Wikipedia:WikiProject Molecular Biology/Molecular and Cell Biology/Help/Archive 2

Help
I'm having some personal problems that have made me unsuitable to take care of things here for a little while. Can somebody take over temporarily as coordinator until I can get my head straight? Many thanks. –ClockworkSoul 21:44, 2 January 2007 (UTC)
 * Hope you work stuff out OK. If you need anything specific send me an e-mail via my user page and I'll do all I can. Good luck, hopefully see you soon. Looking back at the nominations, Willow is second in line.TimVickers 22:15, 2 January 2007 (UTC)
 * Don't wish to interupt but I just noticed "Collaboration of the Month" needs to be updated. -Tutmosis  20:35, 3 January 2007 (UTC)
 * Thanks for the heads-up. I've dealt with it. TimVickers 21:11, 3 January 2007 (UTC)
 * Should be easy to keep it ticking over since most of the hard work has already been done (thanks!). Not sure how I can help, but right now I'm archiving which at least makes our discussion boards less daunting. Hope everything works out for you in the end, CwS! Seans Potato Business01:51, 14 February 2007 (UTC)

Take a look at gene?
Willow, Filll, and I have been discussing a genetics glossary template for the benefit of the less well-informed readers of basic genetics articles. I've just put this live on gene, but the positioning kind of worries me, because the expanding boxes force the browser to re-layout the whole page when the template is positioned at the top of the article above the main image. Can we get some more eyes to give it a test and see if you have any browser issues? Thanks! Opabinia regalis 07:52, 7 January 2007 (UTC)
 * I put the template into a table with the lead image, and that seems to have taken care of the formatting issues. Am I right that that's what you had in mind? – ClockworkSoul16:33, 7 January 2007 (UTC)


 * Hi, Clockwork, it is so good to see you again &mdash; welcome back! :)


 * I had understood Opabinia slightly differently, as meaning that she didn't like how the lead Figure had to shift so far downwards when the glossary was expanded, so far as to be out of sight for someone reading the lead. That's why I put the glossary template below the Figure; it has room to grow into the white space across from the Table of Contents.  Also, that way, it's still "within range" for people reading the first sections following the lead.  Your Table approach is an excellent idea, though, and would work regardless of whether the glossary comes before or after the lead Figure. Willow 20:23, 7 January 2007 (UTC)


 * Thanks guys - I think combining the two works; putting the template in the lower row of the table sorts out the image-pushing problem and doesn't let the template "float" to the side at high resolution. Also glad to see you back, Clockwork. Opabinia regalis 00:39, 8 January 2007 (UTC)

Help?
Hi, I'm sorry to again bother you all for non-MCB help, but one of my nicest knitting articles, Sweater design, isup for deletion and I need help in understanding the reasons for that and how I might amend it. One thing that leaps out is that I should replace "The knitter should" with "The designer generally" everywhere. :( Anyway, there are so many good writers here and so many people more savvy about WP than me, I'm really hoping that you can help me to understand the objections and salvage the article.  It all comes on a bad day for me; I'll reply when I can.  Many thanks, Willow 12:47, 8 January 2007 (UTC)


 * You want us to write about knitting? ;) David D.(Talk) 16:19, 8 January 2007 (UTC)


 * Very funny and cute! :D Many people are surprised, but I really like spiders; I can't help loving them for the way they wash their faces like little cats, for their beautiful, silky webs and, of course, for Charlotte's Web.  Thanks again ever so much for all your kind help and cheer-me-up! :) Willow 00:09, 9 January 2007 (UTC)


 * How terrible. As ever, I'm late to the party but I'm glad your article never got deleted. Why people want to waste (delete) such useful information that took so much effort to write, is beyond me. I'm happy to be bothered for non-MCB help, particularly if it's to save a worthy article. --Seans Potato Business 10:35, 27 January 2007 (UTC)

Articles for deletion/Douglas Stirling
Professional opinions about this researcher are requested, in particular about the impact of his contributions to the field. ~ trialsanderrors 19:44, 24 January 2007 (UTC)


 * In particular, just the value of his contribution to genetics of the mitotic spindle, not his contribution on the one article with 50 authors. KP Botany 02:35, 28 January 2007 (UTC)


 * Closed as keep. I don't know anything about this guy, but I'm unconvinced. Opabinia regalis02:57, 28 January 2007 (UTC)


 * It's not a matter of personal conviction, though. It's a matter of evaluating it in a way that shows whether or not the researcher is notable--and establishing a precedent for similar researchers in similar areas, if possible.  I don't really think he is, but I do know his area of research is obscure and complex, and internet numbers may not be the factor.  Also, deciding the issue in a useful way for this researcher, may lead to understanding about other researchers in his area and their contributions and their importance.  It also may point out additional deficiencies on Wikipedia, like the sucky article on Mitotic spindle.   Wikipedia has this obsession with numbers that has no bearing on reality--notability is not a numbers count, and it's certainly not a web numbers count, the latter being the reason for so many unnecessary AfDs.  My mom is referenced in almost every major book on a specific subject in every language in the world, but she's not a notable scientist and shouldn't have a Wikipedia article.  However, if there were one about her on Wikipedia, and I wanted it kept, I could simply count out 50 books written withen the past 30 years that have her listed in their indexes.  Wouldn't that be sufficient to make her notable, that she's indexed in 50 books?  However, she's definitaley less notable than Stirling, and I don't think he qualifies.


 * It's very frustrating on Wikipedia, the lack of people who are willing to actually do the work necessary to evaluate something. Folks with backgrounds in MCB should be capable of reading and evaluating Stirling's contribution, so why not let them actually evaluate it, now that everyone has voiced their "keep" or "delete" according to a policy and without referencing specifics from the article?


 * I don't even know what to do with your declaration that you don't know anything about the guy. There's a lot of that running around in AfD.  KP Botany 03:14, 28 January 2007 (UTC)


 * Awesome user name, though. KP Botany 03:15, 28 January 2007 (UTC)


 * I think all the time spent evaluating whoever that guy is could be better spent on articles in the MCB Worklist. If the guy is of 'questionable' notability, as opposed to being unnotable outright, then he's notable enough for me to just leave it alone. --Seans Potato Business 03:45, 28 January 2007 (UTC)


 * Yes, I know ;) I'm a bit confused though; what is it you wanted me (us) to do? I don't know anything about him, so I don't have an intelligent opinion on whether to keep his article or not; the AfD is already closed, so doing extensive research now would be moot unless I intended to expand the article, which I don't. I might've looked further if I had seen this before the AfD closed, but I only posted to let other project members know that the AfD was over.Opabinia regalis 03:49, 28 January 2007 (UTC)


 * Well, it could establish some ideas about the field of research that's an important area in genetics right now, to increase Wikipedia coverage on it. I'm willing to vote to delete all sorts of articles, even on topics I'm interested in, if the article is not up to snuff, and this one is clearly low-grade.  However, that's not the issue for me, deleting this particular article or not.  What's the issue is making the process go more smoothly, leading to appropriate results in general for science articles, notification of users capable of evaluating the aritcles and making sure that deletions aren't based upon someone not knowing anything about it deciding to delete it.  The big picture.  I suspect this article isn't important enough to have even spent this much time on.  Still, the mitotic spindle article deserves something much better.  What related areas are just as deficient?  Do we not have anyone who can read Stirling's paper and tell without research the level of importance?  I can read just about any obscure paper in my areas and know pretty much where it stands in the big picture.  Is this not the case with MCB?
 * On a side note, I have access to a TEM for a while, maybe some spare time later on in my project, is there a place where image requests are posted in this area? Are images needed?  KP Botany 17:51, 28 January 2007 (UTC)


 * Last things first - thanks, and our image requests page is here, though it doesn't get much traffic. What kinds of samples would you have access to? Just off the top of my head, we currently only have one rather low-resolution micrograph for cell nucleus. This is a tall order, but none of the amyloid-related pages have a single micrograph of this very distinctive structure, and a nice image of mature fibrillized amyloid beta would be very useful.


 * I am, on balance, something of a deletionist, and in general I think an article ought to make its own case for being kept; if it's so inadequate that reasonable people can't see what the point of it is, then it's probably also inadequate to serve as a starting point for future expansion by someone who does know the subject. Of course, I'm implicitly asserting that AfD regulars are on balance reasonable people (which may be in doubt ;) I'll point to one counterexample, Articles for deletion/Retrocausality, that went exactly the opposite way; uninformed users voting to keep something that anyone with a clue about the field could see was nonsense. (To be fair, the article was subsequently rewritten about a distinct concept, and kept.)


 * If you ask my boss what I do, he'll tell you computational chemistry, which isn't quite right but it's close enough to explain why I personally can't judge one oldish paper on mitotic spindles without further reading. I notice that one project member TimVickers had a more informed opinion. You're right that mitotic spindle - and, I think, a large number of basic cell biology articles; see the state of cell nucleus before our September collaboration - is quite poor. Opabinia regalis 18:54, 28 January 2007 (UTC)
 * My project is in materials science, but we have plenty of biological samples in the biological section. I've been looking at light microscope slides over there, many of which are tied to TEM prepped samples.  I can certainly get a higher resolution micrograph of a cell nucleus, id'ed to what cell it is the nucleus of.  I might be able to get something along the lines of amyloid beta pictures, but I'm not sure.  I know very little on the topic, but I think that the bio lab is working on some Alzheimer's projects. It'll take time, but I'll keep this stuff in mind. I'll watch the image request page, but if you think of anything else, post on my user page.
 * I think I'm more of a deletionist, in general. There's just too much crap on Wikipedia.  But, sometimes I just want to make an informed decision, so the Nobel Prize winners are already in place.  KP Botany 19:14, 28 January 2007 (UTC)


 * Call me picky or call me shortsighted, but even during the dispute about RNA interference I never thought to create Andrew Fire or Craig Mello till after the prize was announced ;)
 * A nice nucleus from a known cell type would be excellent. The one that's there now was scraped out of a US government publication that didn't really caption it. I'll let you know if I think of anything else; thanks for the offer. (You really don't mind? I've done TEM before and found it to be a terrible pain in the backside.) Opabinia regalis 00:26, 29 January 2007 (UTC)
 * Read a little closer, Opabinia, I'll do images of what has already been prepared, not gather specimens, clean, embed, blah blah blah. I bet on RNAi, right from the start, but not this soon.  That was surprising.  What was the dispute about RNA interference?  I'll go look at it.KP Botany 02:54, 29 January 2007 (UTC)


 * I know. Maybe it was laziness that drove me into computational work, but I never liked staring at green phosphorescence and then waiting around in the darkroom. (I'd rather stare at a computer screen in a dark room?) But maybe you have nicer stuff like CCD cameras, or are just less lazy ;)
 * I was also surprised that RNAi came so early, and that none of the early plant people were included. (There's a thread on this somewhere in my talk page archives too.) The dispute on the RNAi article is long resolved at this point, but involved a former member of Mello's lab who is apparently now in a legal dispute about how much credit he was or wasn't given, and who repeatedly inserted links to his personal website into the article. My removing them identified me as a member of the super-secret Mello cabal, or something. Incidentally, I've recently gotten some motivation to go fix up that article (it was the MCB collaboration in December, but nothing ever gets done thoroughly in December) - so if you feel inspired, come take a look. Knowledge of plant work is particularly useful. Opabinia regalis 06:11, 29 January 2007 (UTC)

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 00:25, 27 January 2007 (UTC)

Article Worklist
Regarding the mathbot-generated worklist: how often do the article entries get updated? The worklist page says that the list is updated every day but I'm wondering about the individual entries (as they move from stub to start etc.).--Seans Potato Business 10:20, 27 January 2007 (UTC)


 * The current status on the worklist is updated every day, I believe, by scraping the contents of the categories. How often articles are reassessed, is pretty much "when someone gets a round tuit". Opabinia regalis 03:17, 1 February 2007 (UTC)


 * I added the MCB template to the discussion page of two-hybrid screening a while ago but it is yet to appear on the article worklist. Why is that? --Seans Potato Business 23:34, 11 February 2007 (UTC)

Anybody knowledgeable about Toll-like receptors?
I swear I've seen this posted here before, but maybe I'm imagining things. There's been an edit war ongoing on this page about the history of their discovery, between two people who are both knowledgeable about the field in general but have little wikipedia experience; see Talk:Toll-like receptor. This is not a field I know at all - any clueful people around? Opabinia regalis 02:52, 28 February 2007 (UTC)

Non-biochemical peer review
Hi all,

Sorry to interlope with a non-MCB request, but it's your own fault for being such good writers and helpful critics! :D After long struggles, I've put Encyclopædia Britannica up for peer review prior to nominating it at FAC. If you can spare a moment to look it over, make suggestions or improve it, I'd much appreciate it! Thanks as always,Willow 21:52, 28 February 2007 (UTC)

Question Concerning Copyrights
I didnt really know where to ask this question actually, but here seems the best place as far as I can see. I created an image of Occludin using the PDB data and the PDB Workshop but I am not sure if I am entitled to release it as Public Domain now. Does anybody here know and can you help me to create a better image if this one is copyrighted?

thanks a lot. --hroest 23:46, 1 March 2007 (UTC)


 * My understanding is that technically, protein renderings cannot be public domain unless the program used to create the image does not itself require attribution. GFDL is safer, but this is really picking nits; the consequences of releasing an image as PD are essentially nonexistent. I usually make sure to cite the PDB ID and link the tool used to create the image in the image description section, though.


 * If you're interested, we do have a PyMol tutorial to help people create images using PyMol. Opabinia regalis 02:43, 2 March 2007 (UTC)
 * I release all of my work (including protein renderings) to the public domain, even though I use proprietary rendering software. Should I be worried? :) An aside: I can't run PyMol on my PC. Is PyMol now the "official" program?Fvasconcellos 02:53, 2 March 2007 (UTC)


 * Worried? I doubt it ;) I've always considered using an image for Wikipedia to be a form of publication, so I follow whatever the program requires in terms of attribution in an online source. (Usually a link to the website, with a citation of the original paper as a second choice.) If your program doesn't require that it be cited when images created with it are published, then you're fine.
 * Pymol is the program we have a tutorial for, after a vote on which program to support, but not 'official' really. (I have to admit it's growing on me compared to VMD.) What's the problem installing it; is it something that other people are likely to encounter? Opabinia regalis 03:39, 2 March 2007 (UTC)
 * Not unless everyone has Cambrian hardware in dire need of upgrading ;) I'm using Accelrys DS Visualizer, it's quite good (although best suited for small molecules) and I don't think there is a citation requirement.Fvasconcellos 01:22, 3 March 2007 (UTC)

GABA receptor
Would any of our illustrious MCB editors be willing to help out at GABA receptor? I updated the reference mechanism and tracked down cites for it way back when, but I'm afraid improving the actual content—specifically, making it clearer and more accessible—is out of my league. A visitor raised a comment on the article Talk page regarding its inaccessibility, and I'm inclined to agree with him. Thanks in advance, Fvasconcellos 21:10, 3 March 2007 (UTC)

Sperm & Co.
I'm not quite sure where to put this question, so I'm putting it here since it involves cells. Basically, I'm inviting comments and suggestions at Talk:Sperm regarding a possible page move/disambiguation. I noticed a while ago thatsperm cell was redirecting to spermatozoon, which struck me as incorrect and mammal-centric. So I went ahead and created a more general page to include other types of sperm as well. I created the new page at sperm and redirectedsperm cell to it. Both of these are former redirects to spermatozoon. I saw in the history that sperm started out as a definition of sperm as semen and at other points was a disambiguation page. Based on the votes of two editors on the talk page, it was redirected to spermatozoon. It seems there's been a bit of reverting back and forth going on based on the conflict between sperm = cells versus sperm = fluid and whether the term is truly ambiguous. I noticed when trying to disambiguate links to sperm after I changed its content that quite a few pages use it meaning "semen" and this is not the only ambiguous meaning. After finding Sperm (album), I went ahead and created a sperm (disambiguation) page to declutter the disambiguation links I had started to add to the sperm page. My question now is: Should sperm itself become a disambiguation page again and its current content be moved to sperm cell? In any case, I don't think redirecting it to spermatozoon is accurate. - tameeria 00:37, 5 March 2007 (UTC)
 * I'd say that sperm should redirect to the disambig page. At the top of each page linked from sperm (disambiguation), place or something similar. Let me know if you want some help.-- Scientizzle 18:08, 5 March 2007 (UTC)
 * Maybe an article is in order for spermatia, too? (currently a redirect) -- Scientizzle 01:09, 6 March 2007 (UTC)
 * No strong opinion, but first instinct is to leave sperm as-is, maybe with the disambig note explicitly linking tosemen as well as sperm (disambiguation). But really, anyone using 'sperm' to mean 'semen' deserves to land in the wrong place. Opabinia regalis 01:19, 6 March 2007 (UTC)
 * An article on spermatia would be cool, especially since they seem to have developed some interesting modes of dispersal. Sperm actually used to be a disambiguation page and has been changed repeatedly to point tospermatozoon, so I thought there might be some need for discussion. Quite frankly, I didn't even think of it being ambiguous when I put the new content at sperm instead of sperm cell, but apparently quite a few people think of sperm as semen. I first had that as a link on top of the sperm page, but then found more ambiguous pages, hence the whole new disambiguation page. - tameeria 01:26, 6 March 2007 (UTC)

DNA replication
This article has morphed over the past two weeks from this to to this. I've nominated it for MCB collaboration of the month, but it might well need significant attention before then. I'm not even sure where to start as it has been rewritten so much and had parts taken out so that it's pretty much been chopped into a completely different article from what it used to be just two weeks ago. Some of its former content appears to reside at prokaryotic DNA replication and eukaryotic DNA replication now, which both are in desperate need of attention as well. -tameeria 03:03, 8 March 2007 (UTC)
 * Any good reason not to just revert to the 17 Feb version and turn the others into redirects? The current version is... hmm... clearly inferior. Opabinia regalis 05:21, 8 March 2007 (UTC)

I have reverted and copied the current version into a sub-page of the user who did the deletion so they can work on a new draft without disrupting the old one. TimVickers 05:33, 8 March 2007 (UTC)
 * Should we revert to the February 17 version instead of the February 26 one? Just from taking a brief look at it, the Feb 17 version has a much clearer structure, in my opinion. Instead of treating it as eukaryotic versus prokaryotic, it has section on initiation, elongation, termination etc. I think that's a much better approach for the topic and I'm not quite sure why it was changed in the first place. The change was done by "Joe" (IP 74.97.31.113) who left a message on my talk page asking for a review of his expansion (which was more like a replacement of the whole article). I didn't really get around to looking at it until recently. He also said there is another DNA replication page different from this one as well. I'm not sure where though. I'm wondering if maybe he accidentally overwrote the old page while trying to created an alternative one. - tameeria 13:33, 8 March 2007 (UTC)
 * Addendum: Just found the alternate and it appears to have the old content: DNA replicate. It was created 5 Feb 2007, should probably be merged/redirected? Another merge/redirect candidate might be: Replication fork and the two proposed mergers from there. - tameeria 13:37, 8 March 2007 (UTC)
 * Be bold, you seem to have a good handle on this, go and do your thing! TimVickers 16:49, 8 March 2007 (UTC)

Animal cell
Could someone, or better yet lots of someones, please have a look at Animal cell? I hope I don't offend anyone, but… Judging from its poor quality and its relative lack of incoming links, I get the feeling that not enough experts are aware of it. Judging from the frequency of IP vandalism and low-quality edits, I also get the feeling that there is a disproportionally large popular audience for the article. Cheers, Melchoir 16:37, 13 March 2007 (UTC)

I was bold and merged it into Eukaryote and replaced it with a stub and a link to eukaryote.TimVickers 17:28, 13 March 2007 (UTC)


 * Looks good! Melchoir 17:47, 13 March 2007 (UTC)

New Daughter Project?
Greetings.

My name is Guido David Núñez-Mujica. Undergraduate student, working on my thesis in Systems Biology, no papers yet in this field, however, got some in a totally unrelated field (Future studies). I would like to suggest some terms we could add to the Wikipedia related to this entry, as they are quite a number and we are under the Molecular and Cellular Biology WikiProject, I would like to know if you think it would be a wise thing to create a Systems Biology WikiProject, to make it a Daughter Project or to remain under the Molecular and Cellular Biology WikiProject to avoid scattering our efforts.

I think these terms should be added or expanded:

Metabolic Flux

Stoichiometric Matrix

Metabolic Control Analysis

Control Coefficient

Elasticity Coefficient

Fundamental Subspaces of a Matrix

Elementary Modes Analysis

Also it would be worthy to detail to some extent the biological implications of topics like Null space or Graph Theory.

I apologize in advance for any mistakes in my English, which is not my first language.

Thanks in advance.

Guido


 * Your English is much better than my Portuguese (guess). There is the Metabolic Pathways task force and some other pages you might find interesting aremetabolic network modelling and metabolic network. Welcome to the group! TimVickers 23:58, 15 March 2007 (UTC)


 * Thanks, Tim. Actually I come from Venezuela. And yes, I saw those entries, and I think are great. Concerning the Metabolic Pathways Project, I think what i am sugesting is slightly different, because those concepts are more related to modelling per se than to specific pathways. Of course, I might be wrong. Guido


 * I think what I would recommend is for you to stay with MCB for now. This project does not have a lot of active members and I think having one general project with a lot of interdisciplinary interactions is better than us creating a lot of small, specific and less-active projects. Perhaps, a sub-project would be a good plan once the systems biology/bioinformatics section of MCB has grown large enough enough to support itself? I'm not sure. Anyway, whatever you decide to do, thanks for joining us! TimVickers 17:00, 16 March 2007 (UTC)
 * P.S. I'm working on the metabolism page at the moment, if you had any suggestions or comments they would be very welcome. TimVickers 17:01, 16 March 2007 (UTC)


 * I am not setting anything new. I mean, I am new here and what I want to do is to become helpful, not to start messing things up. And you are right in your analysis if we have few active members. I will go to check Metabolism right now.Guido

Help needed at Phaseolamin
Having come to wikipedia looking for information on Phaseolamin and finding the article in a terrible state, I decided to improve it. But, not being a biochemist, I can't take it much farther than I have already. I've referenced two journal articles that are relevant and cover all the information in the article, but I suspect there's more relevant information that could be extracted from them by somebody who knows what they're doing. I'm also not sure how to categorise the article; I've left the current category of Category:Dietary supplements in place, but I've removed it from Category:Enzyme stubs, because it isn't an enzyme but an enzyme inhibitor -- as to what other categories it should be in, I don't know. JulesH 19:00, 18 March 2007 (UTC)

Ice-minus Bacteria
I am looking for advice on improving the ice-minus bacteria article.Amkered 23:28, 24 March 2007 (UTC)

License for RSCB snapshots and/or automated image generation
Does anyone know what the license terms are for the protein structure snapshots on RSCB? For examplehere... Can't find any info from a search (of WP and the web), and if no one's inquired before, I'm happy to email the RSCB folks. Obviously a few users have done very nice work creating images for a few proteins, but for our planned effort tocreate protein pages en masse, I'm thinking about less-beautiful and more-automated ways of populating image field in the protein box. Any thoughts?AndrewGNF 19:46, 30 March 2007 (UTC)
 * I've e-mailed them to ask. Their help page states "The contents of PDB are in the public domain. Online and printed resources are welcome to include PDB data and images from the RCSB PDB website, and may be sold, as long as the images and data are not for sale as commercial items themselves, and their corresponding citations are included."TimVickers 20:01, 30 March 2007 (UTC)

Great! I think we're good to go as far as harvesting those images then (right?). (Before I lose it, I thinkthis is the link I need to include with the image upload...) Very cool... AndrewGNF 20:42, 30 March 2007 (UTC)
 * Right. Here's the e-mail I got back: TimVickers 17:06, 31 March 2007 (UTC)
 * Dear Dr. Vickers,


 * Thank you for your email message.


 * Images and data from the RCSB PDB are free for use -- our citation information is athttp://www.rcsb.org/robohelp_f/#site_navigation/citing_the_pdb.htm and our advisory policy is athttp://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/pdb_advisory.html


 * Please let us know if we can be of further assistance.


 * Sincerely, Rachel Green

non-MCB FAC of EB (acute alphabetiasis ;)
Hi, as some of you know, I've been working on the Encyclopædia Britannica article (and its relatives) since early December. About a week ago, it was nominated as a feeatured article candidate, and received excellently detailed reviews from Tim and Opabinia. Unfortunately, it hasn't been reviewed by too many others. :( If any of you have the time, it would be great if you could look the article over and make suggestions on improving it. Please be ruthlessly honest; this future featured article doesn't want a cheap seat in Valhalla. ;) Thank you very, very much, Willow 21:41, 30 March 2007 (UTC)

Equipartition theorem
Hi all,

I know that many of you are very busy with DNA and other articles, but if you could find time to reviewEquipartition theorem, which is now a Featured Article candidate, I would appreciate it very much. :) It's tangentially relevant to structural biology, since equipartition allows us to compute the mean tumbling times of a globular protein about its three principal axes, which is important in determining the feasibility of protein NMR. Many thanks as always, Willow 21:08, 27 April 2007 (UTC)


 * Willow, I'm man enough to say when I have no idea about a subject. Even the title scares me.TimVickers 21:23, 27 April 2007 (UTC)

I understand and thank you nonetheless. You're a stellar Wikipedian in my book, even if you don't care to delve intoneutron stars. If only they'd called it the "share&share-alike theorem", maybe it wouldn't be so scary for people! ;) There's a little blurb about beer haze and proteins, maybe that would be fun for you to read?

I'm sorry that I haven't had time to help out with DNA. :( Here's a thought that might help you, though: somebody should add a Figure showing the numbering of the atoms, and explain why the ribose atoms get the primed numbers and the nitrogenous base atoms get the unprimed numbers.  Such a Figure might help in clarifying the whole 3ˈ, 5ˈ thing for students.  With affectionate good wishes as always, Willow 21:43, 27 April 2007 (UTC)

P.S. I'm surely not "man" enough to tackle something like Evolution; that would require a brave Wikipedian indeed! ;)

Glutathione reductase
I'm trying to put this image into the proteinbox in glutathione reductase. Why won't it display?TimVickers 19:29, 7 May 2007 (UTC)
 * You have to either remove or specify the width parameter. If it's present and blank, the image won't display.Fvasconcellos (t·c) 19:31, 7 May 2007 (UTC)
 * Done. I've no idea as to why this happens, in case you're wondering :)Fvasconcellos (t·c) 19:32, 7 May 2007 (UTC)


 * Thank you, where in the box do I specify or remove this parameter? TimVickers 19:35, 7 May 2007 (UTC)
 * Nevermind, got it. Thanks! TimVickers 19:36, 7 May 2007 (UTC)
 * You're welcome. If you don't mind, which software did you use to create the image? That's an interesting style.Fvasconcellos (t·c) 19:41, 7 May 2007 (UTC)
 * It's just a screenshot of the Jmol visualisation on the PDB website. Good enough for a stub!TimVickers 19:47, 7 May 2007 (UTC)
 * Thanks. Certainly good enough, and quick, too… Fvasconcellos (t·c) 19:49, 7 May 2007 (UTC)

Genetics
I just noticed that is making a big push on genetics. Just thought I'd post it here in case anyone might be interested in helping her out. David D. (Talk) 19:38, 9 May 2007 (UTC)

Dopamine genesis
Can anybody tell me how dopamine (and other neurotransmitters) get to be in the vesicle of the axon? If the Neuron do the synthesis where do the components come from? —The preceding unsigned comment was added by 136.153.2.6 (talk •contribs).


 * There's a lot of good info in dopamine & neurotransmitter. Monoamine neurotransmitters are synthesized in the neurons and packaged into vesicles via VMAT2 (which has a woefully inadequate article). Tyrosine hydroxylasehas some info on the synthesis of catecholamines. Serotonin is also an interesting read... &mdash;Scientizzle 16:07, 6 June 2007 (UTC)

Glucoregulation
I came across Glucoregulation as created by a new user. Homeostasis states "Among the most important mechanisms human bodies need to regulate are: Thermoregulation, Osmoregulation, and Glucoregulation." TheGlucoregulation article needs some care and kindness and I do not know anything about the topic. Thanks! --Jreferee 15:04, 9 June 2007 (UTC)
 * Merged with Carbohydrate metabolism and replaced with redirect. TimVickers 17:13, 9 June 2007 (UTC)

Bioenergetics
I just noticed that Wikipedia's information on bioenergetics got merged into an article called Biological thermodynamics. If you know anything about bioenergetics, please comment at Talk:Biological thermodynamics.--JWSchmidt 14:37, 22 June 2007 (UTC)


 * I wish we had taken the time to look into this back in June. It turns out that the person who created Biological thermodynamics is a scam artist who has been adding pseudoscientific garbage to Wikipedia for the past two years. See:Requests for arbitration/Sadi Carnot/Evidence. --JWSchmidt 05:56, 30 October 2007 (UTC)


 * Thankfully that page doesn't seem to be one of the worst examples. However, is Biological thermodynamics simply a redundant article? Tim Vickers 15:28, 30 October 2007 (UTC)

Molecular evolution (draft |talk)
Hello, I noticed that molecular evolution was of top importance for the Molecular and Cellular Biology WikiProject. I also think it's a very important article and I would like to see molecular evolution get the FA status it deserves. I've started a draft here. Any help is welcome.

- PhDP 08:33, 4 July 2007 (UTC)

Link problem after topic merge
Diacylglycerol was recently merged into Diglyceride, but Version 1.0 Editorial Team/MCB articles by quality/2 is still linking to diacylglycerol. For some reason I can't fix the link by changing Diacylglycerol into diacylglycerol. Please help, link-fixing and no beer make Homer something something. Sakkura 15:12, 12 July 2007 (UTC)

Could use some help with mitotic inhibitor article
I recently started and partially developed the article mitotic inhibitor. I beleive it has a high importance to this project, because of its extreme importance in the research and treatment of cancer. I am new to wikipedia, so any help writing and formatting the article up to wikipedias standards would be very helpful. Also, at the moment, there is still a lot to be said about mitotic inhibitors. It would be great if someone could assess the article for quality and importance. Dancanm 16:02, 12 July 2007 (UTC)

Protein articles for Tuberous sclerosis
Tuberous sclerosis (TSC) is caused by mutations in either of TSC1 and TSC2, which encode for the proteins hamartin and tuberin respectively. It would be great if these had two short articles. I think they should be for Hamartin andTuberin rather than the gene names, but you guys know best. There is some info already on the TSC page. If someone here would like to help create these articles, please get in touch. Thanks,Colin°Talk 13:55, 19 July 2007 (UTC)

Bullitins? (And two other quetsions.)
Thanks for making this great initiative! --Dan|(talk) 07:06, 13 August 2007 (UTC)
 * 1) I read somewhere about bulletins? How can I sign up?
 * 2) Would it be acceptable to 'spam' my project using the bulletin? I am working on a 'database of biological databases', which you can read about here; MetaBase and here; MetaBase homepage.
 * 3) Would it be acceptable to 'spam' this project anywhere on discussion pages? I think the MetaBase project is related to the Molecular and Cellular Biology project, and I would love to attract some users to my project.


 * I can answer 3 with a definite yes, we are always glad for new blood! As for the bulletin I'm not sure who is running it, or even if it is still being produced. Tim Vickers 18:57, 13 August 2007 (UTC)

Exosome complex
The article above was written recently by me with the intention of making it FA. All comments and suggestions on the article are welcome and will be addressed. The FAC discussion can be found here: Featured article candidates/Exosome complex. --Cpt. Morgan (Reinoutr) 15:55, 19 August 2007 (UTC)

Adopting a gene page
Anyone interested in adopting a gene page? Specifically, we're looking for people to help locate/integrateProteinBoxBot content when there are namespace conflicts. As an example, check outthis old PBB log file. You can see that only four of the fifty gene pages could be created outright. The rest either had to be merged with an existing gene page (generally replacing the existing protein box with our PBB-enhanced one) (e.g., CXCR4), or after confirming no gene page exists, starting a new gene page at an appropriate location (e.g., MAPK3). I can obviously provide more details and instructions if anyone is interested, but I'll only bother writing them out if there are willing volunteers. The goal is to get to 3000-5000 gene pages total, and it will go much faster if I'm not the only one doing these semi-automated edits! Reply here if you're interested... Cheers, AndrewGNF 04:08, 30 October 2007 (UTC)
 * No volunteers? Anyone?  Bueller?  It takes roughly 2-3 minutes per gene, and we've broken it up into 20-25 gene chunks.  Easy enough to do in one sitting, or you can break it up over a couple of days.  If you're interested, we're up to 190 genes so far -- check out the list here...  Cheers,AndrewGNF 01:54, 1 November 2007 (UTC)


 * OK, I need something to do over the weekend! What do you need doing and to which articles? The PBB logfile is a bit opaque. Tim Vickers 16:18, 1 November 2007 (UTC)
 * Tim, you're probably the last person that needs additional work. But, I won't turn down the offer either...  I put together some general instructions at User:ProteinBoxBot/Volunteer.  Please let me know if you have suggestions for how to make the process easier (feel free to edit the instructions yourself).  Right now there are only two sets of genes that need to be processed, but knock on wood, we should have several more there by the end of the day... AndrewGNF 17:41, 1 November 2007 (UTC)

Just a quick update on progress. Thanks in large part to the work of Forluvoft, Banus, and Tim Vickers in the last week alone, there are currently 591 genes utilizing PBB content. In addition though, the backlog of genes which require some minimal amount of human interventionis growing. If you'd like to help out to get us to 3000-5000 genes, please see ourVolunteer Page. Cheers, AndrewGNF 18:41, 8 November 2007 (UTC)

adding a note-kinda thing to a page
A non-biologist reading a sequence with degenerate bases, might end up in nucleic acid analogues, what is the wiki-protocol for a warning line at the top to say "If your sequence has Ws and Ss, Ms and Ks, Ns and stuff those are degenerate bases not analogues"? I dont know how common it might be, I could put it at the bottom. e.g. I have heard once or twice people think of degenerate primers not as a mix of reg bases but as if Ψ & co. were used, so I assume it might be quite fairly common.--Squidonius 00:41, 3 December 2007 (UTC)
 * I'm not sure that I fully understand the enquiry, and unfortunately you've had a long wait for this reply, but insomuch as I might understand it, then I should advice that Wikipedia is not meant to be a source of advice for anyone, and nor is appropriate to address the reader (i.e. "if your sequence..."). Seans Potato Business 19:14, 5 April 2008 (UTC)

Thanks, eventually I found it. ((Distinguish|other_article)) tag is used as a warning against confusion with a different topic --Squidonius (talk) 12:16, 13 April 2008 (UTC)

Candidate for deletion?
Hi all, what do you think of this page: Plastid Database? Would this be a candidate for deletion? Or merge somewhere? But where? Should Wikipedia have a page for the NSF Arabidopsis 2010 Project (which this was part of)? -tameeria (talk) 02:49, 9 December 2007 (UTC)
 * In general I am interested in all the MCB databases - I would like to integrate work on WP with the MetaBase project that I run here... I wonder if anyone has any suggestions on a reasonable way to integrate that project and this? --Dan|(talk) 12:35, 3 April 2008 (UTC)

Merge proposal for isotonic, hypotonic and hypertonic
Hi again, I've proposed a merge of these three pages into tonicity. This is the second time I'm proposing this. The first time the merge tag was taken off by another editor with the edit summary "Probably should remain seperate" but no discussion. I'm hoping to gather a few more comments to see what the consensus might be on this, so please feel free to stop by at Talk:Tonicity and leave your comments. Thanks! - tameeria (talk) 20:45, 11 December 2007 (UTC)

Move or merge osmole?
Another request for comments (since there have been none so far): I've proposed to move Osmole (unit) toosmolarity (currently a redirect to osmole), but I'm not sure if that would be the best course of action or if it would be preferable to merge them into osmotic pressure. If you wish to add your opinion, please stop by at Talk:Osmole (unit). Thanks! - tameeria (talk) 16:54, 12 December 2007 (UTC)

Last common ancestor/Most recent common ancestor
Hi there, a discussion is underway on the talk page of Last Common Ancestor on the correct definition and application of these terms. Could somebody with some knowledge of phylogenetics help out here? Tim Vickers(talk) 04:45, 13 December 2007 (UTC)

Merge candidates
I was doing some gene searching here and stumbled on ~400 or so possible duplicate gene pages. I resolved a few of them, but perhaps others would be interested in chipping in too? User:AndrewGNF/Merge_candidates. Feel free to delete entries that you check and/or resolve... AndrewGNF (talk) 02:19, 14 December 2007 (UTC)
 * Quite a few of these are cases of protein families vs. individual members or protein complexes vs. their subunits. For example, CCND3,Cyclin_D is listed as well as CCND2,Cyclin_D.  I agree, some of those on list are "true" duplicates. Forluvoft (talk) 02:30, 14 December 2007 (UTC)
 * Yeah, realized it's probably not quite as enriched for true merge candidates as I would have hoped. But, I also realized that it would also be useful to start wikilinking from the protein family/complex pages to the individual genes/proteins.  Again, in case anyone wants something to do... AndrewGNF (talk) 17:28, 15 December 2007 (UTC)
 * Yes, this may require wikilinking in 90% cases rather than merging. Agree with Foruvoft.Biophys(talk) 17:25, 16 December 2007 (UTC)
 * We have to be very systematic here. If this is an article about a single human gene and its protein products, it should be CSNK2B. Casein_kinase_2 is something different - a family of paralogs. Biophys(talk) 17:37, 16 December 2007 (UTC)