Wikipedia talk:WikiProject Microbiology/Archive 4

Thomas Brock
Help requested with creating a biographical article about microbiologist Thomas Brock. His full name is Thomas D. Brock. Thanks. Viriditas (talk) 00:53, 9 January 2009 (UTC)


 * As for the name, you could put it at Thomas D. Brock (I don't really know if that is better or worse than Thomas Brock (biologist) - see Manual of Style (biographies)). What else did you want help with?  I'm not sure what to say other than generic advice like WP:WELCOME, google scholar, etc. Kingdon (talk) 18:12, 9 January 2009 (UTC)
 * Many WikiProjects have a requested articles queue. I failed to find the one for this project, so I am requesting its creation on this talk page. Viriditas (talk) 11:51, 10 January 2009 (UTC)

I've created the stub, Thomas D. Brock. Please help out if you have time. Thanks. Viriditas (talk) 16:00, 13 January 2009 (UTC)

Proposing delisting of rabies as Good article
I was surprised to find rabies was listed as a Good article. In its present state, I believe it fails to meet the criteria, and would therefore propose delisting. Please add your comments to the appropriate section of the rabies talk page. Espresso Addict (talk) 15:52, 12 January 2009 (UTC)

Sec proteins
Someone created an article on Sec proteins, which was subsequently tagged for speedy deletion. The term appears valid, per Google and Google Scholar search, but I don't have the knowledge or ability to do anything more with this article. --Aude (talk) 17:17, 14 January 2009 (UTC)


 * I've redirected to Translocon, which is the complex that these proteins form. Tim Vickers (talk) 17:27, 14 January 2009 (UTC)


 * Sounds good. Thanks for doing that. --Aude (talk) 17:27, 14 January 2009 (UTC)

Naming convention
It has been suggested that Wikipedia change its naming convention for all articles on biological organisms to use scientific names. This is being discussed here at WP:NC. It may be in your interest to take part. --Jwinius (talk) 15:06, 1 February 2009 (UTC)

Phagocyte
Hi, has anyone got the time and inclination to do a peer review? Peer_review/Phagocyte/archive2. Graham. Graham Colm Talk 20:38, 14 February 2009 (UTC)

Alga Stub Merge and Redirect, Urgent help needed
So if you've been paying attention to the new pages today, theres a bot called Anybot producing dozens of alga stubs with information from Algaebase. Currently there are around 2000 of them. Normally this would be a good thing, but the problem is that many of these have existing articles that are under basionyms. These basionyms need to be merged and redirected into their new articles. However, with the sheer number of stubs, and me being the only one working on it, I need some help. If you find a stub with no species info on it, go to algae base and search the stub name, and look for any basionyms. If you find one, merge and redirect the wikipedia article. You can find more info on the Anybot's talk page. Thanks, FingersOn  Roids  00:16, 22 February 2009 (UTC)

I suggest doing more than that before nominating any of these articles for deletion. To take one of FingersOnRoids' deletion nominations as an example: Xe nominated Abratopdinium for deletion for containing no species, but a quick search reveals the existence of Abratopdinium cardioforme and Abratopdinium kerguelense. It might be worth reviewing the other proposed deletions, all made on these same grounds, too. Uncle G (talk) 02:22, 23 February 2009 (UTC)


 * Well, the reason for that was because Algae base says the species are "of uncertain taxonomic status". I was thinking that it didn't warrant an article if the species wasn't official, and if new information came up, we could review if it warrants an article. I based all of my WP:PRODs off of that, Unless you disagree? I'm open to others' opinions. FingersOn  Roids  02:29, 23 February 2009 (UTC)


 * I removed the prods that I found, as they all said they were prodded because there was no basionym to redirect the article to, which makes no sense. I see it says it vice versa here, which actually makes some sense, redirecting the basionym to the current taxonomically valid name, but I could only go by what is on the prod, and deleting is not the answer.  --KP Botany (talk) 07:08, 23 February 2009 (UTC)

Algae at WP:PROD
A bunch of algal genuses have been sent for deletion at WP:PROD. 76.66.193.90 (talk) 06:31, 23 February 2009 (UTC)
 * This is also being discussed at User talk:Anybot (search for FingersOnRoids, the user who PRODded them) and Wikipedia talk:WikiProject Plants. Personally, I don't have a strong opinion one way or the other.  Since these are bot created articles, there isn't any great loss if they are deleted, but having them stick around until/unless someone can find some accepted species or make them a redirect or whatever is probably also OK. I think FingersOnRoids means "accepted name" or "genus to which all the species got moved" or something of the sort rather than basionym, but the finer points of taxonomy usually get my head spinning, so I could be saying it wrong. Kingdon (talk) 15:57, 23 February 2009 (UTC)

Coordinators' working group
Hi! I'd like to draw your attention to the new WikiProject coordinators' working group, an effort to bring both official and unofficial WikiProject coordinators together so that the projects can more easily develop consensus and collaborate. This group has been created after discussion regarding possible changes to the A-Class review system, and that may be one of the first things discussed by interested coordinators.

All designated project coordinators are invited to join this working group. If your project hasn't formally designated any editors as coordinators, but you are someone who regularly deals with coordination tasks in the project, please feel free to join as well. &mdash; Delievered by §hepBot  ( Disable )  on behalf of the WikiProject coordinators' working group at 06:00, 28 February 2009 (UTC)

Article alerts
This is a notice to let you know about Article alerts, a fully-automated subscription-based news delivery system designed to notify WikiProjects and Taskforces when articles are entering Articles for deletion, Requests for comment, Peer review and other workflows (full list). The reports are updated on a daily basis, and provide brief summaries of what happened, with relevant links to discussion or results when possible. A certain degree of customization is available; WikiProjects and Taskforces can choose which workflows to include, have individual reports generated for each workflow, have deletion discussion transcluded on the reports, and so on. An example of a customized report can be found here.

If you are already subscribed to Article Alerts, it is now easier to report bugs and request new features. We are also in the process of implementing a "news system", which would let projects know about ongoing discussions on a wikipedia-wide level, and other things of interest. The developers also note that some subscribing WikiProjects and Taskforces use the  parameter, but forget to give a link to their alert page. Your alert page should be located at "Wikipedia:PROJECT-OR-TASKFORCE-HOMEPAGE/Article alerts". Questions and feedback should be left at Wikipedia talk:Article alerts.

Message sent by User:Addbot to all active wiki projects per request, Comments on the message and bot are welcome here.

Thanks. — Headbomb {{{sup|ταλκ}}κοντριβς – WP Physics} 09:24, 15 March, 2009 (UTC)

Photosynthetic vs Photoheterotrophy
Hi, I'm Jon and I haven't edited pages since 2006 so I'm not sure how to go about changing things. I wanted to point out some widespread misinformation on organism pages about photosynthesis.

Basically the pages say "photosynthesis" if the organism has phototrophic abilities in general, but the definition of photosynthesis as I've learned it is "using light directly for biosynthesis" or photoautotrophy. These pages are a few examples: http://en.wikipedia.org/wiki/Heliobacteria http://en.wikipedia.org/wiki/Chloroflexi

Also, the Purple Sulfur and Purple Non-Sulfur Bacteria are currently combined into Purple Bacteria and should be separated from each other. My rational for this is that only the sulfur bacteria use photosynthesis (photoautotrophy, while the PNS use photoheterotropy.

I'm basically proposing that all pages with phototrophic bacteria be checked for this misinformation and changed to reflect either the photosynthetic/photoautotrophic or photoheterotrophic metabolisms of the organism.--Jonthecheet (talk) 06:27, 16 March 2009 (UTC)


 * Thanks for bringing this up. Your definition of photosynthesis seems to match the one at photosynthesis and  (although some dictionaries give a more general definition, I wouldn't read too much into that especially in a non-specialist dictionary). I made a stab at fixing Chloroflexi, but I'm a bit reluctant to dive into harder tasks like properly separating Purple bacteria and Purple sulfur bacteria because I'd have to learn a lot of background knowledge to do this properly. As for how to change things, asking here is a good step and if there is anything we can advise on, please ask. Failing that, don't be too afraid to WP:Be bold. Kingdon (talk) 12:42, 17 March 2009 (UTC)


 * Oh, and from the point of view of Make technical articles accessible, watch out for the potential confusion between Phototropism and phototrophy (it doesn't mean to avoid the latter term, just to think about whether the context is one where the reader can be expected to know/learn it versus more of an introductory section). Kingdon (talk) 12:46, 17 March 2009 (UTC)


 * I've always tried to use "photosynthesis" as an equivalent term for photoautotrophy, although this word is sometimes used much more loosely in the literature. Tim Vickers (talk) 16:11, 17 March 2009 (UTC)


 * I've tried to do the same thing, but my motivation is that my professors would fail me on the spot. Plus I feel using photosynthesis so broadly fails to accurately describe an organism's metabolic lifestyle. BTW I was wondering if I could add myself to the microbiology project. I feel I've picked up a significant amount of knowledge through my courses at UC Davis. I'm not sure if I'm supposed to ask permission from someone or if there is someone in charge here.--Jonthecheet (talk) 20:13, 17 March 2009 (UTC)


 * Feel free to add yourself to the project. Whether you are editing microbiology articles and participating on this talk page is actually more important than the list of participants, but the list is for anyone who wants to add themselves (no approval needed). Kingdon (talk) 14:20, 18 March 2009 (UTC)


 * I just made my attempt to remove the mention of carbon fixation from Chloroflexi because of its association with photosynthesis. I think a later edit should either mention that carbon is not fixed, but I'm not sure how detailed this should be mentioned.--Jonthecheet (talk) 20:05, 17 March 2009 (UTC)

Category:Species by year of formal description
Hi, folks. I recently opened a discussion at WT:TOL that needs your input regarding the categorization of species by year of description. See Wikipedia talk:WikiProject Tree of Life for more info. Thanks! --Rkitko (talk) 23:11, 28 March 2009 (UTC)

Fungi at peer review
Hi, I've put this important core article up at peer review, and would be very appreciative of any comments you might have to improve it. Thanks Sasata (talk)

Article request

 * Perhaps someone could create an article about Streptococcus iniae, as I have created a redlink for it at Cutaneous streptococcus iniae infection? ---kilbad (talk) 22:20, 29 April 2009 (UTC)


 * Also Cornyebacterium jeikeium, which I redlink at Group JK cornyebacterium sepsis. ---kilbad (talk) 23:09, 30 April 2009 (UTC)
 * Done... previously... with the correct spelling Corynebacterium jeikeium :) Sasata (talk) 06:23, 5 May 2009 (UTC)


 * Also Helicobacter cinaedi which I redlink at Helicobacter cellulitis. ---kilbad (talk) 15:59, 4 May 2009 (UTC)
 * Stubbed. Sasata (talk) 06:23, 5 May 2009 (UTC)


 * Thank you very much! Also, I moved the second article to Group JK corynebacterium sepsis. ---kilbad (talk) 13:21, 5 May 2009 (UTC)


 * I created two redlinks at Gamasoidosis, and wanted to know if someone would help me by creating article stubs for them? ---kilbad (talk) 21:15, 16 May 2009 (UTC)

Italic article titles
Hi, members of this project may be interested in a discussion at the Tree of Life about making the titles of species/genus articles italicised. The thread with information on how to do it is here. Smartse (talk) 19:51, 31 May 2009 (UTC)

Pageview stats
After a recent request, I added WikiProject Microbiology to the list of projects to compile monthly pageview stats for. The data is the same used by http://stats.grok.se/en/ but the program is different, and includes the aggregate views from all redirects to each page. The stats are at WikiProject Microbiology/Popular pages.

The page will be updated monthly with new data. The edits aren't marked as bot edits, so they will show up in watchlists. If you have any comments or suggestions, please let me know. Thanks! Mr.Z-man 20:31, 9 July 2009 (UTC)

Changes to popular pages lists
There are a few important changes to the popular pages system. A quick summary: -- Mr.Z-man 00:11, 12 July 2009 (UTC)
 * The "importance" ranking (for projects that use it) will be included in the lists along with assessment.
 * The default list size has been lowered to 500 entries (from 1000)
 * I've set up a project on the Toolserver for the popular pages - ~alexz/pop/.
 * This includes a page to view the results for projects, including the in-progress results from the current month. Currently this can only show the results from a single project in one month. Features to see multiple projects or multiple months may be added later.
 * This includes a new interface for making requests to add a new project to the list.
 * There is also a form to request a change to the configuration for a project. Currently the configurable options are the size of the on-wiki list and the project subpage used for the list.
 * The on-wiki list should be generated and posted in a more timely and consistent manner than before.
 * The data is now retained indefinitely.
 * The script used to generate the pages has changed. The output should be the same. Please report any apparent inconsistencies (see below).
 * Bugs and feature requests should be reported using the Toolserver's bug tracker for "alexz's tools" -

HIV GA Sweeps: On Hold
I have reviewed HIV for GA Sweeps to determine if it still qualifies as a Good Article. In reviewing the article I have found several issues, which I have detailed here. Since the article falls under the scope of this project, I figured you would be interested in contributing to further improve the article. Please comment there to help the article maintain its GA status. If you have any questions, let me know on my talk page and I'll get back to you as soon as I can. --Happy editing! Nehrams2020 (talk • contrib) 19:01, 18 July 2009 (UTC)

RfC on swine flu statistics
Link to RfC, input welcome. Tim Vickers (talk) 19:37, 23 July 2009 (UTC)

New article: Optical sectioning
I have just written a new article on optical sectioning (in microscopy) after noticing several of the microscopy-related articles referred to it without making any attempt at a definition. Please take a look if you can and check I havn't made any stupid mistakes! - Zephyris Talk 10:16, 29 July 2009 (UTC)

GA Reassessment of Malaria
Malaria has been nominated for a good article reassessment. Please leave your comments and help us to return the article to good article quality. If concerns are not addressed during the review period, the good article status will be removed from the article. Reviewers' concerns are here.

Proposed text for new treatments in development section on clostridium difficile page
I’d like to propose a new section on the Clostridium difficile page for treatments in development since there are several currently. You’ll find my suggested text in full here: kdrichards. Following yesterday’s TIME article on the desperate need for new antibiotics, more clarity on the progress that’s taking place would be helpful for Wikipedia users. KDR 22:08, 1 October 2009 (UTC)

Offering access to histology images (public domain)
I have equipment and access to government histology and pathology slides, and can provide public domain images of most tissues and many common pathologies at large size and good resolution on request (light microscopy to 40x, generally). I don't know how extensive the microbiology-specific portions of the collection are, but certainly some of the more common infections, such as tuberculosis, have good slides showing histological tissue changes from microbial infections.

I would be delighted to provide as many images as possible to this and other interested projects, but I don't have the time to check individual talk pages across many projects. If you'd like microscopic images of tissues, please send an email to histology.request@gmail.com with the request in the subject line (ex: "artery wall" or "tuberculosis granuloma"). Happy regards, Glacialfury (talk) 15:02, 20 October 2009 (UTC)


 * How about Rhinosporidium seeberi? Kingdon (talk) 00:55, 21 October 2009 (UTC)
 * I don't think so, unfortunately. Glacialfury (talk) 16:44, 23 October 2009 (UTC)


 * Well, you did say "more common infections" so I'm not too surprised. Thanks for checking. Kingdon (talk) 01:53, 24 October 2009 (UTC)

Household antibacterials
I am hoping to get some comments from knowledgable people (and hopefully refs) here about household antibacterials and antibiotic resistance. Is there a connection? I am asking because there is an ongoing rewrite of antibiotic resistance and there is an uncited claim to this fact in the article. Thanks! :)-- Literature geek |  T@1k?  17:57, 16 November 2009 (UTC)


 * The livestock part of that sentence was easy, as sources cited elsewhere in the article confirm that. As for household antibacterials, I didn't dig too deeply but I did find a CDC webpage which seemed clear about what is and is not known.  Perhaps someone else knows this area better, or wants to do some more looking around, and can find more. Kingdon (talk) 15:33, 17 November 2009 (UTC)


 * Thanks very much Kingdon for taking the time to answer and find those refs. :)-- Literature geek |  T@1k?  17:19, 17 November 2009 (UTC)

Clostridium difficile - treatments in development addition
Since there are several treatments in development for clostridium difficile infection, I'd like to propose adding some text to that end. Please take a look at my suggested text here: kdrichards. While you're there, please also take a look at my proposed page for Optimer Pharmaceuticals, the company developing fidaxomicin, one of the late-stage drugs in development. With fidaxomicin and the company's other lead drug candidate, prulifloxacin, already in Wikipedia it seems like the right time to get a page started. What do you think?KDR 00:35, 18 November 2009 (UTC)

Species problem
I was looking at the species problem article the other day and was surprised by how limited it is. It would really benefit from a microbiological perspective; I think an entire section on microbial considerations related to defining species would be appropriate. I also looked for an article on 'operational taxonomic unit' and found that this redirects to type (biology). OTU may not warrant its own article but could be discussed in both articles (the biological type article does not really explain the OTU concept but links to the Wiktionary entry). I would be interested in and willing to start a section in the species problem article, where I think it would be most useful, but would love some input and for help writing/expanding it. Do people think this would be a worthwhile addition to the existing article/s? Would anyone be interested in contributing to the new section? Is there anything in particular that should be mentioned in a section on microbial issues related to the species problem? I'm not sure whether this falls within the scope of WP:Microbiology since the articles in question pertain to broader topics in biology, but lack a microbiological POV. Please let me know if this is inappropriate, and if so, I apologize. Myceteae (talk) 01:21, 6 December 2009 (UTC)


 * Part of the problem with Species problem is that it has a lot of verbiage which doesn't seem to say much (perhaps a philosopher would disagree, but I would expect more discussion of gene flows and less talk like "raises the question of whether such things are real"). At least to my eyes, the shorter section Species actually has a lot more information (at least, more per word). I don't know what you had in mind in terms of microbiology, but what springs first to my mind is asexuality and horizontal gene transfer (both of which are mentioned at Species, and which I suppose are prokaryote vs eukaryote as much as macroscopic versus microscopic). Kingdon (talk) 20:07, 7 December 2009 (UTC)


 * The species problem article is highly philosophical in tone and scope, and while this is not a problem per se it does seem rather out of touch with the actual the concerns of actual working biologists. Asexual reproduction and horizontal genet transfer are the primary micro-related issues, and I was thinking of talking about some of the ways that microbiologists have attempted to address these, and some of the micro-specific issues.  For example the relative importance of genetic homology vs. ecological similarity when defining a species.  Different molecular criteria often yield different results (e.g. OTU based on SSU rDNA homology vs. species based on whole genome identity).  Myceteae (talk) 03:24, 8 December 2009 (UTC)