Talk:Polyclonal B cell response/Archive 2

Archive 1

Archive 2

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)

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)

Well-written

• It is (supposed to be) well written. In this respect:

  (a) the prose is clear and the spelling and grammar are correct; and

  (b) it complies with the manual of style guidelines for lead sections, layout, jargon, words to avoid, fiction, and list incorporation.

• • 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)

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;

  (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; 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 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)

Images

• It is illustrated, where possible, by images. In this respect:

  (a) images used are tagged with their copyright status, and fair use rationales are provided for non-free content; and

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

• (b) the images are appropriate to the topic, and have suitable captions.

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
  • 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

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)

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.

 Done I have rewritten most of the section. —KetanPanchal^taLK 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.

 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. —KetanPanchal^taLK 18:19, 27 May 2008 (UTC)

• The clonal selection picture's page still needs its description page referenced.

 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. —KetanPanchal^taLK 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.

—KetanPanchal^taLK 18:19, 27 May 2008 (UTC)

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.

—KetanPanchal^taLK 16:07, 26 May 2008 (UTC)

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.

—KetanPanchal^taLK 17:28, 27 May 2008 (UTC)

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)

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.—KetanPanchal^taLK 12:20, 26 May 2008 (UTC)

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)

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.

—KetanPanchal^taLK 12:20, 26 May 2008 (UTC) !!!

REPLY to "GA review 10 May 2008"

writing

• Well written: some things to improve
  • "treatment meted out to" this expression is hard to understand
    •  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
    •  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)
    •  Done I have rephrased the entires section itself.
  • Don't put sup tags around references, it makes lines overlap
    • Thankfully, User:WhatamIdoing has already done that for me. —Preceding unsigned comment added by KC Panchal (talk • contribs) 17:46, 12 May 2008 (UTC)

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
    •  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.
    •  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.
    •  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.
    •  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.

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?
  • •  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)

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.  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)

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)

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)

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)

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)

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 2008-05-12. {{cite web}}: Cite has empty unknown parameter: |coauthors= (help). 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)

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)

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)

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>...} 22:13, 13 May 2008 (UTC)

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.

KetanPanchal^talk-TO-me 16:08, 14 May 2008 (UTC)

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.

KetanPanchal^talk-TO-me 06:25, 23 May 2008 (UTC)

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)

• Gah. Okay, I'm full of crap. I never considered the fact that someone actually did copyedit and forgot to remove the templte. Ten Pound Hammer and his otters • ^{(Broken clamshells•Otter chirps)} 18:39, 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)

GA Review

The GA Review has been archived here. Dr. Cash (talk) 21:57, 17 June 2008 (UTC)

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 (2003). Immunology Fifth Edition. New York: W. H. Freeman and Company. p. 67. ISBN 0-07167-4947-5. {{cite book}}: Check |isbn= value: length (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)

could be shortened to:

Goldsby et al, Immunology, p. 67.

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

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.

—KetanPanchal^taLK 22:56, 27 May 2008 (UTC)

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 (2003). Immunology Fifth Edition. New York: W. H. Freeman and Company. ISBN 0-07167-4947-5. {{cite book}}: Check |isbn= value: length (help); Unknown parameter |coauthors= ignored (|author= suggested) (help)

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.

—KetanPanchal^taLK 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)

How about citing to the chapter in the book instead of the page number? That should reduce the number of refs somewhat, but still provide useful direction to a searcher. Also, there are a couple of refs that are entirely repeated, or which could be switched from "pages 1-2, 7-8" to two pre-existing refs, "pages 1-2" and "pages 7-8". WhatamIdoing (talk) 20:58, 13 June 2008 (UTC)

Hi!

Thanks, Cylonenim and WhatamIdoing!

• • • • Well, I have no problems with incorporating WhatamIdoing's suggestion, but don't see an advantage in doing that. Also, I agree that some references must have got repeated "as is", but I really don't know what to do about them. If one of you could look into it, and make the required edits, that would be nice. I'll introduce the chapter numbers when I get time (mostly, today).
      • The "Infection" section is bound to be short as it's not the thrust topic in the article, but only meant to "ease" the reader into the topic.
      • Other subsections are short as they don't have much information that requires to be put into them. "Basis of polyclonality" has been written in a way that the subsections are actually the bases (reasons) of polyclonality, and the text under each section is just the further expansion of each basis.
      • Again, somehow had missed this thread (particularly Cyclone's response), hence the delayed response. I don't know if it's appropriate to request this, but if it's not much trouble could you please leave a message on my talk page indicating that a message has been left on this page?

Regards. —KetanPanchal^taLK 08:14, 14 June 2008 (UTC)

I named a bunch of the duplicated refs today. Note that the ref for the image is unhappy using a name from elsewhere in the article, but if you see any other remaining duplicates, then please let me know (or fix them yourself). WhatamIdoing (talk) 23:19, 19 June 2008 (UTC)

Yes, I saw the edits you made. I have added a few more citations. Hope that will make the verifiability aspect stronger. Thanks. —KetanPanchal^taLK 14:37, 20 June 2008 (UTC)

As suggested by you previously, WhatamIdoing, I have clubbed the references into respective chapters and cited them. Also, some other citations I have added (the two FASEB articles) are old, but that shouldn't be a reason for worry, I suppose—those facts are unlikely to have changed in the interim. —KetanPanchal^taLK 21:55, 20 June 2008 (UTC)

Looks good to me. WhatamIdoing (talk) 01:03, 21 June 2008 (UTC)

A-class

How does an article get rated as A-class? One has to nominate it or listing it here like how I have done is alright? I might be adding a few more citations. Please do let me know what more improvements will be required for the article to reach the A-class quality? —KetanPanchal^taLK 05:57, 21 June 2008 (UTC)

I don't honestly know. We don't seem to use that process. The article needs, of course, to be in excellent condition to qualify, but I'm not sure what the process is. GA is as high as I've ever bothered with. WhatamIdoing (talk) 06:20, 22 June 2008 (UTC)

In that case I'm nominating it for FA. Hope that's not too ambitious at this stage. But, from my experience with GA, I learnt that real improvements in the right direction occur only after specific deficiencies are pointed out. I think A-class award is much like awarding B-class that' why there's no clear-cut procedure for it, and may be the A class awarding tends to concentrate more on the verifiability aspect. —KetanPanchal^taLK 10:45, 22 June 2008 (UTC)

---

Top

Image placement

Hi, I suggest not sandwiching text between your figures—it's frowned upon. Graham. GrahamColm^Talk 21:39, 22 June 2008 (UTC)

Was that in reference to the top two images flanking some text between them? If that's the case, then it was a mistake, as I'd simply copy and pasted the first image from down the image, and corrected it immediately. If this remark is for some other image, please point out specifically as I am not able to get you. Thanks. —KetanPanchal^taLK 21:53, 22 June 2008 (UTC)