Wikipedia talk:WikiProject Molecular Biology/Molecular and Cell Biology/Discussion Archive

Here are archived some old discussions from the Molecular and Cellular Biology Wikiprojection discussion page. Do not reply. If you wish to continue a topic, please copy and paste it back into the discussion page.

Members

Recruiting

What do i need to do to join the project? BorisTM 09:09, 25 October 2005 (UTC)

Please add your name to the list at Wikipedia:WikiProject Molecular and Cellular Biology#Participants.

User Box

This user is a member of the Molecular & Cellular Biology WikiProject

We need to have one. But i can't find a good image for it. I like the image for the cell_biology stubs. What about the background color? The brown that we have in the protein info boxes? And the name is so long i just couldn't fit it, so i had to end up with this variant. Any ideas? -- Boris 17:14, 29 January 2006 (UTC)

Possible cell-bio userbox picture

I think you need a square image to make sure it fills all the available space. I did a quick search and i thought this image looked pretty cool. David D. (Talk) 22:46, 29 January 2006 (UTC)

I just went ahead with some bold edits. See what you think. David D. (Talk) 23:01, 29 January 2006 (UTC)

Not all images that are used by the user boxes are square but their background color matches the background color of the first table cell. I just could not figure out what the background color of that image was. I like this new image better, although i wanted to have the brown color for the reason i amentioned. I also changed the border color which was dark brown before to a new one - dark gray. -- Boris 00:31, 30 January 2006 (UTC)

I'm not wedded to any particular background colour. If the brown is a colour associated with this project then that would work well. I'm glad you like the picture as the cell diagram did nothing for me. In fact, I am now thinking it may be more approriate for the cell bio stubs too. David D. (Talk) 00:44, 30 January 2006 (UTC)

That's the only colour we have. I agree about the stubs - actually i think that the stub template and the coresponding user box template have to use the same image - WikiProject_Chemicals have it that way. What stub are we going to use it for? -- Boris 13:44, 30 January 2006 (UTC)

I don't know anything about stubs but above you mentioned the cell diagram was used in a cell biology stub. That was the one I referring too, although I'm not sure I have ever noticed it. David D. (Talk) 16:01, 30 January 2006 (UTC)

Are you sure you have the right background colour coded in the user box (see here, below)? The info boxes above look a lot lighter. It appears to use the background colour #FFFFFF. David D. (Talk) 16:09, 30 January 2006 (UTC)

WikiProject Molecular Biology/Molecular and Cell Biology/Discussion Archive

Yes i am, #FFFFFF stands for white. This orange-brownish kinda color is set by the {{chembox header}}-template. We can't see the background color (#FFFFFF) of the table because it is "overwritten" by the style rules for the one and only table cell. If a make a change in the code you have presented:
{| align="right" cellspacing="10" cellpadding="3" style="background: #FFFFFF; border: 1px solid #C0C090; border-collapse: collapse; margin: 0 0 0.5em 0.5em; width: 320px;" ! {{chembox header}}| '''{{PAGENAME}}''' |}

WikiProject Molecular Biology/Molecular and Cell Biology/Discussion Archive

Then you'll see the background color of the table (#FFFFFF):
I wanted to use #F8EABA; but it was already in the {{User WPChem}}. -- Boris 01:16, 31 January 2006 (UTC)

Miscellaneous

Biocrawler

What the hell is this (biocrawler.com)? Does anyone know anything about it? Why is this site using the Wiki design? Is Wikipedia going to have some freaky clones out there? -- Boris 14:38, 23 December 2005 (UTC)

The "about" pages for that wiki are not very informative. You could try contacting the owner directly to try to find out what they hope to accomplish. --JWSchmidt 02:20, 24 December 2005 (UTC)

Science pearls

Hello, Please notice this project. I hope that the List of publications in biology will be adopted by the molecular and cellular biology project. Thanks,APH 06:50, 13 September 2005 (UTC)

The free dictionary by Farlex

Do these guys copy/paste from wikipedia? It seems so or are they in some relation? -- Boris 11:18, 9 January 2006 (UTC)

Wow, i guess they are. They got everything from Wiki. Well. -- Boris 11:27, 9 January 2006 (UTC)

Way down near the bottom, in fine print, I found this:

This article is copied from an article on Wikipedia.org - the free encyclopedia created and edited by online user community. The text was not checked or edited by anyone on our staff. Although the vast majority of the wikipedia encyclopedia articles provide accurate and timely information please do not assume the accuracy of any particular article. This article is distributed under the terms of GNU Free Documentation License.

...so at least they seem to be adhering to the conditions of the GNU license, even if they are using the disclosure as more of a "CYA" disclaimer. – ClockworkSoul 00:09, 11 February 2006 (UTC)

Lactase problem

I would like to finilize a solution to the lactase argument I been having with Boris and another transient over the issue of stating the difference between lactase and Beta galactosidase. Now I'm willing to agree to stating a brief 1-2 sentence statement on the Beta galactosidase and remove the affiliated statements for lactase, All I ask is that Boris and others agree and will not make a edit war over it. For others see discussion on lactase page for details.

Heh, i totally forgot about this uhhh "edit war" we had there. So, BerserkerBen, what is your solution for the problem? -- Boris 21:22, 17 January 2006 (UTC)

I think i stated it both there and here, already --BerserkerBen 23:57, 17 January 2006 (UTC)

New lead image for DNA

The general structure of a section of DNA

Hi, there has been discussion about the quality of the various old lead images on the DNA article. I now created a new one, which you can see to the right. This picture is meant to give a general overview, it's not a "Structure of DNA"-chart (I'm still working on that). I'd appreciate any feedback! Mstroeck 03:34, 8 February 2006 (UTC)

Good view of base pairing and minor/major grove. What is that sticking out of the ribbons (apart from the nucleotides). If it is the phophate group it is very misleading. The phophate is an integral part of the ribbon not attached to the ribbon as the diagram suggests. David D. (Talk) 08:54, 8 February 2006 (UTC)

After looking at the close up i see you have superimposed the ribbon onto a ball and stick model (this should be described in the legend). Is it possible to only have the nucleotides and the ribbon, without the ball and stick backbone? David D. (Talk) 08:59, 8 February 2006 (UTC)

Well, the phosphate group, as I see it, is not "part of the ribbon". That's exactly what I was trying to avoid. There is no such thing as a "ribbon" in a physical DNA molecule, the ribbon is just a visual aid. Imagine for a second that you don't know the structure of DNA already and look at a chart with a flat ribbon and just the nucleotides. You'd have to read a caption to find out that there the backbone in reality consists of just the same "balls and sticks" that the rest of the molecule does. I'd rather leave out the ribbon completely than getting rid of the phosphates. Mstroeck 13:01, 8 February 2006 (UTC)

I'm assuming you made this figure. Do you have the structure ball and stick structure without the ribbon to compare? Possibly you could have the two side by side. For me, the ribbon represents the backbone (obviously a cartoon that is not accurate), but the phosphates would be part of the cartoon ribbon. Is your point to show that the real backbone is not as smooth as a ribbon? David D. (Talk) 17:33, 8 February 2006 (UTC)

Yes, that is my intent. I can't think of a way to make the backbone completely part of the ribbon without losing the immeadiacy of actually using balls and sticks to show that each strand is in fact a single molecule. I think that using just a ribbon is a bad idea and a confusing representation for people unfamiliar with the subject matter. I'll upload some alternative pictures, though. Mstroeck 21:47, 8 February 2006 (UTC)

I like the image and i like the ribbon too. But:
- Could you make the ribbon transparent?
- The image is too big > 900K. Not everyone has a good internet conection. If you cut the size in half that would make it ~300K. By the way all the amino acid images you have uploaded look very nice but they are huge in size. An amino acid image that is "200px" in size is as informative as a "900px" one.
- Some of the phosphate groups look strange (DNA image). The ones circled in red have a bond between two Oxigen atoms. The phosphate group has a nice tetrahedral structure - those circled in blue don't seem to have one.
- You love the green carbons, don't ya?
- DNA can exists in 3 forms - A, B and Z. If you can make such an image for each of them that'll be great. -- Boris 22:24, 8 February 2006 (UTC)

Excellent idea re: the transparency. I assume you are working with photoshop. If so try setting the ribbon at 50% it might make the ball and stick back bone more obvious. The bases at the top and bottom look a little cluttered. i might be tempted to edit out the last one or two pairs at each end. David D. (Talk) 22:33, 8 February 2006 (UTC)

Chromium in diabetes

Chaps, I'm having a difficult discussion on Talk:Diabetes mellitus on the role of chromium in insulin signalling. One editor there maintains that chromium influences insulin action independently from insulin receptor transduction, something that is only partially reported by the studies he quotes.

Could you kindly weigh in on this discussion, and also pass a verdict on the matter whether this issue is important enough to mention in the intro of an important health-related article. JFW | T@lk 15:45, 20 July 2006 (UTC)

Combine all the Articles

If everyone could please look here [1] Now i think you guys will agree all of these articles should be combined in to ONE CELL CYCLE page...it makes no sense to have these seperate.

It does make sence. Otherwise we would have 20 different terms pointing to the same article. How would then readers, who don't know what the terms mean, be expected to find what they are looking for? Can you solve this problem? Hmmm? -- Boris 05:03, 1 April 2006 (UTC)

Articles for the Wikipedia 1.0 project

Hi, I'm a member of the Wikipedia:Version_1.0_Editorial_Team, which is looking to identify quality articles in Wikipedia for future publication on CD or paper. We recently began assessing using these criteria, and we are looking for A-class, B-class, and Good articles, with no POV or copyright problems. Can you recommend any suitable articles? Please post your suggestions here. Cheers, Shanel 20:15, 9 March 2006 (UTC)

Hide/Show

What is the browser and the Wikipedia style that you (the members) use? I'm with Opera 7.5 and the "monobook" style. I'm asking because i'd like to show you what i've created and i need you opinion. Boris 13:58, 20 December 2005 (UTC)

I always use monobook and Firefox. --JWSchmidt 15:32, 20 December 2005 (UTC)

Here's what i got. I created a script that inserts a search box called "mol-bio search" (MBS) between the "search" and the "toolbox" fields on the very left where the Wiki site links are. Right now MBS is very simple - it has a text field, a select filed with few simple options and a "submit" button. The string that is typed in the text filed is compared to the content in a small MySQL database and if a match is found it is displayed in a table. Well, you might say - why do that? Well if the reader types "fructose" in the wiki search box they can continue with either "Go" or "Search" - the first one sends the reader stright to the article, as long as there is one; the second one finds all the pages in wiki that have the word "fructose" in it and sorts them by relevancy. I don't like neither of them. Do you know how to use your "monobok.js" file? -- Boris 17:30, 22 December 2005 (UTC)

• I think there is information at the meta-wiki, I'm not sure where. A starting place: try this. --JWSchmidt 02:28, 24 December 2005 (UTC)

Proteins

Info boxes

The current protein info sub boxes are pretty general, perhaps it would be a good idea to create sub boxes for specific protein types such as one for receptors, one for enzymes etc. Fuelbottle | Talk 12:25, 30 September 2005 (UTC)

I agree. I selected the current info box system because it is modular. We can easily create new modules that are appropriate for any particular class of protein. I agree that Category:receptors need special attention.

I made a receptor infobox here Template:Protbox receptor Fuelbottle | Talk

I'm having somewhat of a problem with the infoboxes for the amino acids. When I try to put images showing the biosynthetic pathways for the amino acids, the information box will generally cover part of the image (e.g. see threonine). Is there any way around this other than adding extra spaces or resizing the picture? Inositol|talk 23:36, 23 December 2005 (UTC)

I wonder if any of the trouble you are having might be related to use of the gif file format. --JWSchmidt 02:11, 24 December 2005 (UTC)

It's b/c of the way the browsers render the page - Firefox (i forgot to check it for Netscape) does it right, while Opera and IE overlap/overstep/overcover (i'm not sure about the proper word) the table and the image, Opera puts the image on the top, IE does the opposite. I added "float: right;" to the set of style properties of the "info table". This forces everything (in this case the image) that can't fit between the table and the left side ot the page to go under the table. I read somewhere that using this style property on Wikipedia is not recomended b/c sometimes it produces poor (wierd) results, i checked it before saving the change and it looked perfect on all 4 majot browsers that i have. -- Boris 09:16, 25 December 2005 (UTC)

Greetings, troops. I made some changes to Template:Protein which allow it to check for an image and its caption and if they are provided as "|image=file_name.extension |caption=text" to display them. I also added an "id" just in case for a future use of javascript function that will control the protein's infobox. The image width is set to 300px, the same as in Template:Protbox start. I like the images that Blastwizard has made (Plasmepsin, Aspartate transaminase, etc), the program he uses "PyMOL" adds depth, shadows, and makes the surfaces shine which "transform" the 2-D images into 3-D on my screen - awesome - actually the look of his PyMOL images made me change Template:Protein. The only minor problem they have is the black background which will eat a lot of ink when they are printed. Here is an example of what the changes do - Ornithine transcarbamoylase.
What is the difference between having the images under the GNU license and relesing them into the public domain? -- Boris 21:24, 11 March 2006 (UTC)

Propsed Infobox format change

I have an unpopular take on the protbox format. I believe that it should not be modular. I do agree, that modularity does offer the advatage of being easily adapted to different protein types which makes the current format appealing, but it also has a few disadvantages. The modular ability allows the various modules to be arranged in an ad hoc manner. A user creating a protbox is only forced to use the protbox start module, the remaining modules can be arranged in any order the creator chooses. This is counter to one of our goals which is to have a standard fomat for protein pages. The other disadvantage is the protbox creator needs to be aware of all the modules. The creator may not remember to include a module, even if they have information that can be used in a particular module.

I believe that the taxobox is a nice example of any infobox that we can model protbox from. If one were to complete all the fields in a taxobox it is large, but one is not required to fill in all the fields. Only those fields that have information relevant to a species are displayed. Templates can be easily modified, and if new fields are required for a particular type/class of proteins a single protbox should be modified, instead of creating a new template. In addition, we can arrange the order of the fields, such that they appear in the same, logical order in all pages for all proteins. For example I believe the fields 'recent publications' and 'related articles' should be next to each other.

I have made a protbox sample that includes all the fields on the main project page (except for the Template:Protbox codes because I feel that as it stands it needs revision). I think it should have functionality like the Template:Protein). I propose that we deprecate the current format and adopt a single protbox template. I made two examples using my proposed change to the template one using the Myoglobin example and the other using a protein missing some of the fields (such as image). They can be found at :User:GAThrawn22/Sandbox/. I also made an example of a hormone(insulin) and an enzyme(alpha ketoglutarate) they can be found at: User:GAThrawn22/Sandbox/protboxtest2. The code for the template can be found at User:GAThrawn22/Sandbox/protboxtest. I will be adding some other fields if others agree with my proposition. Tell me what you guys think. -- GAThrawn22 01:27, 29 June 2006 (UTC)

I propose an infobox which takes advantage of the new parserfunctions capability... With this i could put together a template which only displays sections which have information filled in for... Ill make a sandbox version at some point in the next week to illustrate this. Zephyris 16:02, 11 August 2006 (UTC)

Thanks for the suggestion. The protbox was already created using the parser function capability, so only those fields that have information in them is visible. A description of its usage can be found at: Wikipedia:WikiProject Molecular and Cellular Biology/protbox usage, while the template can be found at: Template:Protbox. if you have experience using parser functions and creating templates, and you have any suggestions for modifications your help is welcomed. Thanks again. GAThrawn22 00:16, 12 August 2006 (UTC)

Awesome, though the wikiproject page needs updating to change it from the current modular style infobox. Im also preparing a section for better representation of enzymatic reactions, see my work in progress wikiproject/templates wikipedia:wikiproject metabolic pathways. 80.225.195.54 13:23, 12 August 2006 (UTC)

Lol, not signed in and cant do links... Wikipedia:Wikiproject Metabolic PathwaysZephyris 13:31, 12 August 2006 (UTC)

L- and D-isoforms

Each compound has L- and D-isoforms, which chemically are indistinguishable, but biologically they are totally different. Are we going to have two articles for each one or just one article for both? BorisTM 13:49, 9 November 2005 (UTC)

Some observations:

• there can be multiple isoforms (e.g. zeaxanthin has three stereoisomeric forms)
• working within the existing framework, I modified the infobox in glucose to account for the L- and D- isoforms; I considered having a full infobox for the natural form, with a supplementary infobox for the secondary form, but it proved to be difficult to implement (e.g. the second box popped up in the wrong place)
• a good case could be made for encouraging a one-to-one correspondence between "Canonical SMILES" and wiki pages.

Peak 20:51, 9 November 2005 (UTC)

Names of the files

We can use either the long names, say Methylmalonyl Coenzyme A mutase or the short ones, MUT. Well, there is a problem with each one. When we add an article to a category (or categories), for MUT one of them is [Category:Proteins], the name of the article is added to the list of articles of that category, apparently using the long names will make the category pages huge, but then we can't use the short abbreviation name as the title of the article because the same abbreviation could stand for something totaly differnt in another part of Wikipedia - MUT. One way to go aournd is to ask Wikipedia to change the design of the original "add to category" tag from [ [ Category:"'Category's name] ] to [ [ Category:Category's name|Name of the link] ], where Name of the link will be the name of the link (hehe, a little redundancty here) as we want it to be shown in the "Category Page", so for for "MUT" that would be [ [Category:Proteins|MUT] ] - this is the automated way. The manual way is to add HTML in the category pages to make them look something like this

M

MAPK1 MAPK2 MAPK3 MAPK4

MAPK5 MAPK6 MAPK7 MAPK10

MAPK12 MAPK14 MDH1 MDH2

MTR MUT MYC

Any thoughts? BorisTM 11:18, 25 October 2005 (UTC)

I suggest that we make use of some of the protein categories listed at Whole proteome analysis. Most proteins should be categorized into one or more subcategories of the proteins category. I think we should use either the long or the short name depending on which is most commonly used in the literature unless both are commonly used; if so, I would use the long name. --JWSchmidt 02:26, 6 November 2005 (UTC)

I expected this to happen sooner or later. What are we going to do now? User:Novangelis has created the Human serum albumin article, i guess we should create those for the rest of the albimun having species. There are milions of species and each one with thousands of proteins. Gosh, where are we going to end up with this? Any ideas? -- Boris 19:28, 10 February 2006 (UTC)

I wonder if this was inspired by the letter in nature recently. The author was proposing that the scientific community set up their own wiki for all genes. The idea was to pool published resources to help people find information about certain genes more quickly. I'll try and hunt down the letter. If that wiki is a reality then these types of articles can easily be transferred. The other option is to ignore them since it is unlikely that someone will systematically create all the possible pages. It will be a little background noise and not even seen if it is not linked to a relevent article. David D. (Talk) 20:07, 10 February 2006 (UTC)

No wonder, with all the kids that are playing around. "Wikipedia" is a very serious project or at least the idea behind it. -- Boris 22:59, 10 February 2006 (UTC)

I don't want to see yet another wiki created in this case. I think we should work to accommodate the needs of the scientific community at Wikipedia. I think there's room here, and that would make it available more widely and easily. But the right standards need to be defined so that it isn't a mess. --Fjarlq 10:32, 23 February 2006 (UTC)

The letter was published in Nature 439, 534 (2 February 2006) and titled Gene-function wiki would let biologists pool worldwide resources by Kai Wang Department of Microbiology, University of Washington. I have pasted below some quotes although not an exact reprdouction to avoid copyright issues. David D. (Talk) 23:13, 10 February 2006 (UTC)

Your Special Report "Internet encyclopaedias go head to head" (Nature 438, 900–901; 2005) shows that Wikipedia comes close to Britannica in terms of the accuracy of its science entries.

As a frequent user of Wikipedia and also a biologist, I hope that one day a wiki on gene function will be voluntarily created and maintained by biologists.

After a microarray experiment or a BLAST search, hundreds or thousands of interesting gene names are revealed, but the average biologist has no clue as to the function of most of them. Following up with a literature search wastes a lot of researchers' time and energy.

A wiki on gene function would make life very much easier for biologists. Such a wiki would also be less susceptible to spam, as most users would be biologists. It would also be more accurate, as long as statements are accompanied by references.

Several gene-function databases already exist, but each has certain disadvantages for the average biologist.

The Entrez Gene database contains etc..

The Molecule Pages for signalling proteins and the OMIM database for human inherited diseases etc..

The UniProt Knowledge Base provides an integrated view of gene functions. But etc..

In addition, the entries in these gene-function databases — unlike those in Wikipedia — cannot be conveniently commented on or edited by average biologists. This discourages input from many potential contributors. Concise and accurate gene-function annotations compiled and edited by human experts are preferable in many cases.

Types

Adherins

What are these proteins? I know about "Adhesins" and "Cadherins", but "Adherins". Any links? PubMed gives only 5 search results.
The article was created by an anonymous user. -- Boris 15:04, 6 January 2006 (UTC)

Maybe they meant "adherens", as in macula adherens? --Arcadian 16:58, 6 January 2006 (UTC)

"macula adherens" is in Latin. Most probably the person who wrote the article got "Adhesins" and "Cadherins" all mixed up. And besides the whole article doesn't make sence. It is some mumbo-jumbo sh!t, i'll delete right now untill they provide sources and better writing. -- Boris 17:57, 6 January 2006 (UTC)

CETP

Could someone review cholesterylester transfer protein for me and add what is necessary? JFW | T@lk 23:48, 17 November 2005 (UTC)

Suggesting Fiddle With Protein Category System

I want to have a subcategory of the protein category so that we can distinguish between naturally occurring proteins and proteins that have been designed/fiddled with in some way. 'Natural proteins' and 'Engineered proteins' has been suggested. Would it be possible to move all the existing subcategories (which appear only to deal with natural proteins) into the 'natural proteins' category and create another 'engineered proteins' category for me to fill with with the different categories of engineered protein? Currently when I create an article about say, some engineered zinc finger protein transcription factor, all I can class it as is 'a protein' which is a bit unspecific. --Username132 (talk) 10:42, 27 August 2006 (UTC)

• You say that is "has been suggested", but by whom, and where (I ask because I would hope to find some supporting arguments)? Do you think that there is a sufficiently large number of engineered proteins to warrant such an undertaking? I can't speak for the entire group, but I would need quite a bit of convincing before I would support the change. If a protein is modified in such a way to require encyclopedic mention, does it really require its own article? – ClockworkSoul 06:49, 28 August 2006 (UTC)

Well, 'I' suggested that there is need for the new category on the science reference desk, and someone there made the name suggestions on the basis that 'engineered proteins' covered chimera and other "designer" proteins.

Is creating a new subcategory butween protein and the existing subcategories, really that much of an "undertaking"? I'm not aware of any loss in this change, so I don't understand the need for a whole lot of convincing. I feel as though I've just been asked to "fill in these forms in triplicate" when all I want is a category in which to put a lot of important proteins. All chimera would be included in this category, the article on which gives a few examples of drugs on the market which would also be included. At the very least, an 'engineered proteins' subcategory could be added without affecting the others? --Username132 (talk) 11:38, 28 August 2006 (UTC)

Well, we would have to change the category assignemnts of all the proteins... that's a pain in the, well, you know. An 'engineered proteins' subcat, however, sounds like a very good idea! – ClockworkSoul 15:21, 28 August 2006 (UTC)

What I plan to get done today: I am going to work on finishing the protein info box templates and the infobox example for myoglobin. Also, I will place links to this project from other wikipedia pages. --JWSchmidt 19:28, 28 August 2005 (UTC)

I think Protein purification is important, and should be included in this project, and in some of the 'protein' lists.. Adenosine | Talk 03:59, August 31, 2005 (UTC)

I agree. I added Protein purification to the navigation box for major articles about proteins and put that navigation box on the Protein purification page.

Hey just to mention it, RuBisCO is the sceince project's collaboration article of the week this week Adenosine | Talk 04:01, August 31, 2005 (UTC)

I think the Molecular and Cellular Biology WikiProject should feature illustrations that are created for Molecular and Cellular Biology articles, starting with the Calvin Cycle figure made by Adenosine.

Adenosine, What program do you use to make them? I use ISIS Draw 2.5 to make mines - [TCAC cycle]. BorisTM 11:18, 25 October 2005 (UTC)