and Paint. If you're referring to those images, then, I'd like to say that I might download Inkscape in a couple of days and try to work on them. But, it'd be better if you point out which images in particular. KC Panchal (talk · contribs) 15:20, 29 June 2008 (UTC)[reply]
    • "I'm sure the distinction with monoclonal proteins can be safely left out of the introduction."
      • I'd priorly been told by a user (not from the medical field, which adds some weightage to the opinion) that since most of the people come to know of polyclonal antibodies only by way of hearing about monoclonal antibodies, to highlight contrast between the two would be important. Of course, which part of the article can do this is another issue. May be I can shift that part to the discussion on monoclonal antibodies. KC Panchal (talk · contribs) 15:20, 29 June 2008 (UTC)[reply]
    • "The etymology of "polyclonal" belongs in the lead, not halfway down."
      • I've added a note on etymology in the lead. And removed the related material form the section "Basis of polyclonality". KC Panchal (talk · contribs) 15:20, 29 June 2008 (UTC)[reply]
    • "If there are multiple footnotes referencing to the same source, why is that source in "further reading" and does it otherwise appear in the footnotes in various formats?"
      • "Further reading or Bibliography (paper resources such as books, not web sites)"—that's what the MEDMOS says about such a section. So, I see no reason why a source that has been cited can't be used as a further reading recommendation. The only citation that will be seen in two different formats is the "Goldsby:Immunology" citation. It's not in two formats. Just that the first time it is used, it's in its expanded form so that the reader would know what's "Goldsby, et al: Immunology", and for the rest of the article it's in its abbreviated form as it was pointed out that in its expanded form it was making the References section appear too cluttered. KC Panchal (talk · contribs) 15:20, 29 June 2008 (UTC)[reply]
    • "Why are some facts referenced to unreliable web sources, such as undergraduate teaching material?"
      • These are the undergraduate courses:
        • Davis, Cheryl. "Antigens". Biology course. Western Kentucky University. Retrieved 2008-05-12.
        • Ceri, Howard. "Antigens". Immunology course. University of Calgary. Retrieved 2008-05-12. But, the same piece of information is also supported by a published source (textbook): Khudyakov, Yury (2002). Artificial DNA: Methods and Applications. Florida: CRC Press. p. 227. ISBN 0849314267. {{cite book}}: Unknown parameter |coauthors= ignored (|author= suggested) (help). So, I think that should be alright. Moreover, this is what one of the dispatches on reliability had to say: "If a site is written by a noted expert who has been independently published by reliable sources in the field, or is hosted by a college or university institute concerned with the field, it may be reliable, depending on the text cited or whether there should be other, more reliable (for example, peer-reviewed) sources available.". So, I suppose those college web sites have cited "Goldsby" as their original source. But, if still their inclusion is contentious, I can remove them as that won't much difference to the verifiability of the concept they were backing up (that the secreted and membrane-bound antibodies of a clone bind to the same epitope). KC Panchal (talk · contribs) 15:20, 29 June 2008 (UTC)[reply]
    • "What is the point in the one external link, which appears to be someone's personal web page?"
      • I suppose your objection was to this citation: Deem, Michael. "Michael W. Deem". Official Web Page. Rice University. Retrieved 2008-05-08., which is not really a personal web page, but that of the Rice University. But, if still the objection persists, I can remove it and add some other source. KC Panchal (talk · contribs) 15:20, 29 June 2008 (UTC)[reply]
Thanks a lot, JFW, for your detailed review in spite of your time crunch. KC Panchal (talk · contribs) 15:20, 29 June 2008 (UTC)[reply]
The above discussion is preserved as an archive. Please do not modify it. No further edits should be made to this page.
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