Talk:Polyclonal response

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Polyclonal response is currently a good article nominee. An editor has placed this article on hold to allow improvements to be made in order to satisfy the good article criteria. Recommendations have been left on the review page, and editors have seven days to address these issues. Improvements made in this period will influence the reviewer's decision whether or not to list the article as a good article.

Date: 18:35, 27 May 2008 (UTC)

This is the talk page for discussing improvements to the Polyclonal response article.
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Good article Polyclonal response was a nominee for Natural sciences good article, but did not meet the good article criteria at the time. There are suggestions below for improving the article. Once these issues have been addressed, the article can be renominated. Editors may also seek a reassessment of the decision if they believe there was a mistake.
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Contents

[edit] An open request

Since many times the replies become pretty long, I request every one contributing on this page to add a heading or subheading whenever they deem fit to make navigation through and editing of the article simpler.

Ketan C. Panchal, MBBS talk.TO.me>>> 22:19, 13 May 2008 (UTC)

[edit] Criteria

Let's do a step-by-step review to see what needs improving. I'll make six subsections, and we can discuss anything that applies in each separate section.

Just for convenience, I think the spelling/grammar/related stuff should be done last, because if we make any changes, we'll have to re-check all the spelling and grammar for typos at the end anyway! WhatamIdoing (talk) 05:53, 8 May 2008 (UTC)

Though what you've analyzed about the article required quite a bit of effort, it leaves me confused. That's because in all the criteria you've mentioned, the article scores well (at least according to you), and begs the question "what more needs to be done?" Though I don't completely agree with you on all the counts, which of course I mention here in the format you've prepared. Also, one more thing that I haven't understood is that the GA assessment sounds so much like an all important exam, when your work would be scrutinized. I'm alright with that. But, I don't understand WHO will scrutinize it? And WHEN? Why for instance, YOU, or for that matter, Delldot or Chzz, cannot scrutinize the article (this just a question, not a suggestion or request), and pass the verdict--whether it qualifies or it does not? It confuses me because on one hand it is said and mentioned that any one can assess the article and pass ones' judgment, but on the other hand, NO ONE is actually doing that. I'm not distraught or discouraged, but just that am not understanding this aspect of article assessment. May be I haven't understood the procedure well in spite of having read the concerned articles.
Ketan Panchal, MBBS (talk) 21:00, 8 May 2008 (UTC)


[edit] Well-written

    • You really think that the article explains the jargon used well? That has been my greatest concern and the biggest challenge.
Ketan Panchal, MBBS (talk) 22:26, 8 May 2008 (UTC)
No, actually, I haven't assessed that. This is just the list of requirements. I've only looked at parts of them. Let's leave this section for the last, though: if we make any changes, then we'll just have to re-do it anyway. WhatamIdoing (talk) 05:13, 9 May 2008 (UTC)

[edit] Accurate and verifiable

  • It is factually accurate and verifiable. In this respect, it:
    (a) provides references to all sources of information, and at minimum contains a section dedicated to the attribution of those sources in accordance with the guide to layout;[2]
    (b) at minimum, provides in-line citations from reliable sources for direct quotations, statistics, published opinion, counter-intuitive or controversial statements that are challenged or likely to be challenged, and contentious material relating to living persons;[2] and
    (c) contains no original research.
Will specific citations be required for some pieces of information like the frequency of mutation in somatic hypermutation? Ketan Panchal, MBBS (talk) 22:27, 8 May 2008 (UTC)
Very likely. Perhaps as we see such specific facts, we can tag them with {{fact}}, which will put a little flag like this[citation needed] on the text. That will give us a list of what we need to find. WhatamIdoing (talk) 05:28, 9 May 2008 (UTC)
I have a specific query: how does one cite the same reference at many points in an article.Ketan Panchal, MBBS (talk) 14:42, 12 May 2008 (UTC)
See Wikipedia:Footnotes#Naming_a_ref_tag_so_it_can_be_used_more_than_once Bazzargh (talk) 14:45, 12 May 2008 (UTC)

[edit] Images

Y Done I checked the five images in the article and all five have suitable copyright tags. WhatamIdoing (talk) 06:08, 8 May 2008 (UTC)

[edit] GA review 10 May 2008

  • Well written: some things to improve
    • "treatment meted out to" this expression is hard to understand
      • Why is the bit about secondary immune response talking about memory cells? The text is confusing.
    • "This binding requires both the paratope and the epitope to undergo slight conformational changes in each others' " "These"= the weak binding or both?
    • "Of course, some or the other clone" something is misspellt or missing
    • "but the clone as of now would consist of naive cells, and because of an unfortunate phenomenon, such cells are not allowed to proliferate by the weakly binding antibodies produced by the priorly exposed clone" reword into something more comprehensible (and cite)
    • Don't put sup tags around references, it makes lines overlap
  • Verifiable: not quite there
    • Specific statistics need citations (you have already added citation needed to the two spots)
    • "1 in 1700 cell divisions" need source
    • the link to [1] is broken and lacks access date.
    • "Such epitopes are known as conformational epitopes and tend to be longer in length than the linear epitopes" could use a scholarly cource.
    • "only when the peptide in question would be small (to the order of 10 amino acids long)" citation pls.
    • "Since these native molecules will not be eliminated in course of time" is this covered by one of the references?
  • Broad: yes
  • Neutral: yes
  • Stable: yes, should be ok, even with listing at WP:Peer review as well
  • Pictures: some tings to do

Remarks that aren't part of the GA review:

  • I prefer black text and white background in illustrations, it makes it easier to read.
  • Many of the bolded words would be better in italics.
  • I don't think the large white spaces between paragraphs is a good idea.
  • The references could be written in a tidier way, e.g. with template:cite journal
  • ancillary - difficult word, could you reword?
  • The article is divided nicely into sections, but the titles aren't very helpful if you are looking the section for a specific fact, in great part because they are so long that one wouldn't read the table of contents
  • It wouldn't hurt to also get the basic things cited, especially if you can find free papers.

I'm putting it on hold. Narayanese (talk) 20:57, 10 May 2008 (UTC)

I've failed the GA nom, as the article is still lacking in terms of clarity.

Some specific remaining problems:

  • The description of affinity maturation is much too hard to understand, especially regarding the involvement of memory B cells.
  • The antigen-receptor (epitope-paratope) interaction section's two first sentences are still in so poor shape that they can be misleading.
  • The clonal selection picture's page still needs its description page referenced.

Narayanese (talk) 15:22, 16 May 2008 (UTC)

[edit] Reply to GA-assessment by Narayanese and renomination

I've failed the GA nom, as the article is still lacking in terms of clarity.

Some specific remaining problems:

  • The description of affinity maturation is much too hard to understand, especially regarding the involvement of memory B cells.
Y Done I have rewritten most of the section. —KetanPanchaltaLK 18:19, 27 May 2008 (UTC)
  • The antigen-receptor (epitope-paratope) interaction section's two first sentences are still in so poor shape that they can be misleading.
Y Done Shifted the section, so that now it fits better in the context of the entire article. Also, rewrote the opening of the section providing better context. And, added a note on recognition of pathogens by the macrophages employing TLRs. —KetanPanchaltaLK 18:19, 27 May 2008 (UTC)
  • The clonal selection picture's page still needs its description page referenced.
Y Done I've provided reference for the caption. Don't know if it would be appropriate to have a superscripted reference for the description page that lies in the domain of "Wikimedia commons". Moreover, I have never seen the description of any image being referenced up till now. —KetanPanchaltaLK 18:19, 27 May 2008 (UTC)

Apart from the above changes have made many changes in the text trying put things better in perspective and context. Have put the "unalphabetical" glossary in a navigation bar, so that it does not interfere with the overall readability of the article.

Hope that these changes satisfy you.

As I have addressed all the objections raised resulting in the failure of the article to meet the "good article" standards, I am renominating it.

Regards.

—KetanPanchaltaLK 18:19, 27 May 2008 (UTC)

[edit] New changes

Hello Narayanese! I've made some changes to the article keeping in view your suggestions. Do let me know if these satisfy you to any degree, and also what else requires to be done.

Regards.

—KetanPanchaltaLK 16:07, 26 May 2008 (UTC)

[edit] Narayanese replies to new changes

Since it has had so large changes I won't be able to go through it until friday or so when my exam is over. You could always renominate (minus the cleanup tag) in the meantime, other editors are probably better at layout and grammar than me.
One thing I noticed: you imply leukocytes don't differentiate when they change tissue (first section), I thought monocytes did. And I would recommend against anything over three lines per entry in that section. Narayanese (talk) 16:32, 27 May 2008 (UTC)
Thanks for your prompt reply. Secondly, all the best for your exam.
Yes, you are right about monocytes, they differentiate. But, a monocyte will still retain its function, i.e., differentiating into a macrophage irrespective of whether it is, say in the liver or the lungs. All the macrophages (or related cells) they differentiate into serve the same functions, viz., nonspecific phagocytosis, antigen presentation and production of interleukins again irrespective of the harboring tissue. What you have mentioned is somewhat an exception to the statement, but for readers unbeknown to this concepts, explaining a generalized concept is better than highlighting an exception.
Regards.
—KetanPanchaltaLK 17:28, 27 May 2008 (UTC)

[edit] Academic issues

(Added this section heading for better readability and ease of adding and replying to comments)

About the Images: What kind of ref are you looking for? A ref actually in the graphic? Or a citation in the caption? Don't you think that citations about the same information, actually in the main text, would be good enough? WhatamIdoing (talk) 04:45, 11 May 2008 (UTC)

[edit] Affinity-maturation

Just the caption for Image:Original antigenic sin.png, and for the text in the picture Image:Stimulation of specific clone of B cells and its proliferation.PNG. But it would be nice if you could write on the image page what the soluble antibodies are doing in the maturation (are they doing anythng at all, or is it just to say they get to bind better afterward?).Narayanese (talk) 07:40, 11 May 2008 (UTC)
I suspect that the main article, Original antigenic sin, will have at least one ref that supports everything in that caption. That could just be copied and pasted into the caption here, and it's a rapidly solved problem. Perhaps if KC has a minute in the next few days (KC: I mean after you write that exam!) then we'll be able to identify the best of the available sources there. WhatamIdoing (talk) 21:28, 11 May 2008 (UTC)
Thanks, WhatamIdoing, for the wishes. The soluble antibodies bind more strongly, and that itself is one of the aims of affinity-maturation. Better bound antigens are more likely to be eliminated. Trying to explain what the antibodies do would be somewhat beyond the scope of the article (though, now am thinking of adding a note on antibodies' functions), but most definitely beyond the scope of the image. It is to be assumed before going through the figure that stronger binding antibodies is a "good thing". The "concept of original antigenic sin" has an in-text reference now. It had one a few days back, too.
Ketan Panchal, MBBS (talk) 04:56, 13 May 2008 (UTC)
  • KC, the "soluble antibodies bind more strongly" than what? Than the membrane-bound IgD receptor on the mother cell? Sounds extremely unlikely to me. Than some antibody that's not being produced due to original antigenic sin? Maybe. (Could go either way with that, as the suppressed cell line is randomly different and therefore 50-50 odds of being a stronger or weaker bind -- although we only care about the stronger affinity cells being suppressed.) WhatamIdoing (talk) 00:56, 16 May 2008 (UTC)
  • WhatamIdoing, sorry, I seemed to have missed this part of conversation. I meant the antibodies produced as a result of affinity-maturation bind better (more strongly) than the ones produced before affinity maturation. Membrane bound and soluble antibodies of a particular clone are likely to bind with the corresponding epitope with same (at least comparable) strength as they would both have exactly the same paratope.—KetanPanchaltaLK 12:20, 26 May 2008 (UTC)

[edit] Broken link

About the broken link: It works for me, but it was slow to load. Can you try it again?
I've removed the unnecessary <sup> tags and rephrased the sentence about autoimmunity ("these native molecules"). WhatamIdoing (talk) 05:02, 11 May 2008 (UTC)
It was a stray "|", fixed now. Narayanese (talk) 07:40, 11 May 2008 (UTC)

[edit] Lymphocyte and Toll-like receptors

The article says B cells are white blood cells, are you sure? Another bit that makes me wonder is "Whatever the cell type, recognizing an antigen or a segment thereof (an epitope) requires the antigen to bind with the corresponding paratope that is present on the receptor, which is in turn present on the surface of the recognizing cell. In the immune system, these are the T cell receptor (TCR) and the B cell receptor (BCR).", given that leukocytes can recognize microorganisms just fine, both by Toll-like receptors and by finding bound antibodies. Narayanese (talk) 04:39, 12 May 2008 (UTC)

I don't know why one would doubt that. B cells are (B) lymphocytes, which are most definitely WBCs. Referring to them as WBCs and not lymphocytes has this advantage that more people have heard of terms like red blood cells and white blood cells.Ketan Panchal, MBBS (talk) 04:56, 13 May 2008 (UTC)
Seems I confused the term with granulocytes... or something. What about the second bit though?Narayanese (talk) 10:55, 15 May 2008 (UTC)
  • Narayanese, toll-like receptors are part of the activation mechanism for the innate immune system. TCR and BCR binding is required for a B cell response (acquired immune system). I assure you that if a B cell does not first bind its antigen, and then get approval from a T cell, it will not secrete antibodies. Macrophages are happy to go berzerk without any outside approval, but properly functioning B cells do not. Having said that, perhaps we'll be able to find a somewhat clearer way to say this. WhatamIdoing (talk) 00:56, 16 May 2008 (UTC)
Narayanese, I absolutely agree with WhatamIdoing. It is the macrophages that employ TLRs to recognize patterns (small repeating molecules of certain carbohydrates, etc. and not peptides or proteins) present on pathogen surface, and not the B lymphocytes. This recognition is much less specific than a usual epitope (peptide)-paratope interaction. So, the TLRs don't find a mention in the article.

—KetanPanchaltaLK 12:20, 26 May 2008 (UTC) !!!

[edit] REPLY to "GA review 10 May 2008"

[edit] writing

  • Well written: some things to improve
    • "treatment meted out to" this expression is hard to understand
      • Y DoneI have changed that part.
    • Why is the bit about secondary immune response talking about memory cells? The text is confusing.
      • It's simple, I believe. Because the first secondary response is due to the proliferation of memory cells. Every subsequent response is also called a secondary response, which are also because of the memory cell proliferation. (I see, you have a biotechnology background), so please do feel free to let me know what specific flaw did you find with that part.
    • "This binding requires both the paratope and the epitope to undergo slight conformational changes in each others' " "These"= the weak binding or both?
      • "This" refers to binding of the antigen with the paratope on the BCR as well as the secreted antibody molecules.
        • If this sentence doesn't have any obvious practical importance to the article, then I think we should delete it. At minimum it should wikilink to conformational change if kept. WhatamIdoing (talk) 01:05, 16 May 2008 (UTC)
    • "Of course, some or the other clone" something is misspellt or missing
      • Y Done In my view nothing was missing or misspelled, but I have simplified the section. Hope that satisfies you.
    • "but the clone as of now would consist of naive cells, and because of an unfortunate phenomenon, such cells are not allowed to proliferate by the weakly binding antibodies produced by the priorly exposed clone" reword into something more comprehensible (and cite)
      • Y Done I have rephrased the entires section itself.
    • Don't put sup tags around references, it makes lines overlap

[edit] verifiable

  • Verifiable: not quite there
      • In which specific context?
    • Specific statistics need citations (you have already added citation needed to the two spots)
      • Those pieces of information were not put by me. But, will try to find references for them. Apart from the frequency of somatic hypermutation I haven't provided any numerical information.
    • "1 in 1700 cell divisions" need source
      • Y Done Well, the info I provided was a wrong, and have corrected that with appropriate citation
    • the link to [2] is broken and lacks access date.
      • Y Done It worked for me too.
    • "Such epitopes are known as conformational epitopes and tend to be longer in length than the linear epitopes" could use a scholarly cource.
      • Y Done Now I have cited several sources. Only one of them is a published source. But, the rest are part of courses of genuine Universities, so I think their genuineness shouldn't be suspect.
    • "only when the peptide in question would be small (to the order of 10 amino acids long)" citation pls.
      • Y Done
    • "Since these native molecules will not be eliminated in course of time" is this covered by one of the references?
      • I don't think such a piece of information requires reference. Since, the antigens are a part of the body's tissue involved in day-to-day functions, they cannot be eliminated completely. Even if the antigenic molecules, to which the autoantibodies bind are eliminated transiently, they will be synthesized back again. It's comparable to asking for reference for a statement like "if a person is bitten by a mosquito, and since the person continues to stay where he/she was, can be bitten by the mosquito again! I hope you get the point.

[edit] more

  • Broad: yes
  • Neutral: yes
  • Stable: yes, should be ok, even with listing at WP:Peer review as well
  • Pictures: some tings to do
    • Image:Stimulation of specific clone of B cells and its proliferation.PNG (the primary response box and the soluble antibodies in particular) and Image:Original antigenic sin.png should have references
      • One of the requirements of Wikipedia policies is to either use images from the public domain, or that they be original works. How can I provide citation for an image that I originally created. The fact that the concepts in the figure are in accordance with the text, which is adequately spplied with references should be adequate attestation to the soundness of the concepts in the figure. If you still are skeptical about this logic do let me know, but nowhere in entire Wikipedia have I found references for figures drawn by users themselves.

Remarks that aren't part of the GA review:

  • I prefer black text and white background in illustrations, it makes it easier to read.
      • The same point was raised by a user above (#Inexpert review). It wasn't possible to show subtle differences among epitopes of nine different colors. But, they contrast better against a dark background.
  • Many of the bolded words would be better in italics.
      • Well, I have tried to follow a pattern. New terminology has been written in bold, whereas, concepts or keywords have been written italicized.
  • I don't think the large white spaces between paragraphs is a good idea.
      • The spaces have been kept deliberately to highlight that they're two different paragraphs. But, all this amenable to popular opinion.
  • The references could be written in a tidier way, e.g. with template:cite journal
  • ancillary - difficult word, could you reword?
      • Y Done I have replaced the word with "additional", but thought "ancillary" made better sense. "Additional" seems to belittle the role of complement system.
  • The article is divided nicely into sections, but the titles aren't very helpful if you are looking the section for a specific fact, in great part because they are so long that one wouldn't read the table of contents
      • Specific suggestions in this regard are most welcome.
  • It wouldn't hurt to also get the basic things cited, especially if you can find free papers.
      • I have tried hard, but that is a very difficult thing. Most of the high-quality research is cutting-edge and doesn't deal with the basic stuff. My information has been largely based on "Goldsby et al Immunology fifth edition, W. H. Freeman and company". The basic stuff is available only in published books, which for obvious (business-related) reasons isn't made available for free on the net.
        • Narayanese, can you pick a few specific "basic" things that you'd like to have cited? We can certainly use textbooks -- but it would help if you gave us some direction on what to look up. Otherwise, it'll look like we just randomly cited whatever was easy to find. I'd really appreciate it if you'd fact-tag a few things in the article. WhatamIdoing (talk) 01:05, 16 May 2008 (UTC)

I'm putting it on hold. Narayanese (talk) 20:57, 10 May 2008 (UTC)

Your suggestions were most useful. I have tried my best to address all the issues. Hope this satisfies you. I'd be glad to have more problem areas pointed out.

Regards.

Ketan Panchal, MBBS (talk) 17:28, 12 May 2008 (UTC)

[edit] Other complaints

"Major histocompatibility complex is a region on the DNA containing genes present in all the nucleated cells of all jawed vertebrates, that codes for many products involved in antigen presentation (class I and II MHC molecules) and functioning of the complement system." This sentence is bad, as it describes MHC as a gene and not a protein. It's kind of obvious that a gene is found in all nucleolated cells... it's presence of the protein that is interesting. And how can it code for stuff in hte complement system (cite pls)?

Yes, it is most definitely a region on the DNA. The confusion might be arising because two of its important products are called MHC molecules I and II. And, am very confident that MHC class III molecules code for products involved in the complement system and inflammation. I'm citing my source in the main article.Ketan Panchal, MBBS (talk) 10:33, 13 May 2008 (UTC)

Also see my two complaint at the bottom of the review section.

Also, the B7 wikilink goes to disamb page. And B7-CD28 should have a ref.

Narayanese (talk) 22:06, 12 May 2008 (UTC)

Sorry, hadn't seen that. Thanks for pointing out. Y DoneKetan Panchal, MBBS (talk) 10:34, 13 May 2008 (UTC)

--- Couple of quick things (I'm kinda keeping an eye on the development);

  • More references - to avoid accusations of original research it needs lots more refs to books or papers that can back up even well-established facts
  • headings/organisation - As per a previous comments, the headings are currently too long and not very helpful. Needs considerable thought as to the layout. Not my field, but other articles have headings like 'background, history, development, implementation, chemistry, applications in medicine' or that kind of thing.
  • clarity of language - perhaps ask the folk at Copy Edit to take a look?

--  Chzz  ►  22:21, 12 May 2008 (UTC)

Chzz, I appreciate your comments. Do please fact-tag anything in the article that you'd like to see ref'd.
Unfortunately, the section headings you suggested won't work for this topic. I'll give it some thought, though. WhatamIdoing (talk) 01:08, 16 May 2008 (UTC)

[edit] Removed authorlink in cites

Citations shouldn't have an (authorlink = name) unless the author has a wiki article (I think) - otherwise there will be red links (not "appropriate use of wikilinks" in WP:GA). I hope you don't mind my removing them, but I felt it better than just asking for their removal. --  Chzz  ►  22:46, 12 May 2008 (UTC)

Hi! Thanks for pointing out that to me. I wasn't aware of that. Thanks for making the required changes.Ketan Panchal, MBBS (talk) 12:57, 13 May 2008 (UTC)

[edit] More fixes to the references

Using named references doesn't work unless you're using the same reference each time; in this case different pages were being referenced each time. I've shifted those references to the format described here: Wikipedia:CITE#Shortened_notes, so the page numbers appear again.

There were a bunch of other problems with the citations:

  • Don't format the text in the fields of {{cite book}} and the like. The templates are intended to provide a standard formatting with the minimum of additional markup.
  • Dates in the cite templates need to be like yyyy-mm-dd, not yyyy-mm-d. Zero pad as necessary.
  • Several of the ISBNs were misformatted in different ways. Its easy to check these in preview - follow the link they generate to the special ISBN page, then follow the worldcat link.
  • Some field abuse, like non-title info in the title field (which leads to wanting to reformat the title, as above) eg, the Edition should go in the edition field; some of the commentary in your citations might be better off in the 'quote' field. Alternatively, sometimes a comment after the {{cite}} template works well, eg <ref>{{cite foo|bar}} More info.</ref>
  • I removed some odd whitespace in the use of {{cite web}}, I think this was just cut and paste usage.
  • lots of unused fields left in the templates? I left those alone in case you're coming back to them. BTW since the subject matter has academic coverage, Zotero might be useful to you; it does a decent job of filling in the cite template for books and journals (its less good for the web, I rolled my own tool for that [3])

Hope this helps. I thought it might be quicker to fix the page number stuff than explain it; the project might have some better suggestions for formatting these, but at least the page numbers are visible now. Bazzargh (talk) 00:52, 13 May 2008 (UTC)

[edit] Thanks, Bazzargh!

Hi! Thanks a lot for the much needed editing you did on the citations front. I haven't used wikipedia much for developing an entire article--this is my first, that's why so many deficiencies.

  • I believe the blank fields weren't interfering with the display of references, so I left them blank. I hope that's alright.
  • I'm aware of the date format. In fact, I've tried to adhere to it. What you encountered must have been an isolated mistake.

Thanks again. But, I'd like to ask you if you went through the text of the article? If you did, what do you think about the article in context of its ease of understanding (that is if you're not much related to the field of immunology)? What do you think of the overall organization? Regards. Ketan Panchal, MBBS (talk) 05:10, 13 May 2008 (UTC)

[edit] Bazzargh's review

No problem. Normally I wouldn't have said so much about fixing these but I can see you're trying to learn the cite stuff. Yes, the empty fields are ok, but they are clutter for editors; not a big problem though. As for review - might it be worth saying "exhibited by the adaptive immune system of jawed vertebrates." In the lead? As a non-medic it would help me contextualize the article.
Having read the article closely now, the main impression I got was that the diagrams aren't helpful in their current state. They're very cluttered and I had to click through into each of them to figure out what is going on. All the figures contain captions inside the image as well as the 'real' caption below the image; this is unnecessary and the one inside the image is illegibly small.
Some suggestions for de-cluttering the diagrams. Firstly, remove boxed captions from inside the diagrams. Secondly, the 'Clone X' labels on figure 2 and 3 seem to add nothing, remove them. Draw less on each diagram: In figure 2, 6 pairs are enough; in Figure 3, 3 clones are enough. Remove the Keys and instead label one of the clones on the diagram, eg compare [4]. Figure 1: split this into several diagrams. Absorb the right hand side of the figure into the article. I'm not entirely sure what's meant to be going on in Figure 4 (the central bit with the plasma cell).
I might be able to help a bit with these a little later today, I can maybe make you some better diagrams in Inkscape. Bazzargh (talk) 10:25, 13 May 2008 (UTC)

[edit] Reply to Bazzargh's review

Thanks for your review. It was useful as you are not associated with the field.

  • As for review - might it be worth saying "exhibited by the adaptive immune system of jawed vertebrates."
    • Already there has been quite a bit of complaining going around about the usage of passive voice. So, implementing your suggestion might worsen the position
The point here is not the voice, it's missing context. What is the scope of the article? Does it cover only humans? The entire animal kingdom? As it stands you can only figure this out if you knew that adaptive immune systems only exist in jawed vertebrates - so you have to leave this article, read another, and come back. That's not helpful in the lead. Bazzargh (talk) 12:30, 13 May 2008 (UTC)
      • You are right about this deficiency. I have not been very specific about what the subjects (organisms) are. I'll try to correct that. Well, to clarify it here, I know these aspects of immunology as they apply to humans, but then, physiology of all other mammal would be very similar. In fact, most of the information that immunologists possess is through their studies on mice. But, I can't vouch for the validity of these principles in all the "jawed vertebrates", except for the fact that all the cells of all the jawed vertebrates (that includes mammals, too) are capable of expressing MHC class I molecules.Ketan Panchal, MBBS (talk) 16:45, 13 May 2008 (UTC)
        • It is certainly true for all mammals; we could say that, and let it be expanded at a later date, if a source is found later. There are B cells in non-mammalian vertebrates, but I don't know how similar their behavior is. There are certainly some differences. WhatamIdoing (talk) 01:21, 16 May 2008 (UTC)
  • "Having read the article closely now, the main impression I got was that the diagrams aren't helpful in their current state. They're very cluttered and I had to click through into each of them to figure out what is going on."
    • Well, I have tried very hard to make diagrams as intelligible as possible. The keys in the diagrams are necessary as if I try to label certain object in the main body of the diagram, it will only end up making it look more cluttered. Reducing the size of the images further will make the notes within the diagram further illegible. I think it should be alright to have to click the image to open it. I didn't want to compromise upon the accuracy of the concept I wanted to convey. I agree that the figures with black background contain too many clones, but if I reduce the number that might confuse the readers as to why B cells do not react against certain colored segments. I hope you get the point. Also, this was necessary to convey the idea that epitopes are recognized in an overlapping fashion, hence so many clones that react against a single protein.
I disagree, and I'll produce diagrams to show you. I'm not asking you to reduce the size of the images, in fact I'm asking you to make more room in the images for the images by moving text out into the caption (not all the text- labels are fine). BTW, there are print versions of wikipedia. Clicking through is not always possible. Bazzargh (talk) 12:30, 13 May 2008 (UTC)
      • Yes, I had not thought of the print versions of Wikipedia. Obviously, the images will prove deficient in those cases.Ketan Panchal, MBBS (talk) 16:45, 13 May 2008 (UTC)
  • "Secondly, the 'Clone X' labels on figure 2 and 3 seem to add nothing, remove them. Draw less on each diagram"
    • Well, that label consolidates the idea that all the B cells shown are distinct clones, and not the progeny of the same cell. The captions within the images support/help understanding the concepts explained symbolically. Removing them may make the reader confused. Also, those notes underline some important concepts like "overlapping" epitopes, which the reader might overlook without pointing out.
There are other ways you could have visually distinguished the clones; in other diagrams you've indicated this by having different shaped receptors; Thats actually another point of confusion with this diagram - it appears (in comparison to the other diagrams) that the same receptor can bind in all 12 places, which I don't think was your intention. I'm not asking you to throw away the text in the internal captions, btw, I'm asking you to turn those into external captions so that there is more room in your diagram. Also consider: this is wikipedia. How are editors going to edit the text on your diagram? Bazzargh (talk) 12:30, 13 May 2008 (UTC)
      • The figures 2 and 3 deal with a grosser concept of clonality and the structure of the epitopes, wherein the complementarity of epitope and respective paratope isn't being highlighted, so its alright for all the receptors to have the same shape (after all, they all are B cell receptors {BCR}). Whereas, in figures 1 and 4, the specific interaction between the BCR and the corresponding epitope is being examined at a micro level. Hence, the differing shapes for the receptors. In fact, to keep the matters simple, figures 2 and 3 don't have receptors that look different, but the clones have been numbered differently.Ketan Panchal, MBBS (talk) 16:45, 13 May 2008 (UTC)
  • "Remove the Keys and instead label one of the clones on the diagram, eg compare [5]"
    • It is a bit unfair to compare the figures in this article with the above image, because the figures in this article deal with a phenomenon/concept, whereas the above figure just labels a structure. It should be compared with the keys in my diagrams as they are also just dealing with structures. A fairer comparison would be with [6], which also deals with a step-by-step phenomenon, and not a structure, and hence, is a bit complicated. Moreover, if you see, the image would be insufficient in explaining the concept to DNA replication without reading the text. Whereas, I have tried to make the images as self-explanatory as possible (and hence the extensive usage of text within them)
Notice that the example you mention there also manages to get by without a key? Its not the labels in the key that are the problem, its the use of a duplicative boxed partial diagram, you can get the same information across more succinctly without it, pointing the labels at the actual diagram, as both examples demonstrate. Keys are useful on maps and graphs but just eat space on simple diagrams like this. Bazzargh (talk) 12:30, 13 May 2008 (UTC)
      • Sorry, didn't get what you meant by "duplicative boxed partial diagram". Well, by that if you mean the "keys", then, I suppose, the figures 2 and 3 use a very small box, so that shouldn't be a bother, and the other two contain recurring elements like the B memory, naive and plasma cells, and soluble antibodies and surface receptors. But, it might be a good idea to remove the notes in the figures 2 and 3, and put them in the caption below as you are suggesting.Ketan Panchal, MBBS (talk) 16:45, 13 May 2008 (UTC)
I hope I am not hurting you by saying this, but because you are not related to the field, you might be finding it difficult to grasp the concepts. I assure you, it is a bit complicated concept to understand, but once you start understanding, you'll simply love it. You can try this link, I think you'll really find it helpful (assuming you have time) Aberystwyth University-web page. Retrieved on 2008-05-12.. Thanks again for your interest and constructive criticismKetan Panchal, MBBS (talk) 11:07, 13 May 2008 (UTC)
And I hope I'm not hurting you by saying this, but expertise in immunology doesn't confer expertise in graphic design? (not that I'm claiming expertise there either - but I work with them a lot). And if you feel you have to point me at another page to explain the concepts better, doesn't that mean that there may be a problem with the explanations here? No matter: the proof of the pudding is in the eating. I'll put some diagrams together so you can see what I mean. Bazzargh (talk) 12:30, 13 May 2008 (UTC)
      • Quite to the contrary, I am no expert in the field of immunology, and obviously, posses no expertise in graphics. Since, I am so intimately associated with this article, I am no one to comment on its quality. But, I had my limitations:
        • I can't get very informal in my explanations, unlike the article I cited.
        • I had to work within a limited scope. I can go on explaining half of immunology (just like the article), but that would be beyond the scope of "polyclonal response".
        • While citing the article, I didn't assume that you didn't gather any concepts while reading the article on Wikipedia, but only that may be same concepts put in different ways could work better for some.
Any way, did you read the cited article by any chance? Moreover, Wikipedia is for everyone. You're free to contribute your own images, and if they turn out to be better, they will only go on to serve the purpose of Wikipedia and the article better.
Thanks again for your time. Regards.Ketan Panchal, MBBS (talk) 16:45, 13 May 2008 (UTC)
  • KC, given how much time and pain it takes to produce these graphics in MS Paint and PowerPoint, you should definitely take Bazzargh up on his offer -- one thing less for you to do! You and I can probably spend our time better finding sources for whatever the other editors choose to fact-tag. WhatamIdoing (talk) 01:21, 16 May 2008 (UTC)

[edit] Test version of image

Yes, I've read the article. Its pitched more at high-school level, whereas this is more like first year Uni? I know some articles on Wikipedia are getting simpler versions written like that, but its more appropriate for main topics (like Immunology) than this page, which readers are less likely to hit. Actually that's why I commented on the lead and the images, since thats what a non-student is most likely to get out of this page.
Just pushed a draft up for you to see with a different image - [7]. Mediawiki has messed up my svg (its missing the arrowheads coming from the labels, its put round caps on the primary structure, and its messed up the receptor shapes. This all looked ok in inkscape, I need to debug it a bit). Anyway - in-diagram caption has been moved to the in-document caption, key has been incorporated into the diagram proper, and the whole is a scalable, editable graphic of the antigen etc so its easier for others to make changes/translations etc. I made it slightly smaller just to demonstrate that; with larger fonts the image could be smaller still.
From your comments above, the change I made to use shape to distinguish B cells here is unnecessary; how about I just put the number in each B cell (eg '12', not 'Clone 12')?
I'm not proposing this goes on the page yet, its just suggesting a direction the diagrams could be taken in to reduce the use of Flyspeck 3. I'll look in again later this evening, and can make any changes you want. Cheers, Bazzargh (talk) 17:14, 13 May 2008 (UTC)

[edit] Reply to: Test version of image

Hi! That is an amazing image. I really liked it. But, there are a few points where I'm dissatisfied:

  • The "original antigen" shows only six domains (colors, in our analogy), whereas the schematic primary structure has eight. Of course, this makes your job easier. Just remove the second (yellow-ocher, may I) and the sixth (violet/purple--I am always very confused as to what is violet and what is purple) segments from the primary structure.
  • It is important to convey that the smaller segments (peptides) are produced following digestion.
  • Even though the figure looks better this way (more natural as the peptides are seeming "thrown about" rather than in a specific configuration), it'd be better if they can be shown in a particular sequence, which would follow the sequence of colors in the primary structure. Like the first peptide should contain segments 1, 2 and 3, the second peptide should contain segments 2, 3 and 4, the third, segments 3, 4 and 5, and so forth. This is important to convey the phenomenon of overlap between peptides.
  • The label below the long primary structure should read "schematic of primary structure of antigen".
  • I personally have no problems with the shapes of the receptors, but it'd be better if the same shape is maintained for all the cell.
  • I too was thinking of Numbering the clones simply as "1", "2", etc, instead of "clone 1", "Clone 2", etcetera. But, we'll have to specify in the legend of the figure that the numbered cells represent individual clones and NOT individual memory cells of the same clone.
  • Understanding would be easier if there'd be greater resemblance of colors between the "original antigen" and the segments in the primary structure and the peptides.

I think it won't be much trouble for you to incorporate these changes. And, once you do, I won't mind your replacing the figure I prepared. But, if possible, please upload your image with a different name so that the image I submitted does not get deleted. Thanks for the brilliant effort. Bye. Take care. Ketan Panchal, MBBS (talk) 19:21, 13 May 2008 (UTC)

Bazzargh, if you want to clearly show the overlap, you might line up the peptides (colors) so that the matching bits align vertically like these letters do:
  CDE GHI KLM
ABC   GHI    MNO
 BCD FGH JKL
I'm not convinced that we need to convey in the image that the peptides are produced following digestion: With the B cell in the picture, this could easily be the initial antigen binding, which most definitely precedes internalization and digestion.
If you don't want to bother removing the unnecessary colors, we can declare that the "missing" colors are on the long, thin loops instead of in the alpha helices.
Personally, I'd label the B cells according to what (colors) they bind: AB, ABC, CDE, etc. (or red-magenta-blue, yellow-orange, or whatever).
The receptors (the bracket-y bits that bind the antigen) must be mirror images. For our purposes, you can deform the "upper arms" of the Y-shaped receptor in any way you like, but both arms on any given cell must match.
Hope this helps, WhatamIdoing (talk) 01:37, 16 May 2008 (UTC)
BTW I havent disappeared from this, its been a busy week and I might not be able to edit the pics again until Monday. Thanks for the comments. In the meantime, I've a question about the digestion aspect: I'm concerned that this picture appears overly-regular, to the point of being misleading. At the moment, we're always splitting into 3 peptides, and we always have one B cell matching 3 peptides and one matching two; this isn't realistic, is it? I'm wondering if it would help the image to break up this illusion of regularity, say add one 2-peptide chain and one 4-peptide chain, and omit a couple of B cells? Bazzargh (talk) 12:14, 16 May 2008 (UTC)

[edit] An open request

Since many times the replies become pretty long, I request every one contributing on this page to add a heading or subheading whenever they deem fit to make navigation through and editing of the article simpler. Ketan C. Panchal, MBBStalk.TO.me>... 22:13, 13 May 2008 (UTC)

[edit] Unavailable!

I'll be out of town and not accessing the net, so unfortunately will be unavailable to reply to any comments for a week. I know I have made some sweeping, unconventional changes like including a glossary. There will be a few repetitions in the body of the article and the Section titled "Explanation of terms and concepts", so any one interested is requested to rectify the same. Bye for now. Happy editing. Do let me know what you feel about the new section of the article.

Regards.

KetanPanchaltalk-TO-me 16:08, 14 May 2008 (UTC)

[edit] Shifted the "Glossary" section

Hello every one!

Well, am back after a nice holiday. So, I see the article failed in GA assessment for seemingly trivial reasons, which is disappointing to say the least that too in my absence when I was unavailable for editing it. But, it's alright, I suppose.

Well, am posting this message to indicate that I have moved the "Glossary" section to the top, where it best serves its purpose--that of making the subsequent portions of the article easier to understand. Also, renamed it to its present heading "Explanation of difficult terms and concepts" as it is not a glossary; a glossary is supposed to be a compilation of terms in alphabetical order. The concerned compilation is not in alphabetical order. The order I have maintained is the one in which the terms and concepts are likely to be encountered within the article.

It'd be nice to make major changes in the article after discussing them in the talk page.

Bye for now.

KetanPanchaltalk-TO-me 06:25, 23 May 2008 (UTC)

[edit] Failed GA

I quick failed the GA nomination for this article today due to the presence of a {{copyedit}} template on the article. Ten Pound Hammer and his otters • (Broken clamshells•Otter chirps) 18:28, 27 May 2008 (UTC)

Reverting the "GA quick fail". While the article still clearly has issues, a quick fail will not help editors to improve the article at this time. More comments are needed. Dr. Cash (talk) 19:05, 27 May 2008 (UTC)

[edit] GA Review

This review is transcluded from Talk:Polyclonal response/GA2. The edit link for this section can be used to add comments to the review.

Hello!

I have renominated the article after addressing the issues raised by Narayanese on the talk page of the article, and also making other changes as thought appropriate by me.

Regards.

—KetanPanchaltaLK 18:43, 27 May 2008 (UTC)

I will be reviewing this article over the next couple of days to see if it adheres to the GA criteria. At first glance, I am doubtful of this. The most obvious issues that I see thus far include:

  • Numerous violations of the manual of style. For starters, the 'explanation of difficult terms and concepts' is not a section normally included in wikipedia articles, and the use of the two templates combined with the small font text do not adhere to the WP:MOS either. Templates such as those two should only appear at the bottom of an article, at the very end. Difficult terms and concepts should be presented in a more user-friendly manner in the article itself, not with a bold and blatant warning like this, which is really going to do little more than discourage less advanced readers from reading the article. The proper way is to explain these concepts in the article text itself, and use internal wikilinks to let readers learn more about specific terms as they go along.
    • You are very right about the violation of manual of style, in particular, because of incorporating a section of difficult terms. It has been a great challenge to explain the terms within the article as firstly this breaks the flow on many occasions, and secondly, it would be quite beyond to explain certain terms within the main body of the article, say for instance, host and pathogen. Both the terms will find repeated mention in the article, but it would be very weird to actually explain the meanings of these terms, which can usually be taken so much for granted by those even remotely related to the field of biology/medicine, but might confuse those who are unrelated to the field. I can think of totally doing away with explaining them, but that might interfere with their understanding by the so called lay person. Likewise, if I try to explain the functions of the antibodies within the article even in the briefest possible fashion, it would be very much out of scope of the article, and also conflict with the subject matter of the article antibody. But, without doing so, a person unaware of their functions might simply respond like "so what?". I'd be very happy to make the article adhere to MOS to the greatest degree, but not at the cost of intelligibility to a general audience. It is in this respect that I'd like to quote the opening of the WP:MOS—"This guideline is a part of the English Wikipedia's Manual of Style. Editors should follow it, except where common sense and the occasional exception will improve an article." I am not using that as a shield, but, I genuinely feel that the concept inherent in the article cannot be explained (to a general audience) without initial introduction to the terms to be encountered in the article. Of course, I'm most open to suggestions. I'd be very glad if a compromise could be reached between intelligibility of the matter and rigid adherence to the WP:MOS.—KetanPanchaltaLK 23:01, 27 May 2008 (UTC)
  • The names of subsections in the article are very long, and combined with the use of multiple subsection headers, make the table of contents look very "scary" and unhelpful. Section & subsection headers should be short and concise, and should not use the article title (e.g. 'Polyclonal response') in the name of the header (see WP:MSH). Try to minimize the use of subsection headers and only use them where absolutely necessary. A reorganization of some of these sections may be in order; try to somehow "tell a story" -- each section should help the next one out, and lead into it. It's difficult for me to see that that's actually happening here, as it appears to be more bits and pieces of random facts.
    • I have tried to shorten the length of a few section heads, but, I personally felt that in some cases, it is the longer heading that made better sense. Like, "Significance of polyclonal response" would put things much better in context rather than simply "Significance". I also agree that some concepts might be appearing as "bits and pieces of random facts", that's because that's what they are in the context of the article. For instance, how a B cell gets stimulated and costimulated has nothing to do with somatic hypermutaion or affinity maturation. It has also got nothing to do with the concept of original antigenic sin. But yet, it appears in the article because polyclonal response is, after all, all about the B cells getting stimulated. I've maintained a pattern—first, I have introduced the concept at a gross level, and then introduced the subtleties like the original antigenic sin, autoimmunity, affinity maturation, etc.—KetanPanchaltaLK 23:01, 27 May 2008 (UTC)
  • I am very concerned about the 'verifiability' requirement of the GA criteria here. I see lots of information that is not cited with an inline citation, and at least half of all citations provided appear to come from the same textbook. It would be good to not depend so heavily on the same source.
    • A few pieces of information were introduced in the article today, so citations for them didn't appear. The text book I have quoted is a standard one, and actually supports the information I've included in the article. Wherever, some relatively unconventional concepts are involved like the original antigenic sin, or the antigen and antibody slightly altering their conformations to make a better "fit" have been backed by research articles.—KetanPanchaltaLK 23:01, 27 May 2008 (UTC)
  • I see several subsections that have very little text in them (e.g. 'T helper cell stimulation and B cell costimulation', 'Costimulation of B cell by activated T helper cell', most of the subsections under 'Basis of polyclonal response', the entire main section of 'Diversity of B cell clones'), which could either be issues with the completeness criterion of WP:WIAGA, or issues with organization (combine these short subsections into a larger main section).
    • That is because, they are merely expanded explanations of the steps enumerated in the opening of the same section. If you'd see the same sections in the table of contents, it'd make much better sense--

3 B cell response

It shouldn't matter if the text serving as explanation of the step is very short because the concept to be explained itself is short. —KetanPanchaltaLK 23:01, 27 May 2008 (UTC)

  • On the bright side, I don't see any issues with WP:NPOV or stability, so those two criterion are ok. The images are also tagged with appropriate copyright tags.

I'll go ahead and change the GA status to on hold pending revision. Dr. Cash (talk) 19:27, 27 May 2008 (UTC)

I'd be very grateful if apart from pointing out the points in which the article departs from the WP:MOS, I'd be also told how to effectively make them reconcile with it. Surprisingly, I had almost the very same points pointed out to me in the past (especially regarding the long section heads), which I'd altered then, too. But the outcome of those modifications wasn't satisfactory. I think that's because whoever quite used to the usual Wikipedia articles, at first only notices how the article has departed from the guidelines, but not that it'd be very difficult to convey what could be conveyed in the present form of the article, by strictly adhering to all the guidelines.
The fact that article has done well to explain the inherent concept to even a person unrelated to the field is of great satisfaction.
Lastly, I feel, it's the long headings only that can give it a feel of a "story". Still, I assure, am not being adamant. Will try my best to meet the [[WP::MOS]] criteria. Looking forward to some help from you and others, too in this regard.
Regards.
—KetanPanchal[[User

talk:KC Panchal|taLK]] 23:01, 27 May 2008 (UTC)

[edit] Re-review by Dr. Cash

The changes that you've already made to some of the subsection headers seem good, and are MOS-compliant. It seems to make sense. The conversion of subsections in 'significance of polyclonality' isn't MOS-compliant, and should probably be converted back to subsection headers. The 'main article' links go at the top of subsections, not at the bottom, per MOS. I don't like the bulleted list there at all.

I'm not sure if any other title for the said section would adequately convey what is to follow. So, if you have any ideas, I'd like to change it yourself or discuss it over here. —KetanPanchaltaLK 16:43, 6 June 2008 (UTC)

The 'historical' section is very short. Usually, this section is simply titled 'History', not 'Historical'. I see some definite issues with completeness here, though.

To be honest, I wasn't aware of the contributions of the named scientists; I found them in the article clonal selection. But, I've confirmed the accuracy of the statements I've made in the section, so I don't feel there are any issues. —KetanPanchaltaLK 16:43, 6 June 2008 (UTC)

The external link the the 'see also' section needs to be moved to an 'external links' section. It is not necessary to put a 'retrieved on' date for links in this section; just put the link. The retrieval date is only necessary for links used as inline citations.

Y Done —KetanPanchaltaLK 16:44, 6 June 2008 (UTC)

The 'Explanation of difficult terms and concepts' needs to be removed. It's redundant, and the use of the drop-down templates is bad form, and not consistent with WP:MOS. As far as difficult terms and concepts are concerned, this is the exact reason to have internal wikilinks to other articles! If a reader needs more information, they click the link to the other article to get it!

Almost Y Done I think I've explained all the important terms in the sections to follow. Converted the entire section into a hidden comment. —KetanPanchaltaLK 16:43, 6 June 2008 (UTC)

I'm not complaining about the use of your textbook to help build the article -- this is good! But make sure you're not just copying text directly from the article word-for-word, that's plagiarism. I still think it's a good idea to use multiple sources. Do you have any other textbooks? Have you checked PubMed for some of the latest journal articles or studies on the topic? Dr. Cash (talk) 16:55, 28 May 2008 (UTC)

Well, I do have another textbook, but that's a textbook of microbiology, and certainly less detailed than the current one. Plagiarism is almost not an issue, as I'd written the article first, and then tried to look for the corroboratory statements from the said book. But, again don't worry about the accuracy of the concepts I've included&mdashI've made sure they're accurate (even though that was a lot of hard work). The problem with PubMed is that their results usually show articles containing recent research, and not review articles that could serve as sources for the article at hand. Thanks for the suggestion, though. —KetanPanchaltaLK 16:43, 6 June 2008 (UTC)

[edit] Re-re-review by Dr. Cash

I'll look over this article in more detail over the weekend, but I have to say I see a huge improvement! I think we're getting close. There's still an 'expand' tag in the history section, which is a red flag for GA status. The 'Significance of the phenomenon' section is also a little scarce of citations. There's also some "for more details" tags that are at the bottom of sections, which should be moved to the top. That's all I notice right now -- I'll look at it a little more closely tomorrow. But overall, I think we're getting close. Cheers! Dr. Cash (talk) 19:05, 6 June 2008 (UTC)

  • Thanks for the comments. I'll remove the "expand section" tag, though I personally never felt that much more of historical background is required for such a theoretical topic.
  • It's not exactly the "Significance of the phenomenon" article that is lacking in citations, but only the first ("Increased probability of recognizing any antigen") that is. I'd tried to find to citation, but couldn't find a reliable one. I also feel that, it is kind of self-explanatory, and further with the analogy I've given, it should not be considered to be "controversial".
    • Well, now I've added a citation for that piece of claim, too the only problem being, the support for the fact is not the main subject of the citation, and hidden somewhere in the middle-paragraphs. Though some citation is better than none. —KetanPanchaltaLK 21:07, 6 June 2008 (UTC)
  • I've tried to maintain a pattern with regard to the {{main}} and {{details}} templates. The subjects, which are not required in their entirety, but only aspects of which have been discussed, have been incorporated in the {{main}} template, and placed at the top of the paragraphs. The subjects which have been sufficiently explained in the discussed article, and the core concepts of which HAVE been discussed in the article in sufficient details, and which are particularly important in the context of the article have been incorporated in the {{details}} or {{details3}} template and placed at the bottom of the sections. This ensures that, the discussion of the "core" concepts is not interrupted by a tag. Well, do tell me if this is also against the WP:MOS.
Thanks for all your time. Regards. —KetanPanchaltaLK 19:49, 6 June 2008 (UTC)

[edit] Section-by-section discussion

I am introducing a new head for section-wise discussion of polyclonal response. Any one interested in the improvement of article may kindly leave comments under the relevant section heading. If a certain section is deleted, merged or altered in any way, I will try to make corresponding changes, here too, but should that not be possible, I request any one noticing a discrepancy to make the required changes. I have made reading the sections from the article simple. If you are a registered user, and have popups, on, simply point to the relevant section, heading, and you'll see a preview of the same section from the article. Depending upon your browser, and its settings, you can also, simply right-click on the section heading/subheading and open it in a new tab/window. So, happy assessing!—KetanPanchaltaLK 21:55, 28 May 2008 (UTC)

[edit] Article in general

Added the templates {{main}}, {{details}} and {{details3}} at relevant places in the article. —KetanPanchaltaLK 13:48, 28 May 2008 (UTC)

[edit] The lead

I would suggest removal of the "This article deals with...", unless the polyclonal response is not unique to mammals. If its presence is necessary, then it probably ought to be formatted using {{dablink}} (to standardise text size) or one of the other disambiguation templates (to point to another article). Rephrase "a very important component of this response" to "a central component of this response", "a key component of this response", or something similar to avoid using the generic phrase "very important". Link to "soluble". –Black Falcon (Talk) 16:40, 29 May 2008 (UTC)

The immune system may respond in multiple ways to an antigen; a very important component of this response is the production of antibodies by the B cells (or B lymphocytes).
I'm sure we can find a much more concise way to say this, but I'm not sure exactly what it is right now. Perhaps One way that the immune system responds to an antigen is the production..."? WhatamIdoing (talk) 20:39, 31 May 2008 (UTC)
Well, I've employed the {{dablink}}. The problem is I don't know about the immune system in other divisions (hope that's the correct taxonomic term) like the aves and reptiles is similar. I'd feel that it must be similar in them too, but am not sure, so I felt the need for clarification. To remove ambiguity with "very important component", I've replaced it by "a key feature". Hope this change should be satisfactory. I didn't follow the suggestion of WhatamIdoing as I thought the repetition of the word "respond" in two contiguous wasn't "sounding" right. —KetanPanchaltaLK 14:31, 6 June 2008 (UTC)

[edit] Explanation of difficult terms and concepts

The fate of this section is undecided. Might have to be removed as Dr. Cash has objected to its existence. —KetanPanchaltaLK 12:54, 28 May 2008 (UTC)

[edit] Infection

Added this new section, which basically elaborates upon the concepts of host, infection, pathogen, etc. It's a bit short, but expanding it might just make certain info in it irrelevant. But, if any one feels more info in it would do justice, you are welcome to add it. —KetanPanchaltaLK 14:49, 6 June 2008 (UTC)

[edit] Body's response to invading pathogen The immune system

Combine the last two sentences of the first paragraph, by placing the explanation of the term "specific" (i.e. the content of the second sentence) immediately after the word "specific". Or, rephrase the second sentence to avoid the passive voice. (For instance, change "By these responses being specific it is meant that two different pathogens..." to "Specificity means that two different pathogens...".) –Black Falcon (Talk) 16:40, 29 May 2008 (UTC)

I've changed the title as I've added some content, and with it, the current title seems more appropriate. I don't remember if I changed the sentences in passive voice to active voice, or if some body else made those changes, but somehow the issue has been taken care ofsomeone or the other has taken care of the issue. —KetanPanchaltaLK 14:37, 6 June 2008 (UTC)

[edit] B cell response

[edit] Recognition of pathogens

I am tempted to expand the title to "Recognition of pathogens by APCs", but that would make it longer. Comments? —KetanPanchaltaLK 12:53, 28 May 2008 (UTC)

Keep the shorter name, especially when APC is an abbreviation not seen outside the field. Narayanese (talk) 17:20, 6 June 2008 (UTC)

You've fixed the bit about TCR and BCR I complained about before, good job. Narayanese (talk) 17:20, 6 June 2008 (UTC)

Thanks for your comments. Yes, I have made many other changes. What do you feel about its status regarding GA? Regards. —KetanPanchaltaLK 18:53, 6 June 2008 (UTC)

[edit] Antigen processing

Started this new section as antigen processing is an important step before antigen presentation. —KetanPanchaltaLK 12:51, 28 May 2008 (UTC)

[edit] Antigen presentation

[edit] T helper cell stimulation

[edit] Costimulation of B cell by activated T helper cell

[edit] Proliferation and differentiation of B cell

The section now explains well memory B cells are involved in affinity maturation. But it leaves out selection, mutation by itself can never result in a shift toward stronger affinity. And it calls mutation itself the maturation, which is a close but not quite right. Narayanese (talk) 17:11, 6 June 2008 (UTC)

You're certainly right. I've added the point in brackets in the sentence: "Some of the newly created paratopes bind more strongly to the same epitope, which is known as affinity maturation. And others bind better to epitopes that are slightly different from the original epitope that stimulated proliferation in the first place". But, I had any way discussed the subject in greater details in one of the following sections. Thanks. —KetanPanchaltaLK 21:59, 6 June 2008 (UTC)

[edit] Basis of polyclonality

[edit] Clonality of B cells

"Memory and naïve B cells normally exist in relatively small numbers. As the body needs to be able to respond to a large number of potential pathogens, it maintains a diverse repertoire of B cells."-->"Memory and naïve B cells normally exist in relatively small numbers. As the body needs to be able to respond to a large number of potential pathogens, it maintains a pool of B cells with wide range of specificities." Thought that the word repertoire would be complicated for many, and the sentence explains the concept better in its present form. —KetanPanchaltaLK 13:44, 28 May 2008 (UTC)

[edit] Single antigen contains multiple overlapping epitopes

[edit] Multiple clones recognize single epitope

[edit] Multiple clones recognize single epitope

[edit] Diversity of B cell clones

[edit] Recognition of epitope by B cells

"Epitope recognition by B cell": changed the section heading to the current one. —KetanPanchaltaLK 21:55, 28 May 2008 (UTC)


[edit] HistoricalHistory

Added this new section as I found additional information from another Wikipedia article clonal selection. —KetanPanchaltaLK 16:13, 28 May 2008 (UTC)

[edit] Significance of polyclonality

Expanded the title to "Significance of polyclonality" form just "Significance" as this better provides the context to read the text that follows. —KetanPanchaltaLK 14:45, 28 May 2008 (UTC)

[edit] See also

Is the external link to the Aberystwyth University web page directly relevant to this article, or does it have more general relevance to the immune system article? (At first glance, it seems to be the latter.) If it is not directly relevant, it should be removed or incorporated as an actual reference. If it is directly relevant, then it should be placed in a separate "External links" section, which should come after the "References" section. If the link is retained, the text that appears should be rewritten to show the title of the page (or something similar that gives an idea of it's subject). For instance: An Introduction to the Immune System – Aberystwyth University. The "retrieved on" date is not necessary, since external links that are not references are not retained if they become nonfunctional. –Black Falcon (Talk) 16:40, 29 May 2008 (UTC)

Since, the same issue was also raised by Dr. Cash, I'd already put the link in a new section. And, with your pointing out, I've also changed the title (with an additional, bracketed comment though). —KetanPanchaltaLK 14:44, 6 June 2008 (UTC)

[edit] External links

[edit] Notes

[edit] References

[edit] Support

I think it meets the GA criteria now. While most is from a single source, there are no obvious differences from my book The Immune System by Peter Parham (which covers all but affinity maturation and original antigen sin). I intend to write out some three-letter abbreviations though (APC, WBC, TCR). Narayanese (talk) 22:43, 6 June 2008 (UTC)

Thanks for the support. You can of course expand the above-mentioned abbreviations. Though, I've tried to make sure that first usage of each term is in its expanded form. Well, I'd be very grateful, if you could find some more information on the historical aspect and to support the fact that polyclonal response widens the capacity of the immune system to recognize antigens. Thanks again. Regards. —KetanPanchaltaLK 23:32, 6 June 2008 (UTC)

[edit] Full citations in the text

I will leave the GA review to someone who is more experienced in that area (for what it's worth: I haven't studied biology since my first year of university, but I found the article understandable, informative, and interesting to read), but I'd like to suggest one change. I don't think it's necessary to provide a full citation in the "Notes" section for every use of a source that is already listed in the "References" section. For instance,

Goldsby, Richard; Kindt, TJ; Osborne, BA; Janis Kuby (2003). Immunology Fifth Edition. New York: W. H. Freeman and Company, 67. ISBN 0-07167-4947-5. 

could be shortened to:

Goldsby et al, Immunology, p. 67.

or something similar. –Black Falcon (Talk) 19:14, 27 May 2008 (UTC)

[edit] Thanks!

That was a great relief—coming from a person who has not been in touch with biology, that he (I suppose got the gender right) could "understand" the article, and moreover, also find it interesting. I take it is a huge compliment because the concepts involved in the article are fairly advanced in their complexity, and being able to explain them without getting very informal in my approach was really challenging.

Regarding the citations: the citations were indeed in that form at a certain point in time, but changed them to current format as they seem to be better complying with Wikipedia guidelines for inline citations.

Thanks again.

Regards.

—KetanPanchaltaLK 22:56, 27 May 2008 (UTC)

[edit] Another citation comment

Excellent work on the article, people. May I suggest that these references are sorted out to just ONE reference template and remove the page numbers? This will significantly clean up the reference list which is cluttered with a huge number of citations from one book.

Goldsby, Richard; Kindt, TJ; Osborne, BA; Janis Kuby (2003). Immunology Fifth Edition. New York: W. H. Freeman and Company. ISBN 0-07167-4947-5. 

Something like that should replace them all, in my opinion. I'm not sure if the current citations meets guidelines or not, I haven't really checked, but i'm a sucker for neatness in pages. Regards, CycloneNimrod talk?contribs? 15:38, 6 June 2008 (UTC)

Well, Cyclonemin, that would reduce the verifiability factor in the article. It would make much less sense for specific facts to cite a whole book rather than just the specific page/pages. I am going to abbreviate the reference to just "Goldsby, et al". I think that should make the references less cluttered. And, thanks for the compliment. How far do you thing the article has reached to the GA-quality?
Regards.
—KetanPanchaltaLK 17:34, 6 June 2008 (UTC)
Ah I wasn't referring to the length of the reference which makes it cluttered, I was referring to the amount of times it's repeated. But if verifiability is your goal, don't change a thing I suppose, no one will criticise you for it. As for GA status, i'm honestly not sure (not in a bad way, but not in a good way either, very neutral). As far as I can tell it is a well written article in good prose. I still find the images a little too intruding for my liking, if you're worrying about the reader not being able to see all the detail in the image thumbnail I wouldn't bother as they will most likely open the full-sized version if they want detail. They can tell what the image's main focus is on from the caption.
There are several little things that bother me too such as the italic 'See also' text in a lot of the sections. My problem with this is that some are placed at the bottom and some at the top, whereas by convention they should always be at the top of the section. My final worry is that some of the sections are too short, such as the History section which is currently undergoing maintenance, but also the sections on 'Infection' and all subsections in 'Basis of polyclonality'. This may be from lack of information available on the subject in which case you should try your hardest to integrate that information into other sections.
You're certainly on the right track, however, and I implore you to keep working as hard as you have done today alone (24 edits and counting, I see). It's great that you've created an article which you have continued to work on and that you're building it up to a very high standard, this will certainly come across well should you ever decide to apply for adminship. Best of luck, any queries feel free to bring them up here (since i've been watching this page since it's creation) or on my talk page. Regards, CycloneNimrod talk?contribs? 17:51, 6 June 2008 (UTC)

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