Wikipedia:Featured article candidates/Virus

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The following is an archived discussion of a featured article nomination. Please do not modify it. Subsequent comments should be made on the article's talk page or in Wikipedia talk:Featured article candidates. No further edits should be made to this page.

The article was promoted by User:SandyGeorgia 01:46, 23 September 2008 [1].

Virus[edit]

Nominator(s): Graham Colm Talk
previous FAC


Nomination - A huge subject and a large article. I have been working on this on and off since the last FAC was archived nearly a year ago. It is a technical and often difficult subject and with this in mind, I wrote Introduction to viruses which was promoted to FA earlier this year. Viruses occupy a world unfamiliar to most of us; the sub-microscopic, and they are best described in the language of molecular biology—the language of DNA, RNA and proteins. I am mindful that this language may render the article difficult for some readers, but I hope that the introductory article will help them break this barrier. My on-going project is to improve the coverage of viruses and virology on Wikipedia and clearly this article is the keystone. I have used the PubMed database, and four textbooks as sources for the article, three well-established and one that is a newcomer. The images were either created by me or have been taken from Commons. I cannot see any licensing issues. As always, I thank all the other editors who have contributed to this and whose names can be found in the article history but stress that any remaining errors are probably all my own work. Graham Colm Talk 12:49, 15 September 2008 (UTC)[reply]

Support I read this prior to nomination, although I am not a contributor apart from a few minor copy edits. It has undergone further refinements since then, and I believe it is now a highly readable article given the complexity of its subject matter. Assuming no major problems being unearthed by others, I am happy to support this. jimfbleak (talk) 05:57, 16 September 2008 (UTC)[reply]

Response Thanks for your pre-FAC comments and support. Graham Colm Talk 14:57, 15 September 2008 (UTC)[reply]

Support—I think it is FA-worthy and can only improve during the FAC. Comment—A good article on the topic, but I have a few suggestions and concerns:

  • Suggestions:
    • There are many brief, single-paragraph sections which give it a cluttered appearance. (See the second paragraph of Wikipedia:Layout#Headings_and_paragraphs.) Could some of these be merged so as to shorten the ToC?
    • It seems like HIV is used a number of times as a sole example. Perhaps a broader mix of examples would be beneficial where that occurs?
    • Perhaps "Lifeform question" belongs in the same discussion (as a subsection?) as "Origins"?
    • Do the "Bacteriophages", "Viruses of Archaea" and "Viruses of plants" belong as subsections of a common section? Perhaps on specialization?
    • "Laboratory diagnosis" seems out of place. Doesn't it belong with "Prevention and treatment"?
    Concerns:
    • "When diagnosing Hepatitis B virus infections, it is important to distinguish between acute and chronic infections." Why is this? How is this relevant to the subject matter? It is unclear to me.
    • The first paragraph of "Epidemics and pandemics" seems polemic as it doesn't bother to explain the section title and it is not clear how it relates to viruses. Can this be explained better in the context of the example? Was it an epidemic or a pandemic? Perhaps the section needs an explanatory paragraph first?
    • Why does "Epidemiology" only cover the transmission aspects? If it is also about control, why isn't that covered? Perhaps it should have a different name?
    • The first paragraph of "Life sciences and medicine" is unsourced, and I'm not sure about the second as the ref. is very specialized.
    • In the reference containing "The British, the Indians, and smallpox", could the format of all the entries be brought in line with the other citations (including links)?
I hope these were somewhat helpful. Thank you!—RJH (talk) 19:54, 15 September 2008 (UTC)[reply]

Responses from Graham Colm Talk

  • Bob, thanks for your very helpful edits, and for these suggestions and comments. I have made these changes to the article based on your review.[2]. I don't think I have overused HIV as an example but I have made good use of it because it's the one virus most people know something about. With regard to the non-animal viruses in one section, I'd rather not. As they stand they can be partially linked to from other articles without having to be fully linked to Virus. Thanks for an useful review; it has kept me busy this morning. Graham Colm Talk 11:29, 16 September 2008 (UTC)[reply]

Inquiry: The article is quite homo-centric, is an Influenza "Infection in other animals" type section not appropriate on this page as well? 69.196.145.66 (talk) 20:32, 15 September 2008 (UTC)[reply]

Response- I agree with you and thank you for this valid comment. Viruses are a very important cause of diseases in other animals. Canine parvovirus and Foot and mouth disease for examples. A section about viral infections of other animals is missing. I will write one. Thanks for pointing this out. Graham Colm Talk 20:53, 15 September 2008 (UTC)[reply]

Comments / borderline object for now minor object for now This is one of Wikipeida 1.0's 150 Core topics, so this article has to be extra exemplary. Certainly up-to Good Article standards but I'm not sure if it is A-class yet content- or organization-wise (I'm not commenting on MoS or minor grammar FA requirements):

    • Lead section: Pretty good; covers the major aspects and is a highly readable to non-specialists. But some inline cites may be needed (figures and facts likely to be disputed need cites). Some short mention of discovery history may be in order, but size of lead is already on the long side, so some reorg/trimming may be needed.
    • History section: May need more. I'd like to see multiple sub-sections on the history of discovery and major advances. As is, the section reads more like a lead section to an unwritten History of... article.
    • Origins section: Good start,but I'd like to see each point expanded on with an evolutionary bent. Any good microbiology textbook should have enough material to use to expand this section. ed: (see below)
    • Structure section: Very good start, but as noted above, is too sub-sectioned. Consider combining similar sections thematically. Then make sure that the newly adjacent paras flow one to the other.
  • Also, the sections about viruses that attack bacteria, plants, animals should be discussed under a single section. Some compare and contrast may be in order to introduce the subsections (perhaps discuss the common modes of infection/integration). A clearer organization may be needed; I'd like to see the ==Replication== section expanded to cleanly go through the whole "life cyle" of typical viruses (with some explanation on how animal- vs plant- vs bacterial-infecting viruses differ), from infection, replication, host defense, and re-infection (how do viruses find other hosts?). As a matter of fact, maybe my thoughts in the last two sentences should be combined to reduce repetition. That should be enough for now. --mav (talk) 03:01, 16 September 2008 (UTC)[reply]

Responses from Graham Colm Talk Daniel, thank you for this helpful review. I have incorporated most of your recommendations. I haven't changed the Replication section much because there is little difference between plant and animal viruses in this respect. The bacterophages should have their own diagram really, but this would be too much to put in a general article on viruses and it would be better to improve Bacteriophage. There is not much more I can say about the origins of viruses. All we have is the two or three half-baked theories. I bought yet another book on virology yesterday, (the Dimmock one),but this has been of little help in this respect. In fact it has less to say.I I could expand this section a little but it would get dangerously close to original research. I have tidied the section on structure and added a new diagram. I took on board you concerns about the flow of the prose and merged a few short sections; it's not perfect but it is much better. Oh, and I added some in-line citations to the Lead. Thanks again for your valuable comments. Graham. Graham Colm Talk 15:43, 16 September 2008 (UTC)[reply]

  • Great work so far. But as I note, this is a core article so more work is needed ; but you are certainly on track. I struck some items but left others; I'll have to dust off my biology textbooks to provide more feedback. I know from experience how hard it is to bring vital articles to FA; I can't imagine how hard it would be to bring a core topic to FA. Kudos to you and all the other authors of this article! --mav (talk) 03:04, 18 September 2008 (UTC)[reply]
  • My microbiology textbooks must still be in storage so I can't look at them (I should buy new ones anyway).
    1. But Campbell's Biology (1996) p. 335 does have a section on evolution of viruses. Sadly, it looks more impressive before one reads it; mostly fluff and it only explains the cellular origin theory. Two interesting bits of info there but not at virus#Origins are a mention of transposons ("jumping genes") as a possible precursor of viruses (along with plasmids) and a plausible-sounding piece of evidence backing-up the theory; that "... a viral genome usually has more in common with the host cell's genome than with the genomes of viruses infecting other hosts." That, along with a sentence or two explaining how plasmids work and are similar to viruses are the type of thing I'm talking about.
    2. Also, I'm a bit surprised that there is no mention of prions or viroids. I'd expect an article on viruses to mention them and have a para or two (I'm not asking for much) that quickly introduces them and explains the most important differences with viruses. The Origins section is probably the best place for that info.
    3. One last thing for tonight: Please quickly explain jargon (linking alone is not enough). For example, "Viruses are released from the host cell by lysis." means next to nothing to somebody not already familiar with biological concepts. Context is needed in the form of an additional phrase or sentence in this article to prevent the reader from loosing interest or breaking the flow of reading by having to click on that link to find out what lysis is and how that relates to the sentence she just read. A better sentence would be "Viruses are released from the host cell by lysis; a process that kills the cell by bursting its membrane." The next sentence is a bit better; "Enveloped viruses (e.g., HIV) typically are released from the host cell by budding." b/c 'enveloped viruses' are explained in a previous section (by that name even) and 'budding' is at least a word also used in a similar context colloquially. But a follow-up sentence would be good to have. Unfortunately, that sentence is rather info-dense and has some more unexplained and, IMO, unnecessary jargon; "During this process, the virus acquires its phospholipid envelope which contains embedded viral glycoproteins." Yikes! This is the first time 'phospholipid' and 'glycoprotein' are mentioned in the article. The sentence really needs to be broken in two and I see no need to even mention phospholipid in this section (that can be done in the section on envelopes): "During this less-fatal process, the virus acquires its envelope by 'stealing' part of the host's cellular membrane. Glycoproteins – proteins that are combined with polymers of carbohydrates – are added to the developing envelope during budding." That is from memory, so the facts may be a bit off, but I hope you get the idea. These are just a couple examples; please look for and fix others.
  • I know that Introduction to viruses exists, but all we need at virus to make it more accessible and readable is to add a few extra words here and there to provide enough context and info to explain the extra jargon. Assume intelligence and a desire to learn in readers, but also assume they have no specialized knowledge of the subject area already. --mav (talk) 04:53, 19 September 2008 (UTC)[reply]

Support For such a complex subject, this is very readable. Well done. One missing small sub-section is Immunoglobulin for prevention of infection within the "Prevention and treatment" section. Do you need the "See also: virology " -- it is linked in the lead? Colin°Talk 17:51, 16 September 2008 (UTC)[reply]

  • Thanks for your support Colin, I will added a cited sentence or two about passive immunotherapy, although it is used, (in the UK), mainly for Varicella infections during pregnancy. I will delete the See Also to virology. Graham Colm Talk 18:53, 16 September 2008 (UTC)[reply]

Oppose. This article should be species-neutral. Although viruses are an important topic in medicine and human disease, they are also important in science in relation to other species. Relating to other animal species, they are important in zoology, veterinary science, and genetics (transfection techniques). They are important also in other types of organism (in plants, relating to agriculture and botany; in bacteria, relating to biomedical science). For this reason, I fail to see why the main virus article should be so human-centered. My suggestion is that the article virus describe viruses in a species-neutral fashion (retaining most of the content of the current article) and human-related content should be moved to a human virus article. In the main virus article, a section would deal with viruses relating to different types of organism (each in subsections): animal (with a "Human" subsection), plant, bacterial, fungus, protist). --Oldak Quill 18:14, 16 September 2008 (UTC)[reply]

    • (If I may) I have to say I disagree. It is only really the disease section that is human specific and the relative importance of that compared to the "in other species" section is appropriate weight for an encyclopaedia read by humans. Colin°Talk 18:36, 16 September 2008 (UTC)[reply]
    • While the section on virus-caused disease is perhaps a bit on the long side, I don't agree that the article on the whole is overly human-specific. Once that section gets much longer, then it should be spun into a daughter article and a good-sized summary left here; this is the natural growth cycle of larger articles. But we are not there yet. I would like to see the 'Infection in other species' section expanded though. So while I do see a valid oppose here, I don't agree that the article must be strictly species neutral. Some work is needed in this regard, but not to a major extent. --mav (talk)
      • As a way to balance this you could add some plant examples to the text. For example in the Penetration section of the "Replication cycle" section you could mention that plant viruses can spread through plasmodesmata. Tim Vickers (talk) 16:00, 19 September 2008 (UTC)[reply]
        • Thanks Tim, I've made a note of this. I will incorporate this later. I can't face any more editing today. :( Graham. Graham Colm Talk 16:47, 19 September 2008 (UTC)[reply]
          • I've added this myself, also expanded the bacteria section (did you know there are up to 3x108 bacteriophages/ml in seawater). Tim Vickers (talk) 18:56, 19 September 2008 (UTC)[reply]

Response from Graham Colm Talk Viruses of species other than humans are described in the article. The disease section does concentrate on infections of humans and bearing in mind WP:Weight, I have gone into more detail in this section because this is what most readers will be interested in. Graham Colm Talk 18:48, 16 September 2008 (UTC)[reply]

      • Taking account these responses and WP:Weight, I still oppose the article in its current form. Even writing an article with human readers and importance to humans in mind, the article gives undue weight to viruses in humans. The term "virus" is not specific to humans and should be defined as broadly. In terms of the disease section, it is misleading to imply that only humans are affected by virus-caused disease. Virus-caused disease in non-human species is important to humans also. Agriculture is an example that comes to mind (crop yield and livestock). I think the "Disease" (treating humans) and "Other species" (treating non-human species) sections could be merged, with human disease as a shorter subsection of "Viruses in animals". A separate article on "human viruses" could be branched off and would serve those looking for information relating only to humans. As the article stands, it uncomfortably treats the general characteristics of viruses (as they affect all species) and the characteristics of human-specific viruses together and without clear demarcation. This is particularly noticable in the "Viruses and disease" section where humans are solely dealt with and little suggestion that viruses cause disease in all types of organism is given. --Oldak Quill 19:59, 16 September 2008 (UTC)[reply]
Response I have expanded the section on other species and added this template below the header:
Main article: Animal virology
Graham Colm Talk 20:04, 16 September 2008 (UTC)[reply]
  • ...and I see that you have changed the heading to Viruses and human disease. This is a good idea. Thanks for this. Graham Colm Talk 20:23, 16 September 2008 (UTC)[reply]
*I strongly contest this opposition. The article gives a broad definition of viruses. The first viruses mentioned are those that infect plants. The historical section describes the early research on bacteriophages; the viruses of bacteria. The sections on classification, structure and replication pertain to all viruses of all species. There is a good section on viruses of non-human hosts; other animals, plants, bacteria, and archaea. I agreed to the renaming of the viruses and disease section: this was a good idea. The links are sufficient to aid the readers' finding articles on viruses of non-human hosts. This is an entry in an excellent and respected encyclopedia; written in summary style. Graham Colm Talk 22:17, 17 September 2008 (UTC)[reply]
I have withdrawn my opposition. The sections which emphasize humans are more clear that they emphasize humans in particular, and other species are reasonably dealt with in other sections. Thank you for your work on this. My concern that a separate article should focus on viruses which affect humans is unrelated to this featured article candidacy. I do think that this article should be more species-neutral, but that is an opinion tempered by the the quality of the article and by the consensus that the current article reasonably balances human-specific and more general information. --Oldak Quill 00:44, 21 September 2008 (UTC)[reply]

Comment — This is a pretty good article. I nevertheless have spotted an issue that should be fixed: in the lead, it is said that "Plant viruses are often transmitted from plant to plant by insects and other organisms, which are known as vectors." As I understand it, the use of the word "vector" is not limited to plant virii, as the sentence there implies. This sentence, and/or perhaps those immediately following it, could clearly use some rephrasing. {{Nihiltres|talk|log}} 15:49, 17 September 2008 (UTC)[reply]

Response - from Graham Colm Talk Thanks for the praise; it is much appreciated. With regard to your concern about vectors, I don't think the article gives the impression that this term is solely used in the context viral transmission. I could change the "are called" to just "are", but it's linked to a good definition which clearly defines their role in infectious diseases. Graham Colm Talk 18:55, 17 September 2008 (UTC)[reply]

Comments

  • Current ref 22 has no publisher or last access date (ICTV list of virus ..)
  • Current ref 67 (ICTV Master Species list) has no publisher or last access date
Otherwise sources look good, links checked out with the link checker tool. Ealdgyth - Talk 19:27, 17 September 2008 (UTC)[reply]

Response - Thanks Ealdgyth, I have fixed these. Graham Colm Talk 20:31, 17 September 2008 (UTC)[reply]

Support—Generally well-written; haven't looked at anything but 1a.

  • "Electron M/micrograph"—inconsistent, and the M unnecessary. Is "H/herpes" necessary as H? Tony (talk) 09:47, 18 September 2008 (UTC)[reply]

Response —Thanks Tony. I've audited for Herpes: if it's the name of the virus, as in Herpes simplex virus it's upper-case; when it means the disease herpes, it's lower. I think I've got them right. Graham Colm Talk 11:23, 18 September 2008 (UTC)[reply]

Status - from Graham Colm Talk 15:13, 18 September 2008 (UTC) I have edited and expanded the article in light of the helpful reviews above. Two of Mav's comments remain unresolved. The difficult one is the Origins section. I cannot give the detail that Mav has suggested—it doesn't exist really. I think if I made an attempt to expand this section further I would be in danger of breaching WP:OR. I experimented with subsections of the History but reverted them; they didn't work. I have broken up the text with two images instead. In contrast, joing-up the Structure section, (as suggested), made it too complicated; I prefer to have smaller digestible sub-sections here. In short, I think all the major issues have been addressed. Graham Colm Talk 15:13, 18 September 2008 (UTC)[reply]

See my responses above. A bit more can be added, me thinks, w/o going into OR. Specifically, more context to explain jargon. History is now fine. I'll have to look at the Structure section closely to see what can be done, if anything. --mav (talk) 04:53, 19 September 2008 (UTC)[reply]

Response - I have made these changes [3]. I have elaborated the discussion on Origins and described how viroids, transposons and prions support the theories without, I hope, introducing any of my own ideas. I am constantly tweaking the text to clarify jargon but it's often hard for an expert to spot. I have been speaking this crazy language all my adult life ;-) Thanks again for your comments; they have helped to improve the article, so it has been a pleasurable challenge for me. Graham Colm Talk 12:47, 19 September 2008 (UTC)[reply]

  • Great work! I struck-out some more completed items from my comments. I'll have to re-read the whole article and its Encarta and Britannica counterparts a few times before I can consider striking my now minor objection through. Perfection is not needed, but a core topic FA really needs to shine well above our competition. If needed, we can reboot this FAC if it becomes inconclusive. But I'm certain we will get to FA so long as you keep up your excellent work! --mav (talk) 14:23, 20 September 2008 (UTC)[reply]
        • It can't go on commons, but low-resolution images of famous historical figures are perfectly acceptable under the Wikipedia fair-use policy. We can use a local version of this image instead. Tim Vickers (talk) 18:26, 19 September 2008 (UTC)[reply]
          • Note: I have written to Delft University of Technology in The Netherlands, where the Beijerinck Collection is housed and asked if they could release a free image to the project. Graham Colm Talk 13:19, 20 September 2008 (UTC)[reply]
    • Image:Rosalind Franklin.jpg - the image's source page does not assert federal authorship; what is the basis for that claim? The {{PD-USGov-NIH}} template (also used on this image) explicitly warns that "NIH frequently uses commercial images which are not public domain" and requires verification of federal authorship.
    • Image:Tobacco mosaic virus structure.png - needs a verifiable source
    • Image:Icosahedral Adenoviruses.jpg - appears to be a derivative (combination of "two adenoviruses" and a "cartoon"); are both the background adenoviruses and the cartoon original creations by the stated author, or did the stated author merely combine existing images?
      • They are both mine, I took the original electron micrograph and drew the icosahedron in PowerPoint and combined them using Paint Shop Pro. I have tagged the image to this effect.
    • Image:Influenza geneticshift.jpg - needs a verifiable source
    • Image:Phage.jpg - needs a verifiable source
      • This is one of mine and I have tagged it as such. Graham Colm Talk 17:43, 19 September 2008 (UTC)[reply]
        • This was uploaded and released under the GNU license by the author. Unless you have reason to doubt their statement of authorship (and they have produced a lot of other illustrations) there is no reason not to accept this. Tim Vickers (talk) 18:12, 19 September 2008 (UTC)[reply]
          • GrahamColm fixed it. Please read comments critically; I didn't say anything about its acceptability, I said it did not indicate a source. Эlcobbola talk 18:16, 19 September 2008 (UTC)[reply]
    • Image:Gene therapy.jpg - needs a verifiable source (a hitherto deleted en.wiki image is not acceptable; how can we verify this is the work of the NIH?)

Эlcobbola talk 17:16, 19 September 2008 (UTC)[reply]

Response - Thanks for the audit, I will delete the dodgey images and I have tagged my own with an explicit assertion of authorship. Can you or someone confirm the status of the image I borrowed from Influenza? Graham Colm Talk 17:43, 19 September 2008 (UTC)[reply]

  • I've e-mailed the author/uploader, hopefully they'll add the appropriate tag. Tim Vickers (talk) 18:14, 19 September 2008 (UTC)[reply]

Comment Do you think Virophage are too new to be added? Satellite viruses have been known for a while though. Perhaps a section on virus/virus infections in the "other organisms" section? Tim Vickers (talk) 18:59, 19 September 2008 (UTC)[reply]

  • "Great fleas have little fleas upon their backs to bite 'em, And little fleas have lesser fleas, and so ad infinitum."

We have mentioned satellites, (the delta agent), would it help? I not sure, it might confuse. Graham Colm Talk 19:16, 19 September 2008 (UTC)[reply]

Actually I think you're right. The viroids section covers this adequately. Tim Vickers (talk) 19:23, 19 September 2008 (UTC)[reply]

Status - as I see it. Sources and image issues have been resolved. All of Mav's concerns have been addressed, except a concern with some of the jargon. Consensus has been reached with regard to the opposition based on the length of the human disease section compared to diseases in other hosts. There are no issues with the general prose. The was only a minor objection to comprehensiveness, but this was quickly withdrawn. At least one other expert editor has read through the article. With regard to the percieved problem with jargon, I and others are constantly working on this. As Mav said, "perfection is not needed, but a core topic FA really needs to shine well above our competition" — I think Virus does. Graham Colm Talk 17:16, 20 September 2008 (UTC)[reply]

  • Actually, I changed my 'object for now' to a 'minor object for now'. I won't know for sure if virus beats EC and Encarta versions until I thoroughly go over each. But so far, I'm leaning in your direction. --mav (talk) 20:57, 20 September 2008 (UTC)[reply]
  • ....and I have drawn two new and free-of-charge pretty pictures. Graham. Graham Colm Talk 21:08, 20 September 2008 (UTC)[reply]
    • Wow - I just realized that you created many of the wonderful images in this article. Those look as good as what I've seen in textbooks. Great work! --mav (talk) 21:18, 20 September 2008 (UTC)[reply]

Comment: "The production of interferon is an important host defense mechanism" this needs to be integrated better, preferably near the dsRNA mention. "Viruses are an established cause of malignancy in humans and other species" malignancy is an unnecessarily difficult word. And why the scare quotes around neurotropic viruses? Narayanese (talk) 17:56, 21 September 2008 (UTC)[reply]

  • Thanks for spotting these. I have removed the quotation marks, expanded the sentence about interferon and moved it. I have explained malignancy by adding cancer. Graham Colm Talk 18:16, 21 September 2008 (UTC)[reply]

Status:- as I see it on day eight: The article's candidature is well-supported apart from Mav's minor, borderline objection, which will be resolved, one way or the other, after he has checked-out Wikipedia's competitors, (are there any :-)? I was very pleased to see that an expert on RNA interference, and an editor of virus, has commented on the article. I am particularly pleased that a consensus has been reached about the emphasis placed on human infections. Graham Colm Talk 21:09, 21 September 2008 (UTC)[reply]

Update - I have had a reply from Dr L. A. Robertson, Custodian of the Beijerinck Archive in Delft, and she is sending me a copyright-free photograph of Beijerinck to included in the article. I am very grateful to her. Graham Colm Talk 19:43, 22 September 2008 (UTC)[reply]

  • Note, please review the two dab links identified in the dabfinder (and reviewers should be checking for that, not me). SandyGeorgia (Talk) 01:12, 23 September 2008 (UTC)[reply]
The above discussion is preserved as an archive. Please do not modify it. No further edits should be made to this page.
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