User talk:Peter Znamenskiy

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Now the formalities are out of the way ;), let me address your question. The weasel words policy is a good one to heed, but it doesn't really apply when there is a non-controversial, direct, verifiable, scholarly source at the end of the statement. Consider, for example, the difference between "it has been suggested that DNA forms a double helix" and "It has been suggested that aliens have altered George W Bush's DNA". Both statements are (probably) true, one is clearly a weasely contribution the other isn't. The problem with citing individual scientists, is that a lot of science is reduced down into a single sentence in encyclopaedias and so who to credit becomes a problem (especially with the amount of people who like to have their own work cited around here). With this particular example, however, it was more the unencyclopaedic term "X's lab.." that inspired me to revert. If you really wish to assert who did what i wouldn't be adverse to "According to a recent report by X et al" or the like. However, i expect i will not be long before some one comes along with a namecheck for their paper and before you know it half of the editorial board of developmental biology are listed.

The rest of your work on sonic hedgehog looks good though, so keep up the good work and remember to continue to be bold! Best. Rockpocket (talk) 09:39, 21 May 2006 (UTC)

Cell Signaling
Hello Peter. Thanks for your message. I know quite a few people who use Wikipedia for therapuetic purposes. Be careful though, it can be addictive! I'd be very happy to be a contributor to a Wikiproject on cell signaling. I have refrained from getting too involved in projects in the past, simply because i don't quite know how they work, how they are set up and how much effort is required to set them up in the first place. The idea of a daughter project sounds good, though, as much of the infrastructure would be in place - all that would be needed was a subpage, some contributors and a rough plan of action. How would you propose getting it started?  Rockpock e  t  21:34, 3 June 2006 (UTC)
 * Alea iacta est, there is no turning back. Here it is: WikiProject_Cell_Signaling. Now it just needs some people to work on it :) I hope it doesn't share the fate of the Molecular and Cellular Biology Project, which seems really really quite lately... I've quickly put together a list of articles that are around (its on the project page). Peter Znamenskiy 23:50, 3 June 2006 (UTC)
 * Superb. I'll contribute as best i can and point any other editor who might have an interest in that direction.  Rockpock e  t  23:53, 3 June 2006 (UTC)
 * Sounds great! I'd love to draw some diagrams. I often will just troll wikipedia looking for something to draw, a little direction would be great! My background in cell signalling is not the strongest. Could you just tell me which pathways, etc. you want illuminated and I'll do it! Adenosine | Talk 00:21, 4 June 2006 (UTC)

It would be great, I think, to at least get the basic pathways done, and in my talk space we've been chatting about actually having hyper-linked and animated signaling diagrams. The most obvious pathways to get done are:


 * 1) Ras/Raf/Mek/Erk, and the other MAPK pathways
 * 2) PI3K/PDK1/Akt... and then branches to: GSK3/NFAT and GSK3/eIF2B  ;   Tsc1-Tsc2/mTOR/p70S6k and mTOR/4E-BP (PHAS-1) ; BAD ; FOXO ;  etc etc
 * 3) mTOR pathways - rapamycin dependent and independent
 * 4) IKK/IKbeta/NF-kappaB
 * 5) GPCR signaling ...  Galpha S to cAMP; GalphaQ to PKC
 * 6) cell cycle signaling

those seem like the most obvious to get started in terms of diagrams; if you like, I could sketch some of 'em out for the animators Gacggt 22:14, 18 June 2006 (UTC)

The animation would be to illustrate stuff like phosphorylation, ubiquitination etc. For example, it would be really cool to show that once you polyubiquitinate a protein, it gets shuttled to the proteasome and gets destroyed. Or, when a protein is phosphorylated at a particular site, it then recruits a particular binding partner. Or, in a case like FOXO, or NFAT, when it is dephosphorylated it translocates to the nucleus... Stuff like that would seem to require something like Flash, or actually having a link to an mpeg... And then the pathways themselves could be diagrams in which the proteins were hyperlinked... those are just some ideas... Gacggt 22:41, 18 June 2006 (UTC)


 * I made a start on MAPK/ERK pathway. --JWSchmidt 14:45, 19 June 2006 (UTC)

Gacggt 16:54, 19 June 2006 (UTC)
 * I think the MAPK/ERK pathwayis quite a good start. My only suggestion would be for us to think about the naming of these, and the conventions...   for example, this could have been named the "RAS/RAF/MEK/ERK pathway"...   Erk is one of the MAPKs, so calling it the MAPK/ERK pathway isn't really the convention for how pathways are delineated.   Maybe it can be renamed?  Also, the various parts of the pathway can be pointed to this page...       I don't mean this as a big criticism, but these points need to be thought about so that people can find these pages.


 * What do you think of navboxes such as Template:Lipid signaling to link together key pathway components? I don't think each pathway deserves a separate category and such navboxes are easy to use and set up and not distracting if reasonably coloured and placed. Peter Z.Talk 19:29, 19 June 2006 (UTC)


 * Just a headsup that WikiProject_Cell_Signaling has been revived. Biochemza, 13:23, 3 November 2007 (UTC)

Pathway names
What do you think of these names? (source) --JWSchmidt 03:30, 25 June 2006 (UTC)
 * Two-component system
 * MAPK signaling pathway
 * Wnt signaling pathway
 * Notch signaling pathway
 * Hedgehog signaling pathway
 * TGF-beta signaling pathway
 * VEGF signaling pathway
 * Jak-STAT signaling pathway
 * Calcium signaling pathway
 * Phosphatidylinositol signaling system
 * mTOR signaling pathway

VEGF is simply one of many receptor tyrosine kinases - and these all signal through the RAS/RAF/MEK/ERK pathway and the PI3K/Akt pathway. The MAPK pathway is not a great name, because there are three MAPK pathways: the MEK/ERK pathway, p38 signaling and the third one... Jak-stat is okay; hedgehog and Notch and Wnt are okay. I'm not sure that there is one Calcium signaling pathway. Regards.... Gacggt 23:07, 27 June 2006 (UTC)

Here is the way they are naming things at Science, on the STKE site (source: http://stke.sciencemag.org/cgi/collection/cell_biology)

Adrenergic Pathway http://stke.sciencemag.org/cgi/cm/stkecm;CMP_8762. [Pathway]

Angiotensin II-Stimulated Signaling through G Proteins and beta-Arrestin http://stke.sciencemag.org/cgi/cm/stkecm;CMP_16109. [Abstract] [Pathway]

Dictyostelium discoideum cAMP Chemotaxis Pathway http://stke.sciencemag.org/cgi/cm/stkecm;CMP_7918. [Abstract] [Pathway] [Animation 1] [Schematic]

Dictyostelium discoideum cAMP Receptor, G Protein-Independent Pathways http://stke.sciencemag.org/cgi/cm/stkecm;CMP_11471. [Abstract] [Pathway]

Differentiation Pathway in PC12 Cells http://stke.sciencemag.org/cgi/cm/stkecm;CMP_8038. [Pathway] [Movie]

Drosophila PI3K Pathway

http://stke.sciencemag.org/cgi/cm/stkecm;CMP_7053. [Pathway]

Epidermal Growth Factor Receptor Pathway http://stke.sciencemag.org/cgi/cm/stkecm;CMP_14987. [Pathway]

ERK1/ERK2 MAPK Pathway http://stke.sciencemag.org/cgi/cm/stkecm;CMP_10705. [Pathway]

Estrogen Receptor Pathway

http://stke.sciencemag.org/cgi/cm/stkecm;CMP_7006. [Pathway]

Fas Signaling Pathway

http://stke.sciencemag.org/cgi/cm/stkecm;CMP_7966. [Abstract] [Pathway] [Animation]

Fas Signaling Pathway in Cardiomyocytes http://stke.sciencemag.org/cgi/cm/stkecm;CMP_9993. [Pathway]

Fibroblast Growth Factor Receptor Pathway http://stke.sciencemag.org/cgi/cm/stkecm;CMP_15049. [Pathway]

Filamentous Growth Pathway in Yeast http://stke.sciencemag.org/cgi/cm/stkecm;CMP_14554. [Pathway]

G alpha 12 Pathway

http://stke.sciencemag.org/cgi/cm/stkecm;CMP_8022. [Pathway] [Schematic]

G alpha 13 Pathway

http://stke.sciencemag.org/cgi/cm/stkecm;CMP_8809. [Pathway] [Schematic]

G alpha i Pathway

http://stke.sciencemag.org/cgi/cm/stkecm;CMP_7430. [Pathway] [Schematic]

G alpha q Pathway

http://stke.sciencemag.org/cgi/cm/stkecm;CMP_6680. [Pathway] [Schematic]

G alpha s Pathway

http://stke.sciencemag.org/cgi/cm/stkecm;CMP_6634. [Pathway] [Schematic] [Composite Schematic]

G Protein-Independent 7 Transmembrane Receptor Signaling

http://stke.sciencemag.org/cgi/cm/stkecm;CMP_11470. [Pathway]

High Osmolarity Glycerol (HOG) Pathway in Yeast

http://stke.sciencemag.org/cgi/cm/stkecm;CMP_14620. [Pathway]

Insulin Signaling Pathway http://stke.sciencemag.org/cgi/cm/stkecm;CMP_12069. [Pathway]

Integrin Signaling Pathway http://stke.sciencemag.org/cgi/cm/stkecm;CMP_6880. [Pathway] [Schematic]

JNK MAPK Pathway http://stke.sciencemag.org/cgi/cm/stkecm;CMP_10827. [Pathway]

Mitochondrial Pathway of Apoptosis: Antiapoptotic Bcl-2 Family http://stke.sciencemag.org/cgi/cm/stkecm;CMP_17525. [Pathway]

Mitochondrial Pathway of Apoptosis: BH3-only Bcl-2 Family

http://stke.sciencemag.org/cgi/cm/stkecm;CMP_18017. [Pathway]

Gacggt 00:19, 28 June 2006 (UTC)

Cell ilustration
hi, thanks for your effort. but it would seem there is a problem with the files you made (as with almust all SVG format on wikipedia) the point is that is not posible to see it on the image page. when opening on explorer it opens too deep on the page and one can not scroll. when trying to make a thumb from it, it doesnt apear ( here normally is enough to change the size of the thumb one or two pixels to make it work) butn in your case i went from 270 up to 310, and nothing.

wich program you used to make the images? when you want i can upload them again,you need just those 2 images?

as for what you do on the cell article. i do not mind at all, whenever you need another illustration just let me know. i am out of project right now :P

Maybe you can help me with something. could you have a look on this image Image:Acrosome reaction diagram.svg, i was asked some changes, when you read here you will see what i mean. i would like to hear your opinion.

thanksLadyofHats 09:13, 17 June 2006 (UTC)

HERE you have: 

LadyofHats 09:46, 17 June 2006 (UTC).

Cell (biology)
Hi, I just noticed that you are at Glasgow University. I'm at Strathclyde! What are the chances of two editors working on the one articel being from the same city studying at two of the greatest uni's in Britain!? :P GiollaUidir 23:36, 18 June 2006 (UTC)

I wouldn't have thought so either. But I suppose it does have its charms... Somewhere... Although Glasgow Uni does have a lovely campus. Where've you been for the past year?GiollaUidir 23:45, 18 June 2006 (UTC)

Genetics
Talk:Genetics. :) NCursework 11:49, 17 June 2006 (UTC)

Reverse transcriptase
Hi Peter! You might be interesting in giving the cleaned-up Reverse transcriptase article a once-over for errors. Thanks! --  Serephine   ♠   talk   - 09:03, 21 June 2006 (UTC)
 * Thankyou for the edible appreciation - it was delicious haha. Well done on your improvements to the article too, perhaps if we get enough examples of RT we could stick them all under a separate heading in the article. Also, I hope the format change on your front page image section was to your satisfaction ☺ --  Serephine   ♠   talk   - 01:49, 22 June 2006 (UTC)

Protein info boxes
"expand these templates to add links to database entries for various model organisms, preferably with an option to show/hide this information" <-- I like the idea of pointing to good databases. It is a challenge to keep databases up to date and complete. For example, I wish there were a good database of gene knockout/in, RNA knockdown and transfection-mediated over-expression studies. Wiki technology might be the only real solution to the challenge of producing and maintaining good annotated biology databases. I like the idea of options. Wikipedia articles are often written for some imagined "average" reader. They generally need to be better about providing entry points for students and keeping advanced issues and details off to one side for experts. It may be that another project like Wikiversity is needed to really deal with helping students and provding an open-ended option for advanced readers. An alternative to optional display of information is to be careful about the order in which things are presented. Wikipedia articles could have a section at the bottom called "technical details". A simplified protein information box at the top of the article could link to a second box near the bottom that would have links to the more esoteric databases. --JWSchmidt 20:54, 25 June 2006 (UTC)
 * Arginine is fine, but sometimes people do not know what they are looking for until they see it. As long as an article is not too long, my personal choice would be to see the link out of the bottom of the info box lead to a section at the bottom of the main article; have a section of the same article with the details rather than rely on a link to a second page. My guess is that Wikispecies] is the most well-developed "biological wiki database". [EvoWiki] is the most active biology-related wiki I am aware of that is dedicated to going into a biology subject area in more detail than Wikipedia. I think it is natural for there to be "professional" databases with limited access by editors and then the question becomes if the annotation problem can be helped by "open databases" where you risk some vandalism for the chance to get more participants. --JWSchmidt 22:03, 25 June 2006 (UTC)

Hedgehog
"Is there a specific reason for format you use? Would you mind if I reformatted the references to ?" <-- The format I use just fits my way of thinking about ways make Wikipedia more user friendly. I think the format is a reflection of past days when people grew tired while typing reference lists and journals had to pay $ for dead trees and wanted to save on paper costs. Feel free to change references to if you want to. I just started working on Wnt signaling pathway and I also noticed that a good start has been made on TGF beta signaling pathway. --JWSchmidt 21:12, 29 June 2006 (UTC)

I find myself citing an increasing number of journals that are totally online (no print version) and the articles have no page numbers. That means that the template should have another option such as article  I've been reluctant to make my own template because I fear that it would attract the attention of Wikipedia "standardization police"! --JWSchmidt 13:20, 30 June 2006 (UTC)
 * I think I could make a new template by changing elements of the the template such as   to Volume  

I made Template:Cite online journal. It has some punctuation changes compared to Template:Cite online journal (see Template talk:Cite online journal). I called it "Cite online journal" because it inculdes the option of using an "article" field for journal articles that do not have page numbers (they only have an article number). It explicitly shows "Volume" and either "article", "page" or "pages" depending on if the article has an article number, one page number, or multiple pages.

The thing that I dislike most about these templates is that they use the "PMID" feature. I'd rather use things like the "Entrez Pubmed" template. --JWSchmidt 16:06, 30 June 2006 (UTC)

TGF beta signaling
Thanks for the complements on the pictures. I actually agree with your comments on the format of the article. I was in fact considering the format that suggested. I am going to reformat the you article. I will remove most of the headings. (This was a rough draft and the headings helped me organize the information). I will also remove the 'steps'. Thanks for the suggestions, if you have any more I'll be glad to hear them. --GAThrawn22 03:13, 1 July 2006 (UTC)

Thanks again for the complements on the article. Will start referencing soon. I noticed that you incorporated the style of graphic used in the TGF beta signaling pathway in the JAK-STAT signaling pathway. The pictures look great! Perhaps we can colaborate on designing a framework regarding Cell Signaling Diagrams - in particular regarding your suggestions on drawing diagrams to a single standard. --GAThrawn22 04:29, 2 July 2006 (UTC)

Nice Job
I like the picture of the Lentivirus you supplied. Good work. Viridae Talk 01:20, 2 July 2006 (UTC)
 * Thanks. I made it a while ago but forgot to upload for some reason. Peter Z.Talk 01:25, 2 July 2006 (UTC)

enzymometre
I've never heard of it, but I suppose it would be possible. Ion-sensitive electrodes are certainly used. If this technique does exist it will be mentioned in the book below, it really goes into practical detail well. --TimVickers 04:41, 3 July 2006 (UTC) Eisenthal R. Danson M.J. (Eds), Enzyme Assays: A Practical Approach. Oxford University Press (2002) ISBN: 0199638209

SMAD
Hi: I am now very clear about the merits of the articles on SMAD proteins. But can you PLEASE tell me why they are called "Mothers against decapentaplegic homologues"?--Anthony.bradbury 17:49, 3 July 2006 (UTC)

Biology portal content selection
You asked a while ago about a formal process for selecting content for the biology portal. We now have a process in place for this, although it is still based on willingness to make exceptions in good faith: Portal talk:Biology/Proposed. We look forward to your contributions. - User:Samsara (talk • contribs) 14:12, 19 August 2006 (UTC)

This month's WP:MCB Article Improvement Drive article
– ClockworkSoul 22:54, 4 September 2006 (UTC)

This month's WP:MCB Article Improvement Drive article
– ClockworkSoul 21:07, 2 October 2006 (UTC)

Progenitor cell
Hi Peter, I left some of my rambling opinions on the progenitor cells talk page. I'd be interested in your thoughts Dr Aaron 11:45, 3 October 2006 (UTC)

One more vote for the coordinator of the Molecular and Cellular Biology Wikiproject
Since two of the three editors nominated for Coordinator of the MCB Wikiproject declined their nominations, one more vote has been posted: should the remaining nominee, ClockworkSoul, be named as the coordinator, or should nominations be reopened? Every opinion counts, so please vote! – ClockworkSoul 17:56, 17 October 2006 (UTC)

This month's winner is proteasome!
– ClockworkSoul 22:15, 1 November 2006 (UTC)

Peer review of bacteria
Hi there. I'd value your input on this article. Thank you. TimVickers 05:42, 25 November 2006 (UTC)
 * This article is now a Featured Article candidate, the nomination page is (here). Thank you. TimVickers 04:55, 27 November 2006 (UTC)

This month's winner is RNA interference!
– ClockworkSoul 14:39, 2 December 2006 (UTC)

This month's MCB Collaboration of the Month article is Peripheral membrane protein!
– ClockworkSoul 18:59, 14 January 2007 (UTC)

Biological Value
I noticed you appear to be involved in biology articles or WikiProjects relating to biology and human processes. This article, on a method for evaluating biological utilizations rates of proteins in humans and animals, was started in August and is in need of the attention of an expert. We are having trouble locating one and the article desperately needs it. This method is used constantly in bodybuilding magazines and products and is the subject of much misinformation and half-truths. On the other hand it does appear to have some value. Please help if possible. In case you're wondering why I picked you I just looked through some Science WikiProjects and biology articles and your name appeared a lot in one or both categories. Incidentally if you decide not to do this for whatever reason there's no need to reply. I'll just take it you're busy or uninterested and leave it at that. Thanks. Quadzilla99 23:01, 4 March 2007 (UTC)

Speedy deletion nomination of File:Diagram human cell nucleus no text.svg


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ArbCom elections are now open!
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