Wikipedia talk:WikiProject Molecular and Cellular Biology

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[edit] Please Organise Discussions

Please try to use the appropriate discussion page for your topics of discussion and avoid using this page for help requests, proposals etc. which are catered for by the relevant pages. If you think your post is not covered by an existing discussion subpage, put it here and I might get some time to sort it out. --Username132 (talk) 10:57, 4 September 2006 (UTC)

See my post above. But what do you view is the role of this page. Should it be redirected? David D. (Talk) 21:59, 4 September 2006 (UTC)
I'd say that post belonged on the announcements page. I don't think this page should be redirected, 'cause if we chose, say, the /Proposals page as the target, the Proposals page would be peppered with things that aren't proposals. I think this should just be a page with a menu on it, kind of like the reference desk has, giving links to the different individual pages. I havn't seen any other Wikiprojects that organise their discussions like this which is surprising, 'cause I'm finding it useful. I just wish there were more active members. --Username132 (talk) 17:54, 5 September 2006 (UTC)
I think people are active in the sense they are editing. Patience, now you have reorganised these pages and with the bulletins going out I think activity will rise. David D. (Talk) 18:44, 5 September 2006 (UTC)

[edit] Suggesting good references

Hello fellow biologists!

I used to contribute to a number of biology articles, but as my own studies have intensified, I haven't found the time to continue writing. However, I do often come across good articles that could serve either as references for Wikipedia, or as "further reading" that covers topics in more detail than an encyclopedia article would.

For example, PLOS Comp Bio has an Education series, of which the most recent article provides a good overview of Modularity and Dynamics of Cellular Networks.

Do you think that there's any use in collecting a list of these types of articles for future incorporation into Wikipedia? Is there any established method for doing so? If not, perhaps we could choose a "del.icio.us" tag for these articles? If I were to tag such articles with something like "WikiProjMCB" do you think you would use them?

Have a good one, AdamRetchless 16:24, 8 January 2007 (UTC)

[edit] Cell membrane update

Hi guys, just dropping by to give you the heads up on what's been happening on this high-importance article. I was going to nominate the article for the COTM before noticing that it failed to pass it previously. D'oh. To make it a little more attractive to potential editors I made a few changes:

  1. The discussion page now features a large to-do list: see it here
  2. The introduction has been re-written to provide focus
  3. Structure has been fleshed out substantially, but still needs input
  4. In-line referencing added and no backlog of references remain

So what needs to be done? The "Functions" part of the article is very weak, diagrams are needed, and "Structure" needs a bit more work. Pop over and see if you can do anything, it's a crime to have this fundamental article languishing in start-class! -- Serephine ♠ talk - 02:35, 11 January 2007 (UTC)

[edit] Template talk:Protein

I received a request on my talk page from a user at the Hungarian wikipedia to add a field to Template:Protein. Rather than answer it on my talk page, I've directed the thread to Template talk:Protein, to facilitate your comments and feedback. --Arcadian 14:28, 11 January 2007 (UTC)

[edit] STING

Article has been prod'ed for deletion (reason - not notable). It starts "STING (Sequence To and withIN Graphics) is a free Web-based suite of programs for a comprehensive analysis of the relationship between protein sequence, structure, function, and stability." Can anyone help me to determine whether this is notable. The original author has not been here for nearly a year. Should we let it go, or should we remove the prod and let it go to AfD? I have also asked the Chemistry Project which is more my line than here, but this article could come under both projects--Bduke 04:37, 12 January 2007 (UTC)

TimVickers removed the tag, & I was about to myself. There are lots of unjustified N prods these days. DGG 05:32, 12 January 2007 (UTC)
Thanks. Let us now see whether it goes to AfD! --Bduke 05:45, 12 January 2007 (UTC)
It's notable if someone out there might be looking for information on it. --Seans Potato Business 17:44, 21 January 2007 (UTC)

[edit] Succinate-coenzyme Q reductase

I dropped a note at the talk page [1]. -- Boris 20:44, 17 January 2007 (UTC)

[edit] Titin

There is a problem with this article. Some people, most of them random "stop-by"s and none of them working on this project, insist on keeping the FULL (?!?) name of the protein, which is about 28 K amino acids long, written in "arginyltyrosyl.....etc.yl"-kinda way, which make the article to jump from . The reason - someone came up with the idea that when written like that the name of titin is to be the longest word in English. So people that work on this project keep removing this linguistic junk, while unregistered users and editors that have no idea, including some guy who thinks he is the supreme judge in this case and who isn't convinced that there is consensus to remove it from there, keep putting it back. -- Boris 12:55, 18 January 2007 (UTC)

Makes the article jump from... what? If this isn't covered by some rule somewhere, start a vote on the talk page and call it to the attention of MCB members. To me it seems common sense that such a string of chracters has little or no practical use and should be removed. --Seans Potato Business 17:43, 21 January 2007 (UTC)
This is ridiculous. That guy has had plenty of opportunity to respond coherently and hasn't. Worst case, post an article content RfC and announce it here. Even independent of whether the word should be in the article, the template is so poorly designed that it really shouldn't stay in the article as is. Opabinia regalis 06:31, 24 January 2007 (UTC)
Thanks for bringing this to this page's attention, Boris. I agree with you and Opabinia. It's on my radar now. :-) Keesiewonder talk 10:50, 24 January 2007 (UTC)
"which make the article to jump from...", sorry i must have deleted the rest of it by accident, but here you go - "which make the article to jump from 24k (without the FULL name) in size to >240K (with it)". -- Boris 12:17, 24 January 2007 (UTC)
For what it's worth, as of this post the titin template has a larger file size than this discussion split off WP:AN/I for size reasons. If that much text is unacceptable in a high-post-volume noticeboard that everyone expects to be lengthy, then it's totally unacceptable in an article. Opabinia regalis 06:03, 25 January 2007 (UTC)
Agreed; I cannot understand the perspective of the single proponent who wants to include the complete titin name in the article instead of in a link ... Keesiewonder talk 09:08, 25 January 2007 (UTC)

[edit] Eicosanoid Peer Review

I've asked for Peer review for Eicosanoid. I was spurred to work on it when I saw the MCB template on its talk page. I'd like input from the MCB crowd..David.Throop 00:11, 27 January 2007 (UTC)

[edit] ATP synthase

ATP synthase, V-ATPase, F-ATPase and Transmembrane ATPase seem to be in a confused mess! These articles do not refer to each other at all and seem to spend a lot of time reiterating the same basic concepts in a very human-centric way. Does anyone have a good fundamental understanding of these terms, their definitions and their relationships to help tidy up these very important articles? - Zephyris Talk 12:24, 9 February 2007 (UTC)

[edit] Wikipedia:Scientific peer review

It is nearly 11 months since we established this review process as a minimal process after we failed to reach consensus about a number of matters. During that time it has been largely left alone with nobody really keeping a close watch on it. A couple days ago I cleaned everything up. I archived old reviews, corrected the tags on talk pages and made minimal changes to the process based on what I had learnt. I also reviewed how it had operated. There were some reasonable reviews and some that attracted no interest what so ever, but I guess that is the case even with Wikipedia:Peer review. Some entries may have missed some attention since they were not properly formatted, or had no tag on the article's talk page and hence did not appear in the category. See Wikipedia talk:Scientific peer review for my review and report on the clean up.

Of course, in hindsight, I wonder whether we, and particularly I, could have done better a year ago. In hindsight, does anyone have ideas how we progress this review process. To be worthwhile, it must attract reviews that perhaps would not go elsewhere such as Wikipedia:Peer review and it must attract expert reviewers to add to what might be achieved by the general Wikipedia:Peer review. If it can not do either, perhaps we should close it down and just encourage articles to go to Wikipedia:Peer review. Articles for review are listed on the science WikiProjects such as this one, but they are transcluded in so changes do not appear on watchlists. I have also added recent reviews to Wikipedia:Peer review in the same way that WikiProject reviews such as Wikipedia:WikiProject Chemistry/Peer review are added. In this way both review pages refer to the same page for the review discussion and hopefully more editors will be attracted. The key point is attracting expert reviewers who might look at Wikipedia:Scientific peer review but not look at Wikipedia:Peer review.

If you have any ideas on this, please add your views at Wikipedia talk:Scientific peer review. --Bduke 06:26, 14 February 2007 (UTC)

[edit] Cristae

In reading pretty much every taxonomical article I can get my hands on, I've come across terms such as tubular cristae, discoid cristae, and lamellar cristae. These terms are rampant across the internet (including Wikipedia) and yet I have not been able to find a single article discussing what these terms mean. Can anyone help me out here? And then maybe put that information on the crista page? Werothegreat 17:24, 22 February 2007 (UTC)

The terms simply refer to the shape of the cristae: tubular = tube-like, discoid = disc-like, lamellar = thin layers. There's another type: vesicular = small bubbles. Apparently changes in cristae shape are important in cell death and cancer, so I agree that this information should be in an article about them. - tameeria 23:52, 26 February 2007 (UTC)

[edit] Did I do it right?

I update the collaboration of the month. Did I do everything alright? -- Scientizzle 05:43, 3 March 2007 (UTC)

[edit] Automagic image request

I have been working on some infobox templates in the chemical area lately (mainly {{chembox new}} and {{drugbox}}, and (a.o.) programmed some templates with an automatic image request function. This puts pages with an infobox which do not have the image-field set into categories (subcategories of Category:Chemistry pages needing pictures). I have been so bold that I added the same functionality to the protein box. Pages having such a box now categorise in the subcategory Category:Protein pages needing a picture; this specific subcategory links to Wikipedia:WikiProject Molecular and Cellular Biology/Requested pictures. I have also added a section to this image request page. I hope I have not been too bold in this. --Dirk Beetstra T C 14:20, 4 March 2007 (UTC)

[edit] Chemical synapse FAR

Chemical synapse has been nominated for a featured article review. Articles are typically reviewed for two weeks. Please leave your comments and help us to return the article to featured quality. If concerns are not addressed during the review period, articles are moved onto the Featured Article Removal Candidates list for a further period, where editors may declare "Keep" or "Remove" the article from featured status. The instructions for the review process are here. Reviewers' concerns are here. LuciferMorgan 17:13, 7 March 2007 (UTC)

[edit] Protein domains

A few days ago the page Protein domains was created. This should likely be merged with Structural domain. However the editor who created the page put in a lot of info. It appears that the editor,User:Dicky2206 is Dr. Richard George, a post doc at Victor Chang Cardiac Research Institute, Sydney, Australia. The information is mostly from his dissertation and I think we should go through it and add a lot of it into the structural domain article. I'll try to do this over the next few days so please don't go deleting it all just yet. Thanks. Jvbishop 12:59, 19 March 2007 (UTC)

The very term "structural domain" is very unhelpful - since it doesn't clearly refer to proteins. The "protein domains" article, however, is quite a good start; what is missing is a comprehensive list of protein-protein interaction domains... (that's a huge job, and may be too much for a particular article). I'd keep the new article, and add in what is useful and not out-dated from the structural domains piece, and then refer those searching for "structural domains" to the new article...

Having said that, it does seem that there should be individual articles for particularly important protein domains (this can be a whole new category). For example, there whould be articles on: PH (plekstrin homology domains); SH2 ; SH3; UBD (ubiquitin binding domains); Coil-coil; RING; Fbox; Zing-finger; Transmembrane; signal-sequence; IgG domains; etc etc...

Gacggt 21:41, 29 March 2007 (UTC)

First things first we clean up the protein domains article. Then we make nifty little articles for all the main domains. It would be good to have them though. Jvbishop 16:25, 30 March 2007 (UTC)

[edit] Need help proofreading taxonomic refs

Hi, a few of us are working on a system for generating the taxonomic references for arbitrary taxa, but we need help checking that the references produced are OK, i.e., proofreading them. It's described on my Talk page, if you have time to help out — thank you very much! :) Willow 13:46, 21 March 2007 (UTC)

[edit] New article in bad need for assistance

Oleosin needs attention from this project. It's apparently a protein used in plant oil organelles, but I have no idea what to do with it, especially where under category:proteins it should go. Circeus 19:17, 21 March 2007 (UTC)

[edit] DNA

Hi there, are there any members of the project who would like to volunteer to be additional contacts for verification and sources of the DNA article? In practice, you get a couple of e-mails a month and a bit more traffic on your talk page. TimVickers 23:15, 21 March 2007 (UTC)

[edit] Trophy case

Hi, I'd like to include all of our featured articles in the MCB trophy case on our front page, arranged by their date of promotion. Is that OK with everyone? We could add an extra line for those that have appeared on the front page. If there are no objections, I'll make the change in a few days. Thanks for your opinions, Willow 16:22, 2 April 2007 (UTC)

I thought of doing the same on WP:MED. As I'm not a member I decided against it...if the idea comes through here, I'll bring it up there.
Edit: I just remembered I'm not a member here either, but I still think it's a good idea, FWIW! Fvasconcellos 16:31, 2 April 2007 (UTC)

[edit] WP:MEDMOS

Wikipedia:Manual of Style (medicine-related articles) is a proposed guideline discussed and developed over recent months. Please visit the talk page to indicate whether you support or oppose Manual of Style (medicine-related articles) becoming a guideline. SandyGeorgia (Talk) 20:53, 13 April 2007 (UTC)

[edit] Brocciflower

A bunch of misconception about this cross was inadvertently spread on several wikipedia pages (suggesting it's a genetically enginereed cross) which I have corrected. It's a wide cross of some sort, possibly embryo resuce was involved but I'm not certain. I couldn't find anything (only searched Google) which was clear, if anyone knows please add it Nil Einne 12:41, 22 April 2007 (UTC)


[edit] Lytic viruses??

Glioma says: "Gene therapy using lytic viruses ... is being studied for the treatment of gliomas." -- I've made lytic viruses redirect to Lytic cycle for the time being. Please correct if necessary. IANAV. IANAMB. :-) We apparently need an article on Lytic virus / Lytic viruses. -- Writtenonsand 15:18, 25 April 2007 (UTC)

Link changed and references added. TimVickers 16:45, 25 April 2007 (UTC)
Interesting. Thanks. :-) -- Writtenonsand 14:37, 26 April 2007 (UTC)

[edit] Template for "EC" enzyme links

Do we (or if not, should we) have a template for enzymes based on their EC identifier that links to the ExPASy database? {{ec}} is already used for something else, but {{enzyme}} is open. DMacks 17:58, 25 April 2007 (UTC)

We have one at Template:EC number. --Arcadian 18:26, 25 April 2007 (UTC)
Wonderful! Thanks. DMacks 18:34, 25 April 2007 (UTC)

[edit] Alternative oxidase

I simply cannot believe we don't have an article on the AOX! I'm in the middle of finals revision at the moment so now is perhaps not the best time but I'll get round to making a contribution in the future (it's a lot of work given all the potential roles, etc). In the emantime I warmly encourage anyone else who agrees with me that it would be an important addition and a potentially very interesting article, to get started! Philbradley 10:21, 5 May 2007 (UTC)

Article created, feel free to expand. TimVickers 16:36, 5 May 2007 (UTC)

[edit] Citizendium

I was wondering if anyone had anything to say about [Citizendium] (Sanger's answer to the challenge of vandalism (you have to sign up)). Has anyone thought about this? Anyone who didn't even know it existed? It might be nice if some of our better articles could be moved to a more secure area. --Seans Potato Business 18:52, 12 May 2007 (UTC)

They're free to copy anything they want. I don't know why they don't just import all the FAs. TimVickers 03:17, 13 May 2007 (UTC)
They have their reasons. Context available at http://en.citizendium.org/wiki/CZ:How_to_convert_Wikipedia_articles_to_Citizendium_articles .--Arcadian 14:28, 13 May 2007 (UTC)

[edit] Article development drive on Recombinant DNA and Restriction enzyme

Hi there! Is there any chance that if there is anyone free for the next few hours, that they would be so kind as to help me as i expand and reference both these articles? Would be muchly appreciated! ♥♥ ΜÏΠЄSΓRΘΠ€ ♥♥ slurp me! 21:09, 25 May 2007 (UTC)

[edit] Collaboration interest waning?

Cell (biology) is the current collaboration of the month...and almost no improvements have been made in two weeks. In fact, relative interest in the CotM has seemingly waned in general--the nominating & voting for future collaborations has fallen off. What's the deal? What would encourage more participation? — Scientizzle 21:22, 14 June 2007 (UTC)

I wouldn't lose heart; it may just be a passing fluctuation. On the one hand, some of our best contributors have indeed been sorely missed lately (our coordinator, ClockworkSoul, and Opabinia spring to mind) and we should all do a better job recruiting new people. But we've been as busy as otters this last month; we've just brought Evolution to FA status, the Science Collaboration article X-ray crystallography is not far behind (please help!) and we've just added 574 articles on every major family of RNA, articles that are in desperate need of improvement (see the RNA WikiProject). Not too shabby for May, no? Once these distractions have passed, I'm sure that more collaborators will spring back into action. :) Willow 02:40, 15 June 2007 (UTC)

Interest still appears low... In fact, last month there were only 7 total nomination support votes (or new nominations) from users other than me (4 total users). Come on, people! — Scientizzle 21:01, 3 July 2007 (UTC)

Perhaps we can begin promoting the effort once again? – ClockworkSoul 21:34, 25 February 2008 (UTC)
Yeah. How should we do it? — Scientizzle 21:35, 25 February 2008 (UTC)
When I was more active, I would send out a WP:MCB newsletter every month or so. Part of that would usually mention the successes and needs of the project at large. If people feel like they're contributing to something that's already successful, they're far more likely to contribute more. Everybody wants to be a winner, after all! Unfortunatle, I really don't think I'll have the time to pick up where I left off any time soon, but later this week I can try to start something. – ClockworkSoul 21:55, 25 February 2008 (UTC)
I'm in the process of writing a nifty multifuntional tool that'll provide the following functions:
  1. Provide a simple GUI interface for viewing articles and assigning them class and importance rankings
  2. Allow WP-wide user talk page postings, with opt-out support.
The first part is nearly complete, and when it is I'll make the tool available to all while I work on the second part. As time goes on, I hope to add functions and make it general enough for all WikiProjects to make use of it. – ClockworkSoul 17:52, 4 March 2008 (UTC)

[edit] Article ambiguity

Three similar titled articles covering similar topics could do with a bit of clarification:

It is not clear what each article is about just from it's title. Not sure how to deal with it, though. Suggestions? 82.16.7.63 20:04, 25 June 2007 (UTC)

...and there's the vaguely similar Complement system that isn't massively explanitory. Just to clarify, this query is only about titling. WP:TITLE states "Generally, article naming should prefer what the majority of English speakers would most easily recognize, with a reasonable minimum of ambiguity" - 82.16.7.63 20:19, 25 June 2007 (UTC)
Added a couple of disambiguation statements. Seems to me that complementary DNA has better content but ought to be merged with complementarity (molecular biology). Opabinia regalis 03:52, 27 June 2007 (UTC)
I'd actually suggest that things are appropriate as-is. "Complementation", "Complementary DNA" (or its more common synonym "cDNA"), and "complement system" are biologically precise and distinct things. That is to say, a student might find any one of these things in a textbook or a research article and search WP for their meaning. "Complementarity" is a fundamental concept about DNA that I think doesn't get used as much (perhaps because it's such a given in the field?), but doesn't quite fit into any of the other three to warrant merging. (Not entirely convinced "complementarity" is as different from the other three as I've laid it out above.) Anyway, I vote for keeping things as they are. AndrewGNF 23:02, 27 June 2007 (UTC)
I agree that these are separate concepts... and I can't think of alternate titling for them. I am familiar with complementation and complementary DNA as commonly used terms for different things, it looks like the titles of the articles will just have to follow the ambiguity of scientific terminology on this, not much we can do about it other than add disambiguation links. Madeleine 14:38, 28 June 2007 (UTC)
... I have added/expanded the disambig links to cDNA & complementation (genetics). I think perhaps "Complementation (genetics)" should be moved to "Complementation test", this would also help distinguish the concepts. Madeleine 15:27, 28 June 2007 (UTC)

[edit] eukaryote/cell entry

guys i i'm just exploring this wiki thing and i find it very curious indeed! anyway i cleaned up the intro to the eukaryote page and noticed that god knows the rest of it needs a lot of work. then i noticed there is a cell page. alot of duplication.

what should we do? do we want them to remain independant? Wikiskimmer 01:58, 29 June 2007 (UTC)

You mean Eukaryote and Animal cell? The two do not entirely overlap, but at present I set it up so that there is a notice on Eukaryotic cell suggesting people look at the Eukaryote article for more detail. I think the two should remain distinct though, as here are some topics that you couldn't cover in a comprehensive animal cell article, such as the details of plant cell structure, and animal development and physiology. Tim Vickers 21:08, 3 July 2007 (UTC)
no, i mean Eukaryote and Cell (biology), ALOT of overlap. i'm new here and i've been finding alot of overlap. no managers, you know. i suppose if wikipedia evolved for a coupla hundred years and human history would stay put, maybe it would settle down...Wikiskimmer 21:25, 3 July 2007 (UTC)
Overlap happens a lot. If you think Eukaryote should be merged into Cell (biology) you could suggest a merger. Of course, there is Prokaryote as well, to be fair you'd have to suggest that as a merge as well. Often people are happier with separate articles despite overlap, as they feel a more specific article covers details not appropriate to the more general article. Although I'm not sure what that might be in this case, it might come up in any discussion of a merger proposal. Madeleine 21:32, 3 July 2007 (UTC)
I think the answer to overlap in articles is expansion of the material that does not overlap. I see quite a lot of these biology articles as placeholders for wonderful and detailed articles that will be created in the future, but then I'm an optimist! Tim Vickers 21:36, 3 July 2007 (UTC)

[edit] Mdm2

Mdm2 and MDM2 appear to be the same topic. If so, could someone merge/redirect MDM2 into mdm2 and cross it off on User:Cmh/List of page titles with multiple capitalizations. John Vandenberg 10:37, 17 July 2007 (UTC)

Done. Tim Vickers 16:15, 17 July 2007 (UTC)

[edit] Morphogenetic field

This afternoon, PZ Myers noted on Pharyngula that the WP article morphogenetic field did not discuss the developmental biology concept of that name, but rather the pseudoscientific idea cooked up by Rupert Sheldrake [2]. I moved the page to a new spot and started afresh, but this is quite a bit outside my experience, and I'll probably have to leave it in stub-form.

Assistance with expansion would be greatly appreciated.

Anville 19:48, 18 July 2007 (UTC)

[edit] GA categorization drive

If anyone here is not busy writing MCB articles, can you please help the Uncategorized Good articles task force by adding the |topic=Natsci to the GA templates on MCB articles along with the |oldid= from the date the article was reviewed? Thanks. Tarret 17:26, 22 July 2007 (UTC)

[edit] T-cadherin

Does anyone want to take a look at this article, up for deletion? It needs a mass of work or just let it go and maybe start again later. --Bduke 00:45, 23 July 2007 (UTC)

[edit] Bioinformatics is now at Good Article Review

This article is now at Good Article Review for possible delisting of its Good Article status. Concerns are listed at the good article review page. I'm drawing attention to it here because I've seen how quickly this project works - I'm sure that with some quick work in the inline citations department, the article could remain as a GA. Please remember to assume good faith and improve the article to meet the Good Article criteria. -Malkinann 10:11, 26 July 2007 (UTC)

[edit] Mitochondria - Cristae shapes

Can someone PLEASE (who knows what they're talking about) detail the various shapes that cristae take (discoid, flat, etc.), describing their differences, and possibly the purposes for different shaped cristae, either in the eukaryote, mitochondria, or cristae articles, or even create a new one. I would have done this by now, except the whole subject confuses me, and I don't have any sources that clearly explain them. Werothegreat 19:41, 31 July 2007 (UTC)

[edit] p53 vs. TP53

Please take a look at these two articles. Shouldn't they be merged? The protein is also called TP53, but it is not enough clearly stated and obvious in the TP53, to my opinion. I guess the best thing would be to merge them, or, otherwise, rename them to TP53 (protein) and TP53 (gene). --Maxxicum 09:39, 3 August 2007 (UTC)

I would support a merge. --Arcadian 17:32, 3 August 2007 (UTC)
A merge into p53 with redirect from TP53 seems appropriate to me as well. -- MarcoTolo 19:46, 3 August 2007 (UTC)
p53 is the common name for the protein (43137 PubMed hits for it), while TP53 is the name of the gene for that protein--TP53 (protein) wouldn't be an appropriate name. I think they're distinct enough concepts to warrant separate articles, but a merge can't hurt anything. More clarity on the difference between the two term and their fundamental relationship would be a positive. — Scientizzle 19:56, 3 August 2007 (UTC)
Based on the comments abouve I would support a merge. For protein-coding genes (regardless of how important they are), I am from the school-of-thought that either the protein or the gene deserves an article (my bias is towards the protein... naturally, since I am a biochemist). Of course, that means that there would have to be redirects and rewrites. Antorjal 20:38, 3 August 2007 (UTC)

[edit] Chaperone

I'm intrigued by this edit. It could be an excellent clarification (assuming the editor is who he says he is), but it also could be a violation of WP:COI. I wouldn't have worried too much about it if it was just an addition, but the edit replaced the old content crediting Art Horwich (added Jan 2006), which implies that we may be observing a turf battle. The nuance of the timeline is beyond my capacity to evaluate, and I'd welcome further review from editors with more subject matter expertise. --Arcadian 00:07, 5 August 2007 (UTC)

The info checks out completely and I have expanded it a bit. I think this editor is most probably the man himself! Tim Vickers 03:00, 5 August 2007 (UTC)
Thanks! --Arcadian 18:25, 5 August 2007 (UTC)

[edit] Input requested...

Wikipedia:WikiProject Molecular and Cellular Biology/Collaboration of the Month has received one vote since August 3. C'mon folks! — Scientizzle 19:35, 24 August 2007 (UTC)

[edit] Plant hormones

A few years ago I has a series of essays deleted which were theories on hormonal action based on this site from this user. He seems to be actively editing plant hormone articles again adding material based on his synthesis of scientific literature; these articles are in pretty bad shape regardless so it would be nice if some interested editors could help make these article more reliable. The Arabidopsis book is a pretty good place to find current information on the known biological function of all the major plant hormones. I've started a rewrite on brassinosteroids, but there is lots more to do. Thanks --Peta 03:01, 30 August 2007 (UTC)

v • d • e
Plant hormones

[edit] Exosome complex up for FA

The article above has been up for FA already for some time, but has not attacted a lot of remarks. Any comments and suggestions on the article are welcome and will be addressed. The FAC discussion can be found here: Wikipedia:Featured article candidates/Exosome complex. --Cpt. Morgan (Reinoutr) 18:19, 1 September 2007 (UTC)

[edit] Chromosomal duplication: merge, or better distinguish?

There's some discussion at talk:chromosomal duplication as to how this overlaps with gene duplication, and the like. Could someone knowledgeable have a look, please? My own understanding is that there's several different cases of gene dup. (e.g. involving a number of genes on a single chromosome, of a whole chromosome, and of the entire genome), but I'm no expert, and this could stand to be made much clearer in the different articles. Alai 21:29, 10 September 2007 (UTC)

[edit] Should article titles for enzymes be singular or plural?

I noticed today that some articles on enzyme families have plural titles (like DNA glycosylases and AP endonucleases while others are singular (DNA ligase, DNA polymerase). Is there a standard that all of these should follow? For the plural titles, the article with the singular name is a redirect to the plural. If I want to edit these articles and make them all follow the same convention, what is the correct way to do it? Moving the article from the plural title to the singular title doesn't work because of the redirect pages. Thanks in advance for any help. Amazinglarry 19:21, 11 September 2007 (UTC)

WP:NC is clear on that. Singular when possible, plural only if singular makes no sense, quod non. JFW | T@lk 19:29, 11 September 2007 (UTC)
Thanks, I'll have the redirect pages speedy deleted and move the plural pages to singular. Amazinglarry 19:45, 11 September 2007 (UTC)
[EC]If convinced that a move to a different title over a redirect is appropriate, make a request at Wikipedia:Requested moves. An admin will need to delete the redirect to make way for the move. Wikipedia:Naming_conventions#Prefer_singular_nouns seems to support, for example, DNA glycosylase over DNA glycosylases... — Scientizzle 19:47, 11 September 2007 (UTC)

[edit] Cat:lipid stubs, Cat:carbohydrate stubs; others?

In another attempt to chip a few off the huge Cat:biochemistry stubs, I've proposed types for lipids, and for carbs. If anyone has any additional ideas for further sub-types, I'd be very glad to hear them... Alai 21:03, 28 September 2007 (UTC)

[edit] Gene page versus protein page

I'm sure this topic has come up before, so if someone can point me to any previous discussions of it I'd appreciate it. Opabinia regalis made these changes to the article on Amyloid precursor protein. I understand the concern -- that it is confusing that an article on amyloid precursor protein has extensive text referring to it as a gene. Was it decided that we will have separate pages for the gene and the protein? If so, would anyone support a revisiting of this decision (reasons below). If not, then does anyone have a suggestion on a wording that makes it clear that the page refers to both the protein and the gene? The ProteinBoxBot plans on inserting a similar line to this in all pages it creates (as suggested during the bot approval, so we'd like to get the wording right)...

While I think we all can agree that genes and proteins are different things (genes being the DNA template from which one or more types of proteins are created), from an encyclopedic standpoint I believe that in general they deserve one entry. "Gene function" and "protein function", for example, are often used interchangeably. And knowing about a gene's transcriptional regulation is intimately tied with the role of the protein. I feel that having separate entries as the default unnecessarily and unnaturally splits knowledge on something that most biologists consider a single topic. AndrewGNF 16:15, 2 October 2007 (UTC)

Oh, it's probably worth mentioning that "Amyloid precursor protein" has an entry in the "Entrez Gene" database. [3] AndrewGNF 16:17, 2 October 2007 (UTC)
Thanks for letting me know about this thread; I've only popped in on occasion lately and would probably have missed it :) I'm not sure there needs to be a general policy on the gene vs protein question; by default I'd rather see over-lumping than over-splitting, but there's at least an appreciable minority for which mixing genes and proteins in one article would be clunky. As I understood it, the ProteinBoxBot was (originally?) intended mostly for creation of new articles rather than expansion of existing ones, and if neither the gene nor the protein has an article yet, it's probably safe to put them together until enough information accumulates to split them.
The concern I have about the bot, based on what I saw on the APP article, is the dropping in of the summary as an isolated text bolus, unconnected to the existing article. It's confusing for readers to essentially have two introduction sections - especially when they use different definitions! - and it makes the article look half-finished until a human comes along to (does a better job than I did and) integrate things properly. I actually think the PBB boxes should make more use of the fancy collapsible-section formatting, but that's more of an aesthetic gripe. The easiest resolution would be to either comment out the summary text when inserting into an existing article (or one that's been edited by someone besides the PBB), or to always include the summary in some sort of offset text box that makes it clear that it derives from a source separate from the main text. Opabinia regalis 03:04, 3 October 2007 (UTC)
Okay, so I think the PBB will go ahead and be blissfully ignorant of the gene/protein distinction then. The point you've raised above is a good one though, and after going through the process for the first ~25 semi-automated edits, I agree. (In case the distinction is not clear, automated edits are when PBB detects no conflicts in the WP namespace, and then goes ahead and auto-creates the page. Semi-automated edits happen when PBB does find a namespace conflict, and then it falls to a human to manually choose the correct gene/protein page and add the automatically generated wiki text.) Initially, for semi-automated edits, I was throwing the Entrez Gene summary at the top of the page, even if there was already a summary section there. Later, I decided that I should just leave it out in that case for pretty much the same reasons you mention above. Anyway, if I had to do it again, I would have done it exactly as you'd edited to. So I think we're in agreement, and I'll try to do a better job being smart when merging with existing articles. (Sorry to all to confuse this sound PBB feedback with the gene/protein issue, which turns out wasn't the issue at all here...) AndrewGNF 04:16, 3 October 2007 (UTC)

[edit] Question

I'm a big fan of David Goodsell's amazing illustrations for the PDB's Molecule of the Month series, and I've been experimenting with QuteMol to produce similar images. I just uploaded one and added it to thyroxine-binding globulin, but now it strikes me as a bit of a "copycat" thing. I know that all PDB images are in the public domain, but I'm not talking about copyright infringement; it just sort of feels like ripping off an artist's style. Does anyone have any thoughts? Fvasconcellos (t·c) 03:32, 3 October 2007 (UTC)

I don't think you should worry about using PDB data and taking inspiration from someone else's rendering style. (Something about imitation and flattery goes here...) But personally, that rendering style just doesn't do it for me. I find the cartoon/ribbon style to be much more eye-catching, and it underscores that we have high-resolution structural data. These space-filling models almost look like low-resolution EM structures. My two cents... AndrewGNF 04:29, 3 October 2007 (UTC)
I would agree with Fvasconcellos. I think Goodsell's images are really cool, especially for proteins whose surface features say a lot about their function. Ribbon style images are great, but they aren't as approachable to a lay audience. Non-biochemists want something they could almost touch. Not that I've done a poll or anything, but I'm a non-biochemist and I think the PDB poster rocks! That said, I would error on the side of having both kinds of pictures. I don't know anything about image or "style" copyright infringements though. Forluvoft 04:48, 3 October 2007 (UTC)
Actually speaking of taking inspiration from the PDB, it would really cool if we could figure out a way to make our protein boxes scroll through several images, (for example, [4]). That would allow us to keep and display all available visualizations... Any adventurous javascript hackers? AndrewGNF 14:15, 3 October 2007 (UTC)

Hey

I have created a new daughter project under Wikipedia: WIkiproject Plants titled Wikipedia: WIkiproject Plant evo devo and will be working over the next few months to generate comprehensive information related to the topic. My focus is primarily on the molecular aspects, the genes and gene networks that function in development, and their evolutionary synthesis. The resources on this Wikiproject are enormous, and would like to ask for participation from all the plant biologists out here for the Plant evo devo subproject.

The project would function more like a task - updating existing incomplete and generating new wikis related to plant development while more focussing on the evolutionary aspects of development.

[edit] plant evo devo

Hey!

I have created a new daughter project under WP:PLANTS titled Wikipedia:WikiProject Plant Evo Devo and will be working over the next few months to generate comprehensive information related to the topic. My focus is primarily on the molecular aspects, the genes and gene networks that function in development, and their evolutionary synthesis. The project would function more like a task - updating existing incomplete and generating new wikis related to plant development while focussing more on the evolutionary aspects of development.

The resources on this Wikiproject are enormous, and would like to ask for participation from all the plant biologists out here for the Plant evo devo subproject. Maybe we can work out a collaborative function? Gauravm1312 21:11, 4 October 2007 (UTC)

[edit] Nomination discussion

This is being rather too quiet. Could people register their opinions or even their apathy at the Wikipedia:WikiProject Molecular and Cellular Biology/Votes/2007 director vote? All the best Tim Vickers 20:33, 17 October 2007 (UTC)

[edit] Are we allowed to use molarity in articles?

An editor seems convinced that molarity is an archaic measurement and is insisting on using mmol L-1 rather than just mM in the Ellman's reagent article. Could somebody else try to explain to him that the standard usage is biochemistry is molarity? Tim Vickers 04:06, 20 October 2007 (UTC)

He's popped up again. See Talk:Enzyme_kinetics#Molarity_is_obsolete. Tim Vickers 00:01, 23 October 2007 (UTC)

[edit] Change to Manual of Style on measurement systems

The section on choosing measurement systems has been changed from:

  • In scientific articles, SI units are the main units of measure, unless there are compelling historical or pragmatic reasons not to use them (for example, Hubble's constant should be quoted in its most common unit of (km/s)/Mpc rather than its SI unit of s−1)

Into:

  • In scientific articles, use the units employed in the current scientific literature on that topic. This will usually be SI, but not always. For example, natural units are often used: ångströms (or angstroms) are widely used in such fields as x-ray crystallography and structural chemistry, and Hubble's constant should be quoted in its most common unit of (km/s)/Mpc rather than its SI unit of s−1.

Comments on this change are welcome at Wikipedia_talk:Manual_of_Style#Units_of_measurement. Thank you Tim Vickers 18:11, 23 October 2007 (UTC)

One editor is objecting strongly to this change, some feedback from people writing science articles would be very helpful. Tim Vickers 17:48, 26 October 2007 (UTC)

[edit] Images

Would someone like to add the |needs-photo parameter into the MCB template? Richard001 05:45, 24 October 2007 (UTC)

[edit] Enzyme articles

Hi all!

On kind of a whim, I've decided to fill some gaps in our coverage of enzymes, starting with Cat:EC 1.1.1. Would you all be so good as to look them over, and give me suggestions? You might find this page useful. They're just stubs and I know that the pathways are messed up (the "participates in" sentence) because I only now figured out how it should be presented. The rest of it might not be too bad, but I would welcome any advice to improve them, since there's only, ummm, 3500 enzyme classes left to go. ;) Hoping everyone here is happy and healthy, Willow 01:21, 25 October 2007 (UTC)

PS. One question was whether there were too many external links in the {{Enzyme links}} and {{Enzyme references}} templates found on all the new enzyme pages? I wasn't sure which ones could be safely deleted, though; they all seem good!

PPS. OK, I finished Cat:EC 1.1.1, with the exception of a few enzymes that catalyze more than one reaction, which I was too tired to think through how to do. I hope you like them! Please send along any suggestions for improvments or wish-lists of additional features, Willow 03:38, 25 October 2007 (UTC)

They look good, I'll try to work through some every day to fix redlinks and such. One thing I notice is that the stubs link to the names for ions of organic acids eg succinate, while the standard on Wiki is to use the name of the protonated form eg succinic acid as pagenames. Any simple way to fix this? Tim Vickers 17:51, 26 October 2007 (UTC)

Thanks, Tim, both for fixing them up and for detecting classes of errors that I should work to improve. I'll try to use the protonated form in my future enzyme articles, although I confess that the "ate" ending sounds more euphonic to my ears. :) Willow 14:57, 28 October 2007 (UTC)

Wow, a heroic number of edits. Well done... If you're planning on doing all ECs like this, isn't it about time to make a full-fledged bot? It looks like you've got the format and content pretty well down -- seems ripe for full automation. Just a thought... In any case, I very much like it. I'm thinking now of how we can get all the EC categorization for genes so that our ProteinBoxBot can take advantage of all these categories and links... AndrewGNF 00:45, 27 October 2007 (UTC)
The entry on (S)-usnate reductase seems malformed. Tim Vickers 02:14, 28 October 2007 (UTC)
I tried to fix it, but the name of the compound ((6R)-2-acetyl-6-(3-acetyl... see here) is so huge that it didn't even fit my 1024x768 screen :D Having the reaction explained by images as in the Wikiproject Metabolic Pathways, instead of by long names, would be wonderful... the data are already there (I've seen KLEGG) but generating the images, uploading, avoiding duplicates will be an enormous task.
In response to AndrewGNF: usually Uniprot give the EC number for enzymes (see for example MAPK1 here). I don't know how it can be automated, but maybe searching a pattern like "EC x.x.x.x" in the webpage and classifying the gene as "enzyme" whenever the pattern is found, could do the work --Banus 11:12, 28 October 2007 (UTC)
What exactly is wrong with the article? My chemistry isn't so good as to mentally whip up a structure (apart from a very, very simple one) from the IUPAC name, but isn't (6R)-2-acetyl-6-(3-acetyl-2,4,6-trihydroxy-5-methylphenyl)-3-hydroxy-6 methyl-2,4-cyclohexadien-1-one simply usnic acid? Fvasconcellos (t·c) 14:06, 28 October 2007 (UTC)
Sorry, Willow, but after a look at BRENDA, apparently I was wrong. Scratch that. Fvasconcellos (t·c) 15:08, 28 October 2007 (UTC)

Thanks for pointing out the usnic acid glitch; I'll try to fix that up once I get home from my sister's house! I can also send along a list linking the EC numbers with the human and mouse genes — would that be helpful, Andrew? Please let me know what you'd find helpful, and I'll try to do that. :) Willow 14:57, 28 October 2007 (UTC)

Well, more than the current list of links between Entrez Gene / Ensembl and EC number, I'm more curious to know where you get that data from. Banus mentioned using Uniprot -- I think we index Uniprot data but I'll need to check. Anyway, if you have another source, let me know. We mirror all the source files (from NCBI, UCSC, Ensembl, etc.) here to allow periodic updates of ProteinBoxBot content, so figuring out the source of EC links will allow us to also keep those data up to date... (As an aside, should we be doing this for Gene Ontology too?) AndrewGNF 16:24, 28 October 2007 (UTC)

Umm, well, I think you might be able to use this file for linking EC numbers and human genes, although if you work for a company, they might ask you to get permission first. Hoping it's helpful, Willow 14:48, 29 October 2007 (UTC)

[edit] Amino acids need a template or guideline for the lede

I periodically edit articles on amino acids, which can be lively area. These articles desperately need this group (if there is a group that I am appealing to) to strike some agreement about the guidelines/templates for amino acids, at least the ones that are coded for, otherwise the lede really gets jerked around depending on each editor's prejudices. So can the MCB group set up some sort of guidelines?

  • a recurring struggle occurs between editors that want to represent aa's in their simplest form as an organic chemical vs. those that want to describe their zwitterions. It seems that the guidelines might require a sentence to the effect that "the location of the acidic protons in amino acids depends on pH." Otherwise, some ledes quickly become cumbersome if we list every semi-important zwitterion. Similarly the names are tossed around, e.g. aspartic acid vs aspartate.
  • Some editor has decided that every amino acid article should start with a reference to "IUPAC-IUBMB Joint Commission on Biochemical Nomenclature. Nomenclature and Symbolism for Amino Acids and Peptides. Recommendations on Organic & Biochemical Nomenclature, Symbols & Terminology etc. Retrieved on 2007-05-17." Maybe this is a good thing, but some group should decide.
  • most of the articles now have a section on biosynthesis of the amino acid, which is very nice (an upgraded need now is to specify the biosyntheses for various organisms).
  • there seems to be some difference of opinion about how common are free amino acids (I had assumed that free amino acids are rare) and some vagueness/laxness about the distinction between an amino acid and an amino acid residue (maybe this is too narrow). E.g. myoglobin does not contain histidine, it contains the histinyl residue.
  • of course these articles often contain extensive discussions about diet, sometimes including extensive lists on the amino acid content of various foodstuffs (it would be convenient to have a standard source for this info) and, slightly less scientific commentary abuot the health benefits of consuming certain amino acids.

If such a template could be agreed upon, this could be posted on the talk pages of the 20-21 amino acids. Presumably similar standardization has occured with the articles on other biochemical building blocks. --Smokefoot 14:11, 25 October 2007 (UTC)

[edit] protein and enzyme stub subtypes proposed

Please comment here. Alai 04:00, 4 November 2007 (UTC)

This is now a done deal; I've followed the existing permcat names, to the top-level subtypes are at Cat:oxidoreductase stubs, whereas the narrower ones are at Cat:EC 1.1.1 stubs. The issue of renaming said permcats was mooted during the proposal discussion, but it wasn't quite clear to me what would be the best target. If people can use the most specific tag possible when creating new stubs -- or indeed, look through the remaining unsorted ones to see if they can be categorised and sorted further -- that'd be a boon. Alai 00:32, 14 November 2007 (UTC)

Oh, I also notice that many of these stubs have category redlinks for their "EC" cats. I'd be a good idea to complete those. Alai 00:37, 14 November 2007 (UTC)

[edit] Notice of List articles

Page(s) related to this project have been created and/or added to one of the Wikipedia:Contents subpages (not by me).

This note is to let you know, so that experts in the field can expand them and check them for accuracy, and so that they can be added to any watchlists/tasklists, and have any appropriate project banners added, etc. Thanks. --Quiddity 19:36, 5 November 2007 (UTC)

[edit] Wikipedia:Scientific peer review

This Scientific Peer Review project can hardly be called successful. While there have been a steady but small flow of articles submitted for review, the actual reviews have been either non-existent or in no real way different from those done through the standard Wikipedia:Peer review process. Some editors will recall that the project was started with an enthusiastic discussion about identifying expert reviewers through an elected board. Unfortunately as time went by, it became clear there was no consensus on whether we had a board, or on how it was to be set up or on what it was supposed to do. There was also a lack of consensus on what "sciences" we were covering, and on many other aspects. In the end we sort of lapsed into a minimal review process which has staggered on for about 18 months. I think it is time we decided what to do about the project. Unless people can come up with a new way forward and enthusiastically implement it, I think we have to declare that this project be no longer active in any sense and that editors should ask for review at WP:PR. I am posting this on the talk pages of the major Science WikiProjects. Please feel free to publicize it elsewhere. Please add you comments at Wikipedia talk:Scientific peer review#Is this inactive?. --Bduke 03:40, 14 November 2007 (UTC)

[edit] feedback loops and mathematical biology

Feedback loops are a key element in molecular biology, but they are lost around and are inside general articles, or I did not find them, ergo hard to find. A page feedbacks and oscillations in molecular biology or something similar would be the solution but it would be a mix-mash of ideas and references (original data logo) and most people know it anyway. threshold (stochastic inhibitor) and exponential activation. Plus to actually explain these mechanisms, one needs to build on the mathematical biology page that is small to start with, plus I just saw that the background applied mathematics terms here are confused to put it is lightly. I do not have much free time, and . I think i better leave it to a more seasoned wikipedia editor. so I will just contribute this idea (or add the maths later on). --Squidonius (talk) 18:49, 21 November 2007 (UTC)

I would just integrate the most famous examples (e.g. the cascade theory of coagulation) into the positive feedback article. JFW | T@lk 20:38, 21 November 2007 (UTC)
It could also be a good part of the article on Cell signaling, since such mechanisms are an important part of signaling cascades. Tim Vickers (talk) 20:40, 21 November 2007 (UTC)
I feel there is a gap in Wikipedia regarding the organisation of content relating to mathematical biology, computational biology, bioinformatics and systems biology. I have therefore proposed a WikiProject on mathematical and computational biology (preliminary project page found here) to cover these topics. WP:MCB has done a lot for articles within this interdisciplinary zone (e.g. bioinformatics), so I expect that the two WikiProjects have a lot to gain from each other. The mathematical and computational aspects could be addressed in more detail and in an appropriate context within the new WikiProject. So this may be a good place to coordinate work such as the above-mentioned. Hendrik Fuß (talk) 16:20, 29 November 2007 (UTC)
If anyone starts working on this, please also see Wikipedia:WikiProject Molecular and Cellular Biology/Requested articles#Negative feedback loops and feedback inhibition. ;) - tameeria (talk) 15:59, 13 December 2007 (UTC)

[edit] EMBO article

Great to see the WikiProject recognized by EMBO. [5] Keep up the excellent work. --Aude (talk) 01:15, 3 December 2007 (UTC)

[edit] Miscategorization of Genetic Algorithms

The Computer Science article Genetic Algorithms has a template on it's talk page for membership in the Molecular and Cellular Biology Project, which is confusing some folks. We probably want to remove that template, but I want to mention it here first, and also explain why I think it was put there in the first place.

  • There is some natural confusion between models (of natural processes), and algorithms which exploit the natural model for artificial optimization. Pretty much, it's the difference between natural selection, in the Galapogos, and selective breeding, at a stud farm. In GA we can do things that nature can't, such as pumping up the mutation rate to the equivalent of such gamma bombardment as would disintegrate a living organism.
  • There had been something of a movement at the GA page to give historical credit to biologists (who were early in the use of computer simulations of genetics) where previously we had only mentioned computer scientists (who used very similar software as an optimization technique). I'm happy to recognize the significance of early biological simulations to the development of the optimization techniques, and that historical material has been kept.
  • There is also possible confusion because of Genetic Computing (which doesn't seem to have an article here? a biochemist should write one!) which actually uses molecular biology (enzymes and proteins...yuck) to compute things (the idea was very very slow processing but very very huge parallelism, e.g. Avagadro's Number of tiny slow processors).

So we are talking about using a biological model as the basis of a software engineering technique, and the current work in GA per se is done by Control Engineers (who are basically consumers), Computer Scientists, Software Engineers, and even the occasional deranged mathematician. So, please visit, skim over the page, and then please delete the Molecular and Cellular Biology Project template from the Talk page. And here's to standing on each others' shoulders, and not stepping on each others' toes :-) Thanks. Pete St.John (talk) 20:20, 7 December 2007 (UTC)

We include bioinformatics under the umbrella of Molecular and Cellular Biology. Although genetic algorithms might not be a common algorithm used by bioinformaticians, protein folding and protein/ligand docking are mentioned in the Applications section of your article. As for "stepping on each others' toes", I doubt this will be a problem. Many biology articles are "claimed" by multiple projects including those related to medicine, evolution, etc. Besides, I don't think your article will be a high-traffic area for most of our project members, just a small subset that is more computationally-inclined. Forluvoft (talk) 20:59, 7 December 2007 (UTC)
GAs are also used to build phylogenetic trees based on maximum likelihood analysis, so they also have their application as a tool in molecular phylogenetics. - tameeria (talk) 21:39, 7 December 2007 (UTC)

I put the MCB template on that article, it seems, back when I was tagging a lot of articles. My reason for tagging it was based on an interest in bioinformatics, and GAs are certainly part of that. I can assure you I had no clue about any credit disputes (I certainly didn't read the talk page before placing the template) nor was I confused by the title. Plain and simple: It is likely the page will be visited by people with zero background in computer science, e.g. biology students taking a bioinformatics class. The template is there to indicate that this is a topic of interest to molecular biology and to invite editors from the "bio side" of bioinformatics to look at it and maybe help by making it more relevant and useful to those biology students. I'm not quite sure I understand the reasons for the proposed removal of the MCB template. What is the problem with indicating that a molecular biologist might be interested in it? I don't find it confusing at all, but then I'm reasonably familiar with bioinformatics so maybe I'm missing something. - tameeria (talk) 02:28, 8 December 2007 (UTC)

GAs are used by Number Theorists too; but they are not part of Number Theory. It's a computer technique. Radio Telescopes may fall under "Astronomy" instead of "optics" because only astonomers use radio telescopes, but lots of people in many professions use optimization techniques. I'm happy for the article to have a template like "Category: application software used in bionformatics" (then it would have dozens or hundreds of such templates) but I don't understand why it's in the WikiProject MCB. To me, that seems like putting biology in the Wiki Project Glass Blowing because all biologists use glassware. GA is a technique of computer science. Genetic simulation is a technique of biology. GA is merely inspired by genetic simulation; for example, a population can have 3 sexes, or a mutation rate that would disintegrate natural organisms, or immortal individuals, whatever is mathematically and computationally possible can be used, it's not simulating nature. Pete St.John (talk) 19:08, 10 December 2007 (UTC)
Radio telescopes are part of optics? I'm no astronomer, but that doesn't seem right. ;) Putting a tag on glassblowing would be like tagging computer programming. Genetic algorithms are tools, e.g. the equivalent tag should rather be on Erlenmeyer flask and Beaker (glassware). Now, looking at other algorithms, there are pages for Bayesian inference in phylogeny and Distance matrices in phylogeny, for example. Maybe there should be a page for Genetic algorithms in bioinformatics (since its applications are not limited to phylogeny) or something similar that caters to the biologists interested in GAs. In the meantime, I think I found a more appropriate tag for it. - tameeria (talk) 02:29, 11 December 2007 (UTC)
Do physicists consider optics to pertain only to the visual spectrum? Oh well :-) but I think I communicated the idea that GAs pertain to the subject that builds the tool in a way that they don't pertain to the (numerous) subjects that use the tool. But of course there is tons of interplay, I just think that WikiProject CS is a better fit for GA than WikiProject MCB, and that WikiProjects probably should be narrower than Categories. But anyway your switch to Computational Biology is a good step, thanks. Regarding the specific articles you mention, I think "Bayesian Inference in Phylogeny" should be in WikiProjectPhylogeny (if there is one) but surely the article "Bayesian Inference" should not be in WikiProjectBiology? That's the way "GA" in "MCB" looked to me. Genetic Algorithms do not necessarily have anything whatever to do with Genetics. Instead of base pairs from an alphabet of four nucleic acids, you can have base n-tuples that are entry points of LISP functions. A better name might be "Combinatorial Optimization Algorithms Inspired by Allegory From Genetic and Population Biology". But I appreciate the cordial response, I appreciate the rich rich interaction between the fields, we've improved the article, so thanks :-) Pete St.John (talk) 18:53, 12 December 2007 (UTC)

[edit] Paul Chun (professor) in line for a speedy delete

Paul Chun (professor) seems to be in line for a speedy delete on grounds on non-notability. If anyone has any info to the contrary, now would be the time to add it. -- Writtenonsand (talk) 13:18, 11 December 2007 (UTC)

[edit] Parts of a cell

Caesura (talk · contribs) and I independently redirected the new article Parts of a cell to Cell (biology)#Anatomy of cells. The article creator, Warrior4321 (talk · contribs), however disagrees with the redirect, stating that

the article I have written can help users who are searching for Parts Of A Cell.The article that you have redirected it to doesn't really talk about the specific parts of the cell rather than the whole cell.[6]

I undid the redirect, stating that I would bring the topic here for further input. As I outlined in my redirect edit, I believe the redirect is more appropriate as the article was not an inclusive list—If you look at the section to which it was redirected, it includes detailed anatomies of prokaryotic and eukaryotic cells (particularly, in the diagrams) with links to sub-articles about each.

Perhaps other members of this WikiProject will have some ideas as to the correct course of action...? Thanks, — Scientizzle 23:41, 11 December 2007 (UTC)

I think parts of a cell is incomplete. The same material is well covered in the article to which you redirected it. I'm also concerned about the reference used for "parts of a cell". It seems to be a highschool science textbook, which I wouldn't regard as a WP:RS. JFW | T@lk 23:46, 11 December 2007 (UTC)

Cell (biology) covers the same ground but in a more comprehensive way. I think this should just be redirected to the main page. However, that material here might be useful in Simple Wikipedia (maybe their cell article) since it is a nice, basic summary. Tim Vickers (talk) 00:06, 12 December 2007 (UTC)

That's a great idea, Tim. I hadn't thought about the Simple English Wikipedia... — Scientizzle 00:12, 12 December 2007 (UTC)

In case it's gone unnoticed, everything on the Parts of a cell page that Warrior4321 "wrote" is just copied and pasted from other Wikipedia articles. None of that content is original to Warrior4321. (It's not copyvio or anything, of course, since it's from Wikipedia, but it is uselessly duplicative.) It really doesn't belong there; the redirect should stand. —Caesura(t) 00:26, 12 December 2007 (UTC)

Agreed on the redirect. I'm not a member of this WikiProject, but I saw the page come up on the AlexNewArtBot PlantsSearchResult page and was about to redirect it myself before I saw this discussion. --Rkitko (talk) 20:43, 16 December 2007 (UTC)

[edit] Cell Cycle Ontology

It isn't clear whether or not this project [7] is notable--there's a discussion at Wikipedia:Articles for deletion/Cell Cycle Ontology, and some expert help would be appreciated. DGG (talk) 02:52, 15 December 2007 (UTC)

[edit] Mitochondrion

Mitochondrion (edit|talk|history|links|watch|logs) is on WP:FAC. Please comment at Wikipedia:Featured article candidates/Mitochondrion. JFW | T@lk 21:04, 16 December 2007 (UTC)

[edit] Oxygen at FAC

Please comment at Wikipedia:Featured article candidates/Oxygen. --mav (talk) 21:48, 23 December 2007 (UTC)

The FAC was premature, but the article was listed as a GA and the FAC push continues. See the talk page for details. --mav (talk) 03:38, 9 January 2008 (UTC)

[edit] Random coil --> Random coil (protein folding)

Does anyone else think it might be useful to split the random coil article into 2 separate articles? With the first being used to describe the mathematical theory, and the second to describe the protein related aspects of the model?--69.118.143.107 (talk) 18:33, 30 December 2007 (UTC)

Anyone?--69.118.143.107 (talk) 18:50, 21 January 2008 (UTC)
Its not a very big article, I'd be tempted to leave it as it is until it has expanded a bit. Tim Vickers (talk) 19:09, 21 January 2008 (UTC)

[edit] "For the product of protein aggregation, see Amyloid."

Can someone find a better way to phrase this? I find my own wording slightly awkward, and could benefit from a second opinion.--69.118.143.107 (talk) 19:11, 30 December 2007 (UTC)

[edit] SigmaPlot

I realize this third question is slightly outside the scope of this WikiProject, but could someone take a look at the SigmaPlot article, and hopefully rewrite it in a way that isn't as spammy and self-promotional as the original was? I had to blank most of the content as it was directly copyvio'd from systat's website. Surely someone in this WikiProject has used SigmaPlot and can attest to its notability. --69.118.143.107 (talk) 19:55, 30 December 2007 (UTC)

[edit] Merge in Fe-S land

I propose to merge most of the content Iron-sulfur cluster into iron-sulfur protein. Way too much redundancy. We also have an article on ferredoxin as well as shorter ones on more specific proteins High potential iron-sulfur protein, Aconitase, nitrogenase, and adrenodoxin. Maybe some non-bio Fe-S clusters can be mentioned in the article "iron-sulfur clusters." Someone might set up a category for Fe-S clusters. If people have views or concerns on the merger, drop a note on the relevant talk pages.--Smokefoot (talk) 02:18, 31 December 2007 (UTC)

[edit] Help!

Hi,

I'm not an expert, but I had a go at trying to improve the nucleotide page. Diff. The page had some very odd formatting which I tried to fix, and added some prose, but I'm very far from an expert and I'm sure have either made mistakes, ommissions or added complications that don't need to be there. If someone could have a look at it to try to fix it, it'd be a big favour to me, but more to wikipedia. Given it's way out of my expertise I can't really contribute beyond what I already have. WLU (talk) 15:02, 4 January 2008 (UTC)

[edit] The Philip Greenspun illustration project

The Philip Greenspun illustration project will be paying professional illustrators to create images for Wikipedia. The Wikiprojects have been requested to look over their core articles and think about which new illustrations (particularly line drawings and diagrams) we could ask for. Suggestions please! Tim Vickers (talk) 01:55, 15 January 2008 (UTC)

I find that understanding of signaling pathways is greatly enhanced by figures and diagrams. Generating a library of such figures (e.g., [8]) could probably saturate a good portion of the entire allotment, but probably we could cherry pick a couple dozen of the most important (and most complicated) pathways. I haven't looked specifically at the pathway diagrams already in WP so perhaps we're already in good shape for some/most... AndrewGNF (talk) 18:51, 15 January 2008 (UTC)

Signaling pathways aren't very difficult to draw though. Looking through our core articles, how about a cutaway diagram of a Microscope? Tim Vickers (talk) 19:01, 15 January 2008 (UTC)

Ummm, what kind of microscope did you have in mind? :)
I agree, it should be difficult enough that we ourselves couldn't do it, or could it only poorly. How about animations of the cellular organelles and molecular machines, maybe zooming in to view them on different levels and show them in context? For example, it'd be nice to have Image:Chromatin Structures.png as a animation, or to see the electron transport chain, RNA polymerase II, or the ribosome in action, RNA editing and interference, etc. Pictures and/or animations of the most common experimental procedures would also be great, e.g., PCR and other DNA tricks, electrophoretic gels, various types of chromatography, culturing cells, DNA and protein sequencing, mass spectrometry, NMR spectroscopy, stuff like that. Of course, such animations might be asking for too much. :( Willow (talk) 19:55, 15 January 2008 (UTC)

Just a simple optical microscope, but with a cutaway showing the various elements. The translation animation is a current request, perhaps DNA polymerase and RNA polymerase animations? The electron transport chain would not be all that informative an animation though, just blobs moving between boxes. Tim Vickers (talk) 20:03, 15 January 2008 (UTC)

Well, I managed to locate a hacksaw, but now I'm having trouble finding an optical microscope to cut open... ;) Can you direct me to a picture that I might mimick? Willow (talk) 21:18, 15 January 2008 (UTC)
Animation of an equatorial sundial on midsummer's day in Aberdeen. :)
Animation of an equatorial sundial on midsummer's day in Aberdeen. :)
If we're thinking animations, perhaps this link might a place to troll for ideas? But in the absence of existing non-free examples, creating an animation by someone not in the field I think is hard. While I can mock up a static figure and hand it off to a graphic designer to make it beautiful, I think it'd be much harder to mock up an animation. And never having made an animation, will doing that increased amount of work still make sense under the current anticipated payouts? Finally, does WP support animations? Can't recall ever seeing one here. I like Willow's proposal of common experimental techniques though... AndrewGNF (talk) 20:14, 15 January 2008 (UTC)
I'm not sure of the answers to most of your questions, but I do know that they allow animations here at Wikipedia. I just made the sundial at the left this morning, in training for my New Year's resolution of producing a kappa goniometer for X-ray crystallography. It, ummm, needs work, but that's how we might do it; we could show the professional a crude mock-up and say , "Please make this look pretty and cool." :) Admittedly, making movies would be faster and simpler, but perhaps the files would be too big and the images unnecessarily complex? Willow (talk) 21:13, 15 January 2008 (UTC)

[edit] Dr. Samuel Wood human cloner

Samuel H. Wood needs attention. It is a stub. CM (talk) 19:27, 18 January 2008 (UTC)

[edit] G-quadruplex

This article's only categories where wikiproject (this one infact) related cats which dont belong on mainspace, so I had them moved to the talk page and the article is now categoryless. Since this is not my field I'm not too sure where it belongs (Is there a cat better suited for this than the DNA one?). Would someone be kind enough to go there and add a cat or two? Thanks RIP-Acer (talk) 01:50, 20 January 2008 (UTC)

Done. Tim Vickers (talk) 02:17, 20 January 2008 (UTC)

[edit] fixing grammatical errors in gene names?

Any comments on the changing of official gene names for grammatical errors? For example, [9]... (Clearly, this is a very subtle "error".) On the one hand, I'm all for being technically correct in the use of language. On the other hand, given the choice of using the HUGO-approved name or a variant that is more gramatically correct, I think I'd err on the side of using the version from the naming authority. In any case, perhaps it should be discussed. Since Drphilharmonic appears to be making these changes systematically, this isn't just an isolated case or a hypothetical example. (Drphilharmonic's page moves according to this principle has also been introducing several double redirects, a fact which I've note on his talk page.) AndrewGNF (talk) 02:44, 22 January 2008 (UTC)

[edit] Lipid

I'm a member of WP:Chem, so I'm not a subject expert, but I happened to be looking at Lipid which was assessed (appropriately) as Start-Class in 2006. It appears to have greatly improved since that time (when it was demoted from GA) to at least B-Class, so you may wish to re-assess this. I think perhaps it could even be good enough to go to WP:GAN, but that would be your call. Walkerma (talk) 15:38, 24 January 2008 (UTC)

I upgraded it to B-class. Thank you. Tim Vickers (talk) 16:49, 24 January 2008 (UTC)

[edit] Wikipedia Weekly

I tried to promote the project and highlight a few of the things people are doing in the current episode of the podcast. Tim Vickers (talk) 16:52, 24 January 2008 (UTC)

Beautifully done! I'm actually a little jealous that I didn't get to assist on that one! :) – ClockworkSoul 07:34, 29 February 2008 (UTC)

[edit] Action potential

Action potential has been nominated for a featured article review. Articles are typically reviewed for two weeks. Please leave your comments and help us to return the article to featured quality. If concerns are not addressed during the review period, articles are moved onto the Featured Article Removal Candidates list for a further period, where editors may declare "Keep" or "Remove" the article from featured status. The instructions for the review process are here. Reviewers' concerns are here. Medos2 (Talk) 10:31, 30 January 2008 (UTC)

Is anyone going to look at this article? SandyGeorgia (Talk) 17:27, 23 February 2008 (UTC)
It needs definite love. It's one of our very oldest FA's and has been subjected to the usual article decay and increasing FA standards, but it would be a shame to see it delisted. – ClockworkSoul 09:33, 29 February 2008 (UTC)
I'll try to save it. I have very fond memories of learning the Hodgkin-Huxley model from a friend; she was very patient with me, and her words fell as soft as snowflakes. :) The only difficulty is that I'm leaving tomorrow to visit my sister, to help her prepare for her wedding this summer, and I won't be back for a week or so; can we put the FAR on hold somehow? I'll leave a note there; perhaps someone will be likewise patient with us? Willow (talk) 09:52, 29 February 2008 (UTC)
Action potential was saved. Thanks to everyone who helped! :) Willow (talk) 09:22, 8 May 2008 (UTC)

[edit] Moved Bifidus Factor

I moved Bifidus Factor to Bifidus factor and am updating pages that link to it. I d0n't know whether to alter Wikipedia:Version 1.0 Editorial Team/MCB articles by quality/8 Thank you for your time. ColorfulNumbers (talk) 18:24, 4 February 2008 (UTC)

[edit] Using Wikipedia to advance fringe biosciences?

My guess is that much of Chromium deficiency is fringe science, aimed toward promoting chromium as importantly beneficial biologically. There is no characterized metalloprotein. The credibility of chromium picolinate (Googling "chromium picolinate" gave 1.3M hits) is supported by the wobbly nature of the wiki report which makes it appear that bio-chromium is settled science. This editor is afraid, due to NPOV concerns, to forcefully state that a healthful role for Cr is unproven. Similar problems relate to other possible ultra trace elements, and it is difficult to argue such cases. It would be useful if this group were to develop some guidelines for proof of a biochemical role. The ultratrace proponents will always be able to find a variety of publications in specialized journals that support their claim. --Smokefoot (talk) 16:25, 16 February 2008 (UTC)

[edit] Proposal to create a WikiProject: Genetic History

I have put up a suggestion at Wikipedia:WikiProject Council/Proposals to create a new WikiProject (or WikiSubProject), WikiProject: Genetic History.

To quote from what I've written there:

Description
A wikiproject for articles on DNA research into genetic genealogy and genealogical DNA tests; the history and spread of human populations as revealed by eg human Y-chromosome and mitochondrial DNA haplogroups; and similar. Many such articles can be found in Category:Genetic genealogy and its subcategories, notably the subcategories on human haplogroups.
Rationale
  • My direct motivation for seeking this Wikiproject was a recent run-in at Y-chromosomal Aaron, where I desperately missed the lack of a relevant WikiProject talk page to go to, to attract the input, advice and views of knowledgeable editors in this area.
There's a lot of general public interest in the proposed subject area -- eg the Y-chromosomal Aaron page is apparently getting well over 100 hits a day, and over the last 18 months or so there's been a lot of material added, by a fair number of different editors, mostly editing different pages which are particularly relevant to them. IMO, a central wikiproject would be useful, and also a good place to be able to bring WP:OR, WP:V, and WP:general cluelessness issues for wider informed input.
Wikipedia:WikiProject Molecular and Cellular Biology and Wikipedia:WikiProject Evolutionary biology do already exist, but their focus is much much broader. With regard to those project's charters, I believe the subject would be seen as a rather specialist niche topic area, rather out of the mainstream of those project's normal focus. On the other hand, I believe that there are a number of wikipedia editors (and readers) who are specifically interested in the subject, who would find advantage if there were a specific wikiproject for it. Jheald (talk) 12:56, 22 February 2008 (UTC)

If people think this would be a good idea, it's a target for WikiProjects to have at least five "interested" signatures to show there's some support, before they get going.

Alternatively, if people think it would be a bad idea, please leave a comment in the comments section.

Either way, please show what you think, at Wikipedia:WikiProject_Council/Proposals#Genetic_History

Thanks, Jheald (talk) 13:15, 22 February 2008 (UTC)

[edit] Bioflavinoid

Hi! Pardon the intrusion, but I found this project through Vitamin and was hoping that someone could help me out with Bioflavinoid, which I found via new page patrol. What the article currently is, is a mess. Whether it's notable or not, I have no idea and Google doesn't help. Can anyone here help? Thanks! TRAVELLINGCARIMy storyTell me yours 20:47, 25 February 2008 (UTC)

  • The term bioflavanoid is usually used by media outlets or vitamin manufacturers when they really mean flavonoid. I set a redirect. – ClockworkSoul 20:50, 25 February 2008 (UTC)
    • Thanks! So it was a typo and somewhat of a misnomner, no wonder Google didn't help. Figured someone here would be more knowledgeable. Thanks for the help! TRAVELLINGCARIMy storyTell me yours 21:28, 25 February 2008 (UTC)

[edit] 2 Base Encoding nominated for deletion

Please see Wikipedia:Articles for deletion/2 Base Encoding (2nd nomination). Expert help may be useful to decide whether the article should be deleted or this is just a matter of cleanup. --Itub (talk) 09:46, 28 February 2008 (UTC)

[edit] KCNJ15 / kir4.2 editing

Hi. I just wrote something for the KCNJ15 article. It should be factually correct, but I'm not a wiki-veteran, so if anybody would look over if I did some formatting errors (what with templates and Protein Box Bots and such).--LasseFolkersen (talk) 17:24, 28 February 2008 (UTC)

I've switched off the "auto-update of summary" feature in the bot controls at the top, otherwise the ProteinBoxBot would over-write your additions. Tim Vickers (talk) 20:02, 28 February 2008 (UTC)
You need to start citing your sources better. http://diberri.dyndns.org/wikipedia/templates/ does it for you automatically if you insert the PMID. JFW | T@lk 20:19, 28 February 2008 (UTC)
I've expanded them myself. Another hint for Lassefolkersen (talk · contribs): when you use a reference twice or more, you can fill it only once, give it a name (for example, <ref name="Pearson et al. 1999">..</ref> and then recall it using only its name in a single tag (for example, <ref name="Pearson et al. 1999" />). See my edit for a real world example. When you don't have a PMID, this tool can be somehow useful in place of Diberri's. —Banus (talk) 13:08, 29 February 2008 (UTC)
Thank's all. I'll keep your tips in mind --LasseFolkersen (talk) 16:23, 29 February 2008 (UTC)

[edit] In development: WikiProject Tool

I already posted this as a response to a thread above, but I think that this deserves a thread of its own. I'm currently in the process of developing a nifty multi-funtional WikiProject management tool that'll provide - at first - the following functions:

  1. Provide a simple GUI interface for viewing articles and assigning them class and importance rankings (1200 unassigned articles? Not anymore!)
  2. Allow project-wide user talk page postings, with opt-out support (newsletters made easy, right from the desktop)

The first part is nearly complete, and when it is I'll make the tool available for testing while I work on the second part. As time goes on, I hope to add functions and make it general enough for all WikiProjects to make use of it. Hopefully, a tool like this one will help to make WP's in general somewhat more standardized and easier to manage, hopefully with the effect of increasing project participation and reducing the number of abandoned projects somewhat. Anybody have any thoughts or suggestions regarding features they might want to see? How about a really, really witty name? – ClockworkSoul 18:06, 4 March 2008 (UTC)

Sounds great, how about calling it "Igor" :) Tim Vickers (talk) 18:26, 4 March 2008 (UTC)
Wow... that's actually really, really good! I'll be giving you credit for that, so you can have something a little unusual for your CV. ;) – ClockworkSoul 18:29, 4 March 2008 (UTC)

[edit] State of Igor

It's coming along very nicely. A few bugs to work out here and there, but it's getting close to release for some alpha testing. Here's some screenshots:

Logging in process. Anonymous editing is also supported, but if this tool becomes too abusable, I may make it require a login.

Downloading the article list for MCB, but supports all 1212 WikiProjects

Complete listing of all 11081 MCB articles, sorted by priority. Of course, you can sort any way you like.

Let me know what you think! – ClockworkSoul 21:50, 11 March 2008 (UTC)

So this is a browser plugin running in Java? Tim Vickers (talk) 20:44, 12 March 2008 (UTC)
It's a standalone application, but it is written in Java. The release versions will most likely be in the form of executable JAR files. I'm writing a fairly detailed description list of features now, which will be available here. – ClockworkSoul 20:57, 12 March 2008 (UTC)

[edit] article traffic information

Comment moved to Igor's talk page.

[edit] Suggestions

I'm already getting some great suggestions! If you have any ideas (good or bad, or whatever!), go ahead and post them on Igor's talk page. Thanks! – ClockworkSoul 22:02, 12 March 2008 (UTC)

[edit] System biology images

Some new images are avalible here people might find useful. Tim Vickers (talk) 18:26, 4 March 2008 (UTC)

Hi, I'm from the WikiProject Systems, who uploaded most of those images from a government source, which I think, is very interesting also. I am however not very familair with the field of systems biology myselve. I wonder though if some of these images or others could be used to illustrated the systems biology article. Could anybody give me some suggestions are give it a try. Thanks. -- Mdd (talk) 18:38, 4 March 2008 (UTC)

[edit] Proposed WikiProject Microscopy

This may be of interest to some members of this project – I've recently proposed the creation of a WikiProject on Microscopy. If interested, add your name here: Wikipedia:WikiProject_Council/Proposals#Microscopy. Peter G Werner (talk) 18:46, 7 March 2008 (UTC)

[edit] Protein/gene stubs

I've just proposed splitting up the present Cat:protein stubs, many of which are actually on the (human) genes which code for particular proteins, rather than the proteins themselves. Alai (talk) 04:56, 16 March 2008 (UTC)

We should strive for parsimony here. Unless a gene codes for multiple proteins, we should try to concentrate all gene and protein content on the same page. JFW | T@lk 08:34, 16 March 2008 (UTC)
Splitting up the category (or more precisely, stub type), not the articles! Alai (talk) 16:23, 16 March 2008 (UTC)
Is it okay for me to join in? I understand the protein stubs are going to become a huge list with all those automatically generated by PBB, and that most pages listed as a "protein-stub" actually begin with "...is a human gene". These pages already are automatically assigned to a chromosome by means of what the bot picks up from the gene databases - so I think it is a good idea to separate these pages based on that info and give it a subcategory "stub" label. With the number of new pages being generated, this would definitely have to be an automated process that could detect a conserved element in all the pages, right? Of course, once editors go and build the pages up with info, the "stub" tag will likely get replaced with a more specific "Cat:" tag that is appropriate to cover both gene and protein for that particular page. Hopefully I'm not too far off the mark? ~ Ciar ~ (Talk to me!) 18:20, 16 March 2008 (UTC)
We shouldn't split up very small pages just to get the category right. If a page is about a gene as well as its gene product it can have both stub messages simultaneously. JFW | T@lk 19:41, 16 March 2008 (UTC)
I can't say what Ciar has in mind, but once again, I'm not proposing splitting articles. As it stands the artciles are notionally about the genes, there's a metric shedload of them that's truly swamping the articles on proteins per se, which strongly motivates a number of "human genes" stub types. (All this should be clear from the actual proposal, which this was merely supposed to refer the WPJ to, not to spark off a tangential meta-debate.) Alai (talk) 20:58, 16 March 2008 (UTC)
No, my comments were not about splitting the genes away from the proteins either. How do I say this in a way to make my thoughts more clear, h'mmmm. Right now there are currently many thousand pages ALL labelled as protein stubs. The proposal, in my interpretation, is to look at those that are labeled "protein-stub", and give them a new label (e.g. "protein encoded on chromosome 1-stub") so that the pages can be broken down into managable numbers on a category level. All content within the page would remain the same so that gene info AND protein info would remain in the same article - only the management side of things would be different. Is this what you mean Alai? ~ Ciar ~ (Talk to me!) 23:25, 16 March 2008 (UTC)
Exactly. Alai (talk) 00:11, 17 March 2008 (UTC)

At the moment there are a lot of protein stubs categorised as gene-stub. I think we should follow Ciar's suggestion and rename the category to "protein encoded on chromosome 1-stub". — Tirk·fl  “…”  09:12, 29 May 2008 (UTC)

That sounds like a broadly sensible plan to me, since it appears that these articles are something of a mixture of mostly-about-the-gene, but alluding to the protein as well, and vice versa, mostly about the protein, but with info on the human genetic basis (as tagged/catted as both, in each case). Do we need an actual rename of the categories, or would a change to the scoping text of the category and template suffice? Alai (talk) 14:01, 29 May 2008 (UTC)
I think a rename would be better, because otherwise it is very confusing and simply not correct! What about renaming the category to "gene or protein encoded by gene on chr. #-stub" or "protein encoded by/or gene on chromosome #-stub"? — Tirk·fl  “…”  08:30, 30 May 2008 (UTC)
But that's not what that the permcats that these articles all already use are called! If it's "simply not correct" to place an article that's (mostly) on a protein in a "gene" category, why are there literally thousands of such categorisations, and why is no-one objecting to, or proposing renaming of, those? Certainly I find your proposed category names extremely unwieldy -- if category names is what they are, you seem to be mixing and matching between category and template naming formats. If it is the template names you're concerned with, I'd be happy to have additional templates with variant text feeding into the existing categories: perhaps something like {{protein-17-stub}}, or {{protein-chromosome17-stub}}, and so on. Alai (talk) 13:07, 9 June 2008 (UTC)

[edit] Article importance ranks vs. popularity

I've noticed that some articles have importance rankings that differ greatly from their popularity as counted by page views. Looking at the access stats collected 2/01/08 to 2/23/08 I put together a table of the 500 most-accessed articles in the MCB wikiproject and the outliers for the Top and Low importance rankings — the top ten most accessed "Low" articles were 10 times more popular than the ten least accessed "Top" articles. What do people think about how page views should influence article importance rankings? Madeleine ✉ ✍ 04:07, 18 March 2008 (UTC)

The working philosophy for importance ranking has always (at least unofficially) been that the greater the interest an MCB subject is to the community – scientific and otherwise – the greater the emphasis we should place that article's quality. That being said, though, a number of the articles that are ranked as mid- or low-importance simply don't really belong within the domain of molecular biology. Periosteum, for example, might be better left to the physicians. Even caffeine, the #3 most accessed article, an article I love dearly and which I helped bring to FA status, isn't really an MCB subject (pharmacology, really). Perhaps we should go through your list and reevaluate the rankings and "MCB membership" of each of the articles? – ClockworkSoul 04:26, 18 March 2008 (UTC)
I've reassessed Gliotransmitter as mid-importance. To be honest I'd never even heard of them. Tim Vickers (talk) 04:27, 18 March 2008 (UTC)
Neither have I... I'm pushing it down to "low". I wish we had more categories! – ClockworkSoul 04:32, 18 March 2008 (UTC)
Substrate (biochemistry) is not ever going to be much more than a definition, with enzyme kinetics and enzyme catalysis as articles, so I moved that down to Mid as well. Ditto with RNA structure, which although reasonably important, is clearly less important than the core article on RNA in general. Tim Vickers (talk) 04:35, 18 March 2008 (UTC)
I've changed Organic life into a redirect to Life. Tim Vickers (talk) 04:40, 18 March 2008 (UTC)
Excellent. I've been marking articles as "redirect" class if I can see it becoming its own article one day, or de-listing it if I can't. – ClockworkSoul 04:43, 18 March 2008 (UTC)
This may be a good time to mention somethign I've noticed while working with Igor. We have many, many, many, many articles ranked as "low", most of which are proteins which few people will really look at anytime soon. Perhaps we should re-evaluate our importance guidelines to maybe shift the balance a bit? – ClockworkSoul 04:43, 18 March 2008 (UTC)
What about merging Biological inheritance with Heredity? Tim Vickers (talk) 04:46, 18 March 2008 (UTC)
Sounds reasonable to me. – ClockworkSoul 04:47, 18 March 2008 (UTC)
I pushed Ossification from low to high importance. – ClockworkSoul 04:55, 18 March 2008 (UTC)

Should we keep articles that are mostly pure chemistry, like dimer and oil, or tissue types, like fat and periosteum? – ClockworkSoul 05:03, 18 March 2008 (UTC)

Also, drugs, like caffeine and Aciclovir? – ClockworkSoul 05:04, 18 March 2008 (UTC)

Many of these subjects will be falling under multiple WikiProjects, and that is not a problem. I would leave actual pharmaceuticals primarily under WP:PHARM, but a substance like caffeine is harder to push into that corner because most people using caffeine will not do it medicinally (... little do they know ...). Similarly, subjects like periosteum are primarily WP:MED and WP:Anatomy, but MCB has a role to play when it comes to their molecular/cellular aspects.

Collaboration between WikiProjects is still quite rudimentary, and presently seems to be happening more on a personal basis. I'm not suggesting there should be any other cross-talk at the moment, but it is well possible that an article is "high"-importance for MCB while being of only modest interest to Pharm, Med and Anatomy. JFW | T@lk 06:43, 18 March 2008 (UTC)

It looks like, though not the only criteria for classification, counts are useful for assessing and reassessing importance. I've updated the tables and added outliers the High and Mid categories, sorry, it's only semi-automated. I'm guessing Percy Lavon Julian shouldn't be in MCB scope at all - I'm not aware of any other biographies being within MCB project - should we throw out any biographical articles about scientists as not being within the project scope? Madeleine ✉ ✍ 18:15, 18 March 2008 (UTC)
I removed Percy Lavon Julian. Mind of I ask where you're grabbing the data for this list from? – ClockworkSoul 18:46, 18 March 2008 (UTC)
I got the pagehits for en 2/1-2/23 from [10] - same thing I mentioned on the Igor talk page ... but it looks like you can get the raw data from this place? [11] It's a large amount of data; the "full" version is 59 million lines, more than half of which are only "1" observation, I think due to a lot of mistyped urls? For the importance rank lists, I copy and pasted and parsed from web pages by hand. It's tedious, tell me if there's a trivial way to do that... Madeleine ✉ ✍ 19:56, 18 March 2008 (UTC)
Trivial, no... but I could write a bot that does it. It's too much data to import into Igor, unfortunately. :/ – ClockworkSoul 20:11, 18 March 2008 (UTC)
Looking over the list, I'm still not sure we should keep articles like carbon dioxide or alcohol in our lists. Yes, their biological significance is profound, but the articles written on those subjects are destined to be primarily from a chemical or physical perspective, and not one of MCB. – ClockworkSoul 18:52, 18 March 2008 (UTC)
I'm similarly unsure about complex tissues, like muscle. Looking at the article, only a small paragraph is dedicated to the cellular aspects, with the vast majority covering the major anatomical aspects, and appropriately so, I think. Perhaps we should focus more on more MCB-relevant topics like myofibril and myocyte, and leave stuff like muscle to WP:Anatomy? – ClockworkSoul 19:00, 18 March 2008 (UTC)
I guess the point of putting articles in a Wikiproject is to make sure they get attention, not merely to say "it's important to this subject"? If so, and if an article is clearly getting attention from another more appropriate wikiproject, then you could remove it from this one? On the other hand, some wikiprojects aren't very active, so I don't know how you'd quantify "attention". Madeleine ✉ ✍ 20:03, 18 March 2008 (UTC)
I definitely see what you're saying, and there's a great deal of truth to it, but it think that it the point of a having a topical project is to focus those efforts on a particular subject. So really, I think that it's both: is it important to the subject, and are people looking for it? If it was just a question of attention, it would just be a "WikiProject Most Viewed Articles" (which I think would make a pretty interesting group to be part of!) – ClockworkSoul 20:11, 18 March 2008 (UTC)
I'm not sure how I was misread here, but I was arguing that an article like carbon dioxide can be removed from MCB wikiproject because it's presumably getting attention from a more appropriate wikiproject (Chemistry). (I guess you misread attention-from-another-project as referring to page views.) Madeleine ✉ ✍ 20:13, 18 March 2008 (UTC)
Ah... sorry about that. I guess we're of the same mind on this one then. :D – ClockworkSoul 20:19, 18 March 2008 (UTC)

I'm not a member of WP:MCB, but I'm a chemist who's been heavily involved in the assessments at WP:1.0, so hopefully you'll forgive me intruding a little! Firstly, you may be interested in looking at some of our test output here, this is a collection of 1403 MCB articles ranked by a combination of (mainly) importance and (less) quality. It also shows a hit count for one month (Feb 2008, I think), as well as other measures of importance such as links-in and interwikis. Please note that we are still tweaking the system, but we hope that these data will become official soon, and you will be able to see them updated regularly. Secondly, our system at WP:1.0 expects that multiple projects will tag the same article (many have 6 or more projects). So if you want to tag an article like nitric oxide or oxygen, WP:Chemistry, WP:Chemicals or WP:1.0 certainly won't mind - and it may help you to keep track of topics within your area of interest. Cheers, Walkerma (talk) 00:54, 19 March 2008 (UTC)

[edit] Article importance and class: Igor

The first release of Igor is available, if you want to take a look. It's still early in its development, but it still lets you see all of the project's articles and sort them in order of class and importance. I've used it to assign values to a few hundred articles in the past couple of days :) – ClockworkSoul 06:46, 22 March 2008 (UTC)

[edit] Picture requests

Unanswered query This question or request has not been resolved
Remove this tag when this is resolved.

Is there some way this can be included in the template? For example, on phycocyanin I was going to add a request, but the project's template doesn't have the |needs-photo parameter that many others do. In this case it's not so much a photo that we want though - it's difficult to photograph pigments themselves. Unfortunately Wikipedia's image requests are very photo-centric, so I'm no sure what category this request could go in. Richard001 (talk) 09:34, 2 April 2008 (UTC)

Just to doble check as I am not sure what you are actually asking... There are two questions here right?
  • About the image: pycobilin is a small molecule therefore can be drawn as a nice diagram; pycocyanin is a protein: if someone has studied its structure cryoEM, christallography, NMR and so on, it will be in a database [12], which is the case here, there are lots of structures, so you have a choice of two.
  • the question is not actually about pycocyanin but about the template {{Plant Pigments}} written by a user called Doseiai2. Could you give an example of a page with a template with a picture in it? --Squidonius (talk) 14:40, 13 April 2008 (UTC)

[edit] New template for large talk pages

Unanswered query This question or request has not been resolved
Remove this tag when this is resolved.

Some pages, such as this one have lots of post and it requires some work to see what has been answered or acknowledged. therefore I made the {{Unanswered}} template that can be put above a section allowing one to quickly glimpse what has been answered. For now I will tag mine and any post I am 100% sure is unanswered. If you were waiting for an answer but never got one as the post in somewhere in the middle tag it! please voice any queries or comments in the talk Template:Unanswered (links, talk) and not here. Cheers --Squidonius (talk) 14:03, 13 April 2008 (UTC)

[edit] Desperately seeking editors

This article is really really sad: Post-transcriptional regulation. It has been nominated for deletion, by someone who is obviously not a biologist. I asked that the AfD be closed. But, really, the article should be in far better shape than this. If any editors have some time, please develop this article. I see many of the genetics and protein synthesis articles need major work, so I understand if editors have their own priorities. Still.... --Blechnic (talk) 00:51, 14 April 2008 (UTC)

I bulked up the page by using a project report I had on genome-wide detection on transcription rates. but it still needs TLC. I kind of have too many pet articles, anyone what gene reg & co. as a pet? --Squidonius (talk) 17:36, 15 April 2008 (UTC)

[edit] Journal abbreviations in citations

Better tune in to the discussion at WP:CITE. SandyGeorgia (Talk) 22:16, 14 April 2008 (UTC)

If anyone wants to cook something up for Pubmed, I took a note (badly) of the addresses for NCBI stuff on my user page --Squidonius (talk) 14:09, 16 April 2008 (UTC)

[edit] New NavBox

Someone somewhere said that a better table was needed. here is example. Please modify it freely (vde on top left). --Squidonius (talk) 01:22, 16 April 2008 (UTC)

Unanswered query This question or request has not been resolved
Remove this tag when this is resolved.
Protocol issue: Wikipedia's policies are against protocols (How-To) some methods have protocols (eg. Nuclear run-on (no assay in title)) I recently saw that open wetware site is now full of info on protocols and reagents. what is the policy reguarding linking to another wiki not of wikifoundation? --Squidonius (talk) 17:52, 27 April 2008 (UTC)

[edit] Has action potential reached FA-quality? You decide!

I would appreciate commentary and critique on whether the current action potential article is worthy to be a Featured Article. It's a long article, I know, but please read through it and vote your conscience, Keep or Remove, at its FAR. If you don't like it, then let me know what needs to be fixed! Willow (talk) 19:05, 24 April 2008 (UTC)

[edit] Talk:Lysozyme#T4_or_other.3F

Input requested on potential disambiguation (Please do not respond on my talk page as it is shared by a large number of library computers at Stony Brook University. Please also note that my only edits are to lysozyme, its talk page, and to this WikiProject. All other edits from this IP are the result of other users behind the same router in other physical locations within our library system).--129.49.7.125 (talk) 15:20, 1 May 2008 (UTC)

[edit] Nitroindazole AfD

A very stubby article, nitroindazole, has been nominated for deletion: Wikipedia:Articles for deletion/Nitroindazole. It looks like this WikiProject is the one that would be most likely to supply some informed opinion. —David Eppstein (talk) 03:30, 7 May 2008 (UTC)

[edit] Started new discussion topic (mRNA processing)

Hi, I am new to this Wikiproject. I have started working on the Post-transcriptional modification article, however, I am not deleting anything which was there prior to my editing. I am not sure as to what I should do, so for now I am just leaving the older version in the article with my newer edits in it. Shall I just leave the article for an editor to clear up? SholeemGriffin (talk) 12:38, 9 May 2008 (UTC)

I'd rather see less about mRNA in that article than more... especially when the article is underreferenced. I would be nice if the article moved toward discussion RNA in general rather than specific mRNA processing stuff, since there is better written article at messenger RNA about that. Narayanese (talk) 13:43, 9 May 2008 (UTC)
Concur That mRNA article is well linked (I have seen it now for the first time.. lol). and just like for medicine, aputations are ok if it makes the patient better and wikipedia is not a collection of analysed data but well structured information. It seems like it is find and recycle operation (just like yesterdays new PHD comic strip): tRNA has little. My pet article (Nucleic acid analogues) a small section on the bases. Prokaryotes have Aptamers too...--Squidonius (talk) 14:07, 9 May 2008 (UTC)

[edit] cAMP dependent pathway

Hey guys, can you help improve this article. It seems that Wikipedia talk:WikiProject Cell Signaling is inactive.--Lenticel (talk) 04:31, 21 May 2008 (UTC)

It's been inactive for about a year and a half. A common approach to this problem used by many large projects when smaller ones that are closely related to it become inactive is to reabsorb them as a task force. Perhaps we should consider such an action for Wikipedia talk:WikiProject Cell Signaling? – ClockworkSoul 19:01, 9 June 2008 (UTC)

[edit] Request for Cystatin C image

This article is on the main page in the DYK section, but the image might be improved by someone who knows about structure rendering from the Protein Data Bank... See Image:Cystatin C 1r4c.jpg. --Steven Fruitsmaak (Reply) 14:07, 21 May 2008 (UTC)

What would you like in a new image the the current one is lacking? – ClockworkSoul 16:11, 21 May 2008 (UTC)

[edit] Protein data box

Is there a parameter or any other way to get rid of the category:Human proteins it has automatically added? I'm looking at H19 (gene), which isn't a protein. Narayanese (talk) 11:59, 6 June 2008 (UTC)

[edit] Cite journal, PubMed Central & Diberri's tool

Just a heads up for those involved in biomedical topics, PubMed Central as well as longstanding PMID now both have parameter options (pmc & pmid) in {{cite journal}}. Diberri has also kindly upgraded his tool to take pmc article numbers to generate full cite journal markups too (see example) :-) David Ruben Talk 22:53, 6 June 2008 (UTC)

[edit] Yet more protein stub size issues: membrane proteins/transmembrane receptors

The Cat:membrane protein stubs are very oversized: I've proposed splitting off the Cat:transmembrane receptor stubs from those. Let us know if this makes sense, or if some other scheme would be preferable. Alai (talk) 13:09, 9 June 2008 (UTC)