Wikipedia talk:WikiProject Molecular Biology/Molecular and Cell Biology/Archive 5

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Can we get some help picking articles for a Molecular Biology course project?

I'm helping to run an Education program course for Molecular Biology this coming semester, two sections: section 81 and section 82. We've done this for the past three semesters, and now it's starting to look like we're running out of articles! I have our tentative lists up here, User:Klortho/Articles. If anyone has a chance, could you help us find more good candidates? The best would be top or high importance stubs. But I think that the article ratings from this group are pretty out-of-date. You can either edit the list in-place, or make suggestions on the talk page there. Thanks! Klortho (talk) 13:45, 21 January 2014 (UTC)

Statistics: are stubs being expanded?

In a deletion discussion at the Dutch Wikipedia, I stated that an existing article invites improving, much more than a non-existent article invites creation adding that statistics show the truth of this statement. Naturally, people required me to come up with the facts, but I am unable to find the statement I remember to have read.

If I am true, the statement was not in Wikipedia itself, but in a more or less scientific article defending the creation of large numbers of bot stubs about genes, perhaps by someone who was involved in creating the bot articles. All of this has happened a few years ago. Can anyone remember or find this article or stats about improvement in Wikipedia texts? Regards, Bertux (talk) Bertux (talk) 06:51, 11 December 2013 (UTC)

B.t.w.: As English is not my native language this text will surely not be spotless. Feel free to correct it. Bertux (talk) Bertux (talk) 06:51, 11 December 2013 (UTC)

FYI: I left the same message at Talk:WikiProject Human Genetic History

I think you are referring to the Gene Wiki. That link in turn cites a number of articles published on the Gene Wiki. In particular PMID 22075991 contains some statistics about how these stubs have been expanded by human editors. Boghog (talk) 13:20, 28 December 2013 (UTC)

Hi Boghog, thanks for the interesting article. The article that I remember accompanied the creation of large numbers of bot articles, probably as part of the Gene Wiki as you suggested. If so, it must have been published in 2008. Reassuring contributors about the viability of such articles appeared to be its aim and it presented some statistics to make its point. The article that you linked employs pretty much the same method to achieve the same goal, so you did a very good job indeed. This one will serve my purpose well and the context you provided will help my further explorations. Thank you very much for research and the helpful result! Bertux (talk) 15:09, 25 January 2014 (UTC)

Wikipedia:WikiProject Transporter Classification Database

Please add Wikipedia:WikiProject Transporter Classification Database to "Similar WikiProjects".
—Wavelength (talk) 17:23, 3 February 2014 (UTC)

AfC submission

Could any of you have a look at this submission? Regards, FoCuSandLeArN (talk) 14:42, 30 January 2014 (UTC)

And Wikipedia talk:Articles for creation/Niche (protein structural motif). FoCuSandLeArN (talk) 19:00, 11 February 2014 (UTC)

• Wikipedia talk:Articles for creation/Imaging Cycler Microscopy
• Wikipedia talk:Articles for creation/Toponome

• Wikipedia talk:Articles for creation/Toponomics. FoCuSandLeArN (talk) 23:51, 11 February 2014 (UTC)

Star fish are dying

A story from the LA Times speculates that a pathogen is the likely cause of star fish dying. Is this of interest to this wikiproject?

• http://www.latimes.com/science/sciencenow/la-sci-sn-something-is-killing-the-starfish-scientists-race-to-find-out-what-20140204,0,6767257.story#axzz2tcNaRjVu

XOttawahitech (talk) 00:23, 18 February 2014 (UTC)

Popular pages tool update

As of January, the popular pages tool has moved from the Toolserver to Wikimedia Tool Labs. The code has changed significantly from the Toolserver version, but users should notice few differences. Please take a moment to look over your project's list for any anomalies, such as pages that you expect to see that are missing or pages that seem to have more views than expected. Note that unlike other tools, this tool aggregates all views from redirects, which means it will typically have higher numbers. (For January 2014 specifically, 35 hours of data is missing from the WMF data, which was approximated from other dates. For most articles, this should yield a more accurate number. However, a few articles, like ones featured on the Main Page, may be off).

Web tools, to replace the ones at tools:~alexz/pop, will become available over the next few weeks at toollabs:popularpages. All of the historical data (back to July 2009 for some projects) has been copied over. The tool to view historical data is currently partially available (assessment data and a few projects may not be available at the moment). The tool to add new projects to the bot's list is also available now (editing the configuration of current projects coming soon). Unlike the previous tool, all changes will be effective immediately. OAuth is used to authenticate users, allowing only regular users to make changes to prevent abuse. A visible history of configuration additions and changes is coming soon. Once tools become fully available, their toolserver versions will redirect to Labs.

If you have any questions, want to report any bugs, or there are any features you would like to see that aren't currently available on the Toolserver tools, see the updated FAQ or contact me on my talk page. Mr.Z-bot (talk) (for Mr.Z-man) 05:15, 23 February 2014 (UTC)

Total free access to Royal Society History of Science journals for 2 days on March 4th and 5th !!!

As Wikipedian in Residence at the Royal Society, the National Academy for the sciences of the UK, I am pleased to say that the two Royal Society History of Science journals will be fully accessible for free for 2 days on March 4th and 5th. This is in conjunction with the Women in Science Edit-a-thon on 4 March, slightly in advance of International Women's Day, on Saturday March 8th. The event is held by the Royal Society and the Royal Academy of Engineering, and is fully booked, but online participation is very welcome, and suggestions for articles relevant to the theme of "Women in Science" that need work, and topics that need coverage.

The journals will have full and free online access to all from 1am (GMT/UTC) on 4th March 2014 until 11pm (GMT/UTC) on 5th March 2014. Normally they are only free online for issues between 1 and 10 years old. They are:

• Notes and Records: the Royal Society journal of the history of science
• Biographical Memoirs of the Fellows of the Royal Society

The RS position is a "pilot" excercise, running between January and early July 2014. Please let me know on my talk page or the project page if you want to get involved or have suggestions. There will be further public events, as well as many for the RS's diverse audiences in the scientific community; these will be advertised first to the RS's emailing lists and Twitter feeds.

I am keen to get feedback on my personal Conflict of Interest statement for the position, and want to work out a general one for Royal Society staff in consultation with the community. Wiki at Royal Society John (talk) 12:17, 28 February 2014 (UTC)

AfC submission - 05/03

Wikipedia talk:Articles for creation/TcdA1. FoCuSandLeArN (talk) 12:30, 5 March 2014 (UTC)

• Wikipedia talk:Articles for creation/Solution Structure of Bacillus subtilis MinC N-terminal domain. FoCuSandLeArN (talk) 00:45, 6 March 2014 (UTC)

CYP1A2

Someone from this project should copyedit CYP1A2. See Talk. Thanks, Hordaland (talk) 08:29, 9 March 2014 (UTC)

Thanks for the heads up. Responded there. Boghog (talk) 12:26, 9 March 2014 (UTC)

New stub article

ATP:Cobalamin adenosyltransferase could use some attention from people who frequently edit such articles (which I do not). I imagine it could be expanded greatly with info from RSs. Jinkinson talk to me 02:17, 6 March 2014 (UTC)

I see you have already merged it into Cob(I)yrinic acid a,c-diamide adenosyltransferase. Thanks. There have been 66 publications to date on this enzyme but only one review (PMID 20677021) which I just added. Cheers. Boghog (talk) 12:46, 9 March 2014 (UTC)

"Prokaryotic Diversity" class looking for interaction with editors

Hi! A class (course page here) at Louisiana State University about Prokaryotic diversity will be editing Wikipedia this semester. The professor has used Wikipedia as a teaching tool before, and the students at LSU tend to do pretty great work with the help of their Ambassador Becky. In the last few classes, the students have hoped for more interaction with experienced editors. Since those of you in this WikiProject are likely interested in the articles they'll edit, I wanted to reach out to see if anyone is interested in communicating with these new users during their Wikipedia assignment.

Even if you're only interested in participating very informally, it would be great to have editors who are familiar with the topics comment on the work they're doing! One of the great features of the course page is that you can even use this link to see a feed of their edits, which I find extremely useful for providing good feedback. You can also now leave messages on the talk page of the course, which will notify all students in the class. So if you happen to see a trend about references they're using, have suggestions for topics to edit, etc., that's a great way to reach them. Please let me and Becky know if you're interested in working with them this semester, either by notifying us on a talk page, sending me an email, or pinging us back here! Thanks so much, Jami (Wiki Ed) (talk) 19:02, 6 February 2014 (UTC)

Thanks for your note! Prokaryotic Diversity is outside my expertise, but if there are specific questions concerning the molecular biology aspects of the course subject and how to integrate the content added by the students with the rest of Wikipedia (e.g., MCB navboxes, infoboxes, wiki links, etc.), I will try to help out. Boghog (talk) 12:56, 9 March 2014 (UTC)

Disambiguation question - Herpes Simplex

There is a recent article about a U.S. Navy aircraft squadron called VP-16, which at this moment is named VP-16 (U.S. Navy). It is one of about 20 articles on squadrons named "VP-nn", and the only one that isn't named just "VP-nn". I would love to be able to rename the Navy article as plain "VP-16", and include in it a disambiguation link to Herpes simplex virus protein vmw65. Right now, VP16 is a disambiguation link to that article, which currently has no disambiguation link to VP-16 (U.S. Navy). I think that doing it in the suggested way would be what's best for all concerned, but I don't know if the Herpes simplex virus protein vmw65 people would agree. Who has any ideas? Lou Sander (talk) 14:13, 7 March 2014 (UTC)

Thanks for your note. I was bold and went ahead and converted VP16 from a redirect into a disambiguation page that now contains links to both VP-16 (U.S. Navy) and to Herpes simplex virus protein vmw65. Is this OK? Boghog (talk) 12:34, 9 March 2014 (UTC)

@Boghog:Well, it's a move in the right direction, but there are still some loose ends. I'm not a disambiguation expert, so I'm operating at a handicap here, while trying to do the right thing. There's a VP-16 page that goes to a page about the drug Etoposide. There is a kind of disambiguation page that handles both forms: VP 16 and VP-16, but I'm not sure what it is or how it works. Also, it seems to me that best for all concerned would be to rename the Navy squadron as simply "VP-16", like every other Navy VP squadron, and include hatnotes disambiguating and linked to the virus and the drug. The rationale for that is that "VP-16" is the squadron's actual name, while VP 16 and VP-16 are just alternative names for the other articles. If a user looking for the virus or the drug entered the alternative names VP 16 or VP-16, they would just have to go to one intermediate page (the renamed Navy squadron page), exactly like they do with a regular disambiguation page. So these folks would be where they are now, while the Navy folks would go directly to their page. Lou Sander (talk) 13:26, 9 March 2014 (UTC)

Thanks for the followup. This is slightly more complicated than I thought. Since "VP-16" is the primary name of the squadron and "VP-16" is a secondary name (synonym) of the Etoposide, I think what you are proposing is reasonable (i.e., rename VP-16 (U.S. Navy) to VP-16 and add an "other uses" hatnote pointing to the VP16 disambiguation page). We will need to ask an administrator to delete the VP-16 redirect before we can complete the page move. I will make the request. Cheers. Boghog (talk) 14:22, 9 March 2014 (UTC)

Request filed to deleted the redirect to make way for the page move. Boghog (talk) 14:30, 9 March 2014 (UTC)

Request for help from AfC

Please take a look at Wikipedia talk:Articles for creation/Intrinsically Disordered Protein (IDP) and help guide the writer. The topic seems notable (to this "high school biology only" AfC reviewer) but clearly the draft is nowhere near being an article yet. Roger (Dodger67) (talk) 18:50, 10 March 2014 (UTC)

List of important labs/people in science articles

Looking at the Wikipedia talk:Articles for creation/Intrinsically Disordered Protein (IDP) page reminded me that I've seen a few articles with lists or important labs at the end. Although they do seem useful, particularly for people looking to contact key members of a field, I worry that which labs make the cut as 'important' is very up to the discretion of the writer since no source of authority on which labs are the key players can be cited. Do we reckon that these sections are fine, or should they basically be included as the authors of references through the article?T. Shafee (Evo&Evo) (talk) 22:22, 11 March 2014 (UTC)

It is a good question. For any material to be added to an article there has to be verifiability. Is there a reliable source that says these labs are the important ones? If not, then the list can't stand by itself. In other math and science articles I've seen, lists of important people or institutions in a field are displayed as a list of wiki links to their respective articles. This kind of a list is presumed verifiable, as the underlying articles that are linked to should be based on verifiable sources. --Mark viking (talk) 22:38, 11 March 2014 (UTC)

I agree with Mark that a reliable source should be included with these lists that documents that these labs are important. This is rarely done. In addition, articles should focus on the results of the research, not the researchers:

Do not hype a study by listing the names, credentials, institutions, or other "qualifications" of their authors.
— Wikipedia:MEDMOS#Citing_sources

An exception is in the history section where notable discoveries and who made them should be listed. Finally the list of labs that are doing important work in this field is implicit in the citations that should already be included in the article. IMHO, these lists unless documented by a reliable source should not be included. Boghog (talk) 07:25, 12 March 2014 (UTC)

AfC submission - 19/03

User:Kevincdick/sandbox. FoCuSandLeArN (talk) 15:06, 19 March 2014 (UTC)

Beta-Hydroxybutyric acid

Beta-Hydroxybutyric acid is described as being a ketone body both in the main article and various others discussing ketosis and ketoacidosis. Thing is, it's not a ketone in a chemical sense. I edit chemistry pages and would normally just start correcting all this, but sometimes biochemist have their own terms for things, so I though I'd raise the point here before I did anything. Project Osprey (talk) 10:48, 22 March 2014 (UTC)

Request for help with miRNA target prediction algorithm

Please take a look at Wikipedia_talk:Articles_for_creation/TargetScan and help guide the writer. The topic is mentioned several places in Wikipedia, but the writer of this article is not an experienced member of the Wikipedia community. Since submission, external links have been removed from the body of the text. Much more information is contained, of course, in the references, and the writer would appreciate any recommendations about further content guidelines. — Preceding unsigned comment added by 18.4.1.141 (talk) 19:48, 15 April 2014 (UTC)

Sexual differentiation articles -- redundancy/merge discussion

Opinions are needed from this WikiProject on this matter (WP:Permalink): Wikipedia talk:WikiProject Anatomy#Sexual differentiation articles. Flyer22 (talk) 22:38, 17 April 2014 (UTC)

Article title names

I have ran across a diversity in article title names and I thought I would inquire.

• There are articles such as ACRV1 that includes "is a protein that in humans is encoded by the ACRV1 gene", ACSBG1 that includes " is an enzyme that in humans is encoded by the ACSBG1 gene", ACSBG2 that includes "is an enzyme that in humans is encoded by the ACSBG2 gene", ACSF3 that includes "is an enzyme that in humans is encoded by the ACSF3 gene", ADPRHL2 that includes "is an enzyme that in humans is encoded by the ADPRHL2 gene", AFF3 that includes "is a protein that in humans is encoded by the AFF3 gene, AHCTF1 that includes "is a protein that in humans is encoded by the AHCTF1 gene", AIM1 that includes, "is a protein that in humans is encoded by the AIM1 gene" and AADAC that includes "is an enzyme that in humans is encoded by the AADAC gene".
• Then there are articles such as AADACL3 (gene) that includes "is a protein in humans that is encoded by the AADACL3 gene", AADACL4 (gene) that includes "is a protein in humans that is encoded by the AADACL4 gene, ABRA (gene) that includes "is a protein that in humans is encoded by the ABRA gene", ACTG1P6 (gene) that includes "is a protein that in humans is encoded by the ACTG1P6 gene", and ADC (gene) that includes "is an enzyme that in humans is encoded by the ADC gene.

• Then there is ABI gene family member 3 that includes "is a protein that in humans is encoded by the ABI3 gene"

All these articles have in common that they are orphans and I am trying to de-orphan such articles. A protein or an enzyme may or may not include "(gene)" in the article name. It would seem to me that an article concerning a gene would be better listed with "(gene)" in the title. I would appreciate it if someone would take a look at this and let me know. Otr500 (talk) 05:19, 22 April 2014 (UTC)

Hi. Concerning the lead sentence in Gene Wiki articles, as discussed here and here, we have tried to make clear that the scope of these articles encompasses both the protein and gene encoding that protein. Furthermore these articles are not only about the human gene/protein, but also orthologs that exist in other species. The wording that was reached through consensus is perhaps a little awkward, but it is both accurate and concise:

• <recommended UniProt name> is a protein that in humans is encoded by the <approved HUGO gene symbol> gene.

The "that" in the above sentence is non-limiting implying that the protein (and gene) exists in other species besides human.

Many gene symbols are sufficiently unique that the "(gene)" disambiguation is not required. On the other hand, to having redirects from "<approved HUGO gene symbol> (gene)" makes these articles easier to find. A bot therefore systematically added these redirects (see bot approval).

Concerning article names that contain the disambiguation gene, my suggestion is to rename them to remove the unnecessary disambiguation and leave behind the disambiguated name as redirect. Finally if the corresponding UniProt name is concise, it would probably be better to name the article after the protein name. I know this must sound messy, but unfortunately gene and protein nomenclature is inherently messy and it is impossible to come up with a simple universal rule for naming these articles. Boghog (talk) 11:49, 22 April 2014 (UTC)

AfC submission - 25/04

Wikipedia talk:Articles for creation/Reverse Transcription Loop-mediated Isothermal Amplification. FoCuSandLeArN (talk) 19:47, 25 April 2014 (UTC)

Royal Society journals - subscription offer for one year

I'm delighted to say that the Royal Society, the UK’s National Academy for science, is offering 24 Wikipedians free access for one year to its prestigious range of scientific journals. Please note that much of the content of these journals is already freely available online, the details varying slightly between the journals – see the Royal Society Publishing webpages. For the purposes of this offer the Royal Society's journals are divided into 3 groups: Biological sciences, Physical sciences and history of science. For full details and signing-up, please see the applications page. Initial applications will close on 25 May 2014, but later applications will go on the waiting list. Wiki at Royal Society John (talk) 02:58, 29 April 2014 (UTC)

Endorphin and beta-endorphin restructure proposal

See Wikipedia talk:WikiProject Pharmacology#endorphin and beta-endorphin for details. Seppi333 (Insert 2¢ | Maintained) 08:15, 5 May 2014 (UTC)

Gene page evaluations

Is there an evaluation process to change a gene article from stub to a different category? I have edited this article and it is no longer a stub. Please let me know if there is anything I can do on my part to reclassify this article. Rraju2 (talk) 15:41, 1 May 2014 (UTC)

On the article's talk page, you can change class=stub in the template at top of that page into the appropriate class (C-class perhaps? -> class=C). --WS (talk) 17:59, 1 May 2014 (UTC)

Adding to that: there is no formal process for ratings, you can just go ahead and rate them according to your best judgement, except for good and featured articles for which there are formal processes. --WS (talk) 18:00, 1 May 2014 (UTC)

Thank you for the information! I changed the article from stub to C-class article. Greatly appreciate the help. Rraju2 (talk) 20:52, 9 May 2014 (UTC)

Question about references

I am a new editor on Wikipedia and working on a gene page for a class. Many of the sources we found are primary sources but are cited as secondary sources in the introduction of other papers. There are not many secondary source review articles available. What would be the appropriate way to reference this material?Rraju2 (talk) 15:25, 1 May 2014 (UTC)

Rraju2, you can cite the introduction of other papers as a secondary source. I hope that helps. Best. Biosthmors (talk) pls notify me (i.e. {{U}}) while signing a reply, thx 22:14, 4 May 2014 (UTC)

That does help, I responded further on the article talk page.Thanks! Rraju2 (talk) 20:59, 9 May 2014 (UTC)

Alloenzyme

This needs some work on it, in that it promotes the incorrect concept that alloenzymes are by definition highly conserved. Lavateraguy (talk) 13:58, 15 May 2014 (UTC)

AfC submission - 18/05

Should this be merged with Aequorin? FoCuSandLeArN (talk) 15:36, 18 May 2014 (UTC)

Yes. Apoaeqorin is the apoenzyme variant of aequorin that lacks its prosthetic group. I will make an attempt to merged the former with the later. Thanks for the heads up. Boghog (talk) 17:35, 18 May 2014 (UTC)

AfC submission - 22/05

Draft:XB130 (gene). FoCuSandLeArN (talk) 19:55, 22 May 2014 (UTC)

• Wikipedia talk:Articles for creation/TANGO6: Transmembrane and Golgi Organization 6. FoCuSandLeArN (talk) 00:28, 23 May 2014 (UTC)

AfC submission - 26/05

Draft:TANGO6: Transmembrane and Golgi Organization 6. FoCuSandLeArN (talk) 17:08, 26 May 2014 (UTC)

• See this discussion for plenty more examples. They seem to be part of some university project. Please help with the heavy influx of these submissions. Regards, FoCuSandLeArN (talk) 15:23, 27 May 2014 (UTC)

I reviewed all references and none support the text. I do not think the article is worth fixing. I could not even find one reference in Google Scholar on in Medline about:

• TANGO6
• Transmembrane and Golgi Organization 6
• TMCO7
• Domains: DUF2435, DUF2411
• TANGO6 HEAT domain.

The references point to databases such as Gene2Promoter, and genetic map software: TMAP, NetCGlyc, NetOGlyc, NetPhos. These require the entry of specific -yet unspecified- DNA sequences for analyses. My assessment is that this material is primary research that has not been published yet. Not a single reference can be used to support any entry in this Wikipedia article.

Cheers, BatteryIncluded (talk) 19:00, 2 June 2014 (UTC)

As far as I can tell, none of these gene are notable. Furthermore the drafts contain mostly original research. Therefore all should be rejected. Boghog (talk) 20:04, 2 June 2014 (UTC)

Circadian clock

Perhaps someone would look at the "High-importance" article Circadian clock. On the Talk page it says:

• This article has been rated as Start-Class on the project's quality scale.
• This article has been rated as High-importance on the project's importance scale.

It may have been a stub once, but it now appears to be well-developed. --Hordaland (talk) 01:08, 3 June 2014 (UTC)

AfC submission - 03/06

Draft:Q8N5Q1. FoCuSandLeArN (talk) 01:53, 3 June 2014 (UTC)

AfC submission - 08/06

Draft:Partition system. FoCuSandLeArN (talk) 17:48, 8 June 2014 (UTC)

Leaflet For Wikiproject Molecular and Cellular Biology At Wikimania 2014

Hi all,

My name is Adi Khajuria and I am helping out with Wikimania 2014 in London.

One of our initiatives is to create leaflets to increase the discoverability of various wikimedia projects, and showcase the breadth of activity within wikimedia. Any kind of project can have a physical paper leaflet designed - for free - as a tool to help recruit new contributors. These leaflets will be printed at Wikimania 2014, and the designs can be re-used in the future at other events and locations.

This is particularly aimed at highlighting less discoverable but successful projects, e.g:

• Active Wikiprojects: Wikiproject Medicine, WikiProject Video Games, Wikiproject Film

• Tech projects/Tools, which may be looking for either users or developers.

• Less known major projects: Wikinews, Wikidata, Wikivoyage, etc.

• Wiki Loves Parliaments, Wiki Loves Monuments, Wiki Loves ____

• Wikimedia thematic organisations, Wikiwomen’s Collaborative, The Signpost

For more information or to sign up for one for your project, go to:
Project leaflets
Adikhajuria (talk) 13:29, 13 June 2014 (UTC)

Identifier templates?

Hi,

I remember using PDB ID templates before to link to specific structures, i.e. PDB: 1dan​. I'd like to start building links to sequences in ENA/GCA/etc. is there a page within MCB that lists all the different recommended 'identifier' templates?

Many thanks, --Dan Bolser (talk) 12:03, 27 May 2014 (UTC)

I am not sure this is complete, but this link may help: Category:Biology_external_link_templates. Boghog (talk) 19:23, 2 June 2014 (UTC)

Thanks @Boghog:! BTW, did I do that right?

@Dan Bolser: Your welcome. If you want to alert someone to a reply, {{ping|user name}} is a good way to do it. Boghog (talk) 19:21, 24 June 2014 (UTC)

Here is my first attempt at an ENA linking template (based on the RefSeq linking template, e.g. {{ENA|FN595246}}. This lets you link to anything in ENA, including GCAs, for example. i.e. {{ENA|GCA_000003745}}. Should we also create an INSDC template to link to NCBI, ENA and DDBJ? Also, any value in making explicit templates for sample, gca, etc.? --Dan Bolser (talk) 11:39, 10 June 2014 (UTC)

BTW, seems the Template:NCBI should be moved to Template:NCBI Taxonomy (or similar). Should I be bold? --Dan Bolser (talk) 11:45, 10 June 2014 (UTC)

The {{NCBI taxonomy}} template was already taken, so I moved it to {{NCBI taxid}} (note that 'taxid' is the term used by the NCBI in their URLs). The template redirect is working fine. --Dan Bolser (talk) 11:57, 24 June 2014 (UTC)

Looks good (both the name and the link). I agree that the {{NCBI taxonomy}} template is probably misnamed. In analogy to Wikipedia:Medical disclaimer, {{NCBI taxonomy}} should probably be renamed to {{NCBI taxonomy disclaimer}} or something similar. The disclaimer itself looks a bit over the top, but I am not a taxonomist. Boghog (talk) 19:21, 24 June 2014 (UTC)

If you need a template, create it. That is the only justification required. Boghog (talk) 19:47, 24 June 2014 (UTC)

AfC submission - 02/06

Draft:Family with Sequence Similarity 163 Member B. FoCuSandLeArN (talk) 17:17, 2 June 2014 (UTC)

Non-notable (no sources that are specifically about this gene). Draft contains largely original research. On that basis, the submission should be rejected. Boghog (talk) 20:02, 2 June 2014 (UTC)

What is this page? --Dan Bolser (talk) 11:17, 24 June 2014 (UTC)

The draft page is about a human gene with unknown function. The link I provided above is to PubMed citations about this gene. Boghog (talk) 22:12, 4 July 2014 (UTC)

EC numbers, "synonyms" , and readability

I am not a biochemist. I looked up cellulase and found a previous version of the article that began this way:

Cellulase (EC 3.2.1.4, endo-1,4-beta-D-glucanase, beta-1,4-glucanase, beta-1,4-endoglucan hydrolase, celluase A, cellulosin AP, endoglucanase D, alkali cellulase, cellulase A 3, celludextrinase, 9.5 cellulase, avicelase, pancellase SS, 1,4-(1,3, 1,4)-beta-D-glucan 4-glucanohydrolase) refers to a suite of enzymes produced chiefly by fungi, bacteria, and protozoans that catalyze cellulolysis (i.e. the hydrolysis of cellulose). However, there are also ...
Reaction: ...

I saw several problems with this text:

• The EC number in the text is superfluous, since it is also given in the infobox. Moreove, the "EC number" template links to a database that may be important to specialists, but is quite unhelpful to the interested non-specialists. Since Wikipedia is meant for the latter, the link does not deserve so much evidence.
• That database has its own division of the "enzyme space" into pages (EC numbers), which surely will not and should not be the division of Wikipedia articles. That is to say, one should not assume a one-to-one correspondence of WP articles and EC numbers. This is another reason for not giving such prominence the EC number. (The Cellulase article may be a case in point: to reduce the reader's confusion, perhaps it should be split in two: one about "Cellulase" as a generic enzyme name, and another about "cellulase complex".)
• The multi-line list of names within parenthesis breaks the sentence and makes the text completely unreadable. The first line of an article should be a readable definition of the article's topic, in good English, as clear and concise as possible, and accessible to the interested non-specialist. One or two synonyms in parentheses (in boldface, not italics) are acceptable, but beyond that the synonyms should be placed in a separate sentence, later in the head section.
• That list of "synonyms" is taken verbatim from the EC database page, and apparently contains not only synonyms, but also subclasses and specific enzymes, related molecules, and maybe even commercial names. That indiscriminate list may be appropriate for the EC database, but is not for Wikipedia. Synonyms should be distinguished from other related but non-synonymous terms, and the latter shuld be given as links in the text or in the "See also" section.
• Boldface in the head section should be used only for synonyms of the topic, not for related terms or for titles of pseudo-subsections.

Some of these same problems were present in the article Glucan 1,4-beta-glucosidase, presumably they occur in many other articles. I tried to improve the cellulase article, but I am unable to sort out the list of "synonyms"; it would require some specialized help. Thanks... --Jorge Stolfi (talk) 20:21, 4 July 2014 (UTC)

Point #1: Agreed that in-line link to EC number should not appear in the text.

Point #2: "which surely will not and should not be the division of Wikipedia articles" – You must be kidding. Per WP:V, Wikipedia articles must be based on reliable sources. Enzyme Commission number database is the definitive way of classifying enzymes. There is no question that Wikipedia enzyme articles should mirror this classification system. What alternative classification system would you propose?

Point #3: "indiscriminate list may be appropriate for the EC database, but is not for Wikipedia" – not an indiscriminate list per point #2.

Point #4: "The multi-line list of names within parenthesis breaks the sentence and makes the text completely unreadable" – agreed. This sentence should be split out as a separate nomenclature section and converted into a bulleted list minus the bolding.

Boghog (talk) 21:21, 4 July 2014 (UTC)

First, many nodes in the EC system are clearly classes of enzymes, not individal enzymes. But it would make sense for Wikipedia to have separate articles for certain individual enzymes, since the articles contain more information than the EC pages, and it will often be confusing to write about different enzymes in the same article. The cellulase is an example -- the EC class is a mixed bag of several enzymes and enzyme suites, that should be sorted out in WIkipedia. Conversely, some mid-level nodes in the EC system may not be worth separate articles in Wikipedia. Second, in such a rapidly evolving field any classification scheme will be perpetually inadequate, since changing its classes to reflect scientific progress would be extremely disruptive to users (think of all papers out there that refer to EC numbers). Wikipedia does not have this problem, its articles can be updated, split, merged, and renamed according to the most current knowledge and understanding. Organizing its articles on enzymes by the EC criteria would be as inappropriate as organizing other areas by the Dewey classification used in libraries. Third, the EC system may be an important 'reliable source', and it may be used to generate a starting set of articles; but it is not the ONLY reliable source. There must be thousands of quality articles and books that can be used to legitimize Wikipedia articles that do not correspond to a unique EC class. (The same happens in chemistry, for example: not every substance that readers may look up in Wikipedia and is supported by reliable publications has a number in the Chemical Abstracts database; but this is no excuse for excluding a Wikipedia article on it.) Fourth, the EC classification was defined to be useful for specialists; but Wikipedia is primarily directed to a very different public, for which that classification may hinder more than help.
As for the name list in the EC pages being "indiscriminate", I stand by that claim: that list is obviously a keyword list, placed there so that people who search for any of those "names" will find that page. It is a search trick used in many other scientific databases, e.g. of chemical substances, living species, etc.. The keyword list is obviously not meant to be an authoritative or systematic list of synonyms or class members; lists of different classes may overlap, and the list may include obsolete or deprecated names (e.g. a database for living species may list "bear" as a keyword on the Koala page.) Finally, it has been clearly stated since day one that "Wikipedia is not a database", so its articles should not be mechanically derived from a database, not forced to mirror it. All the best, --Jorge Stolfi (talk) 03:10, 6 July 2014 (UTC)

As discussed here and here, there is consensus within the MCB project to create enzyme articles based on EC numbers. I strongly support that consensus.

The EC system is more than a database, it is a system of enzyme nomenclature. Strictly speaking, a terminal EC node refers not to a class of enzymes but rather to a specific type of chemical reaction that is catalyzed by enzymes. While there are a few other classification systems (e.g., MEROPS), the EC system is by far the most comprehensive and widely used. In addition, while there have been updates to the EC system, these changes occur slowly and the rate of change has slowed down. Most changes involve addition of new EC nodes. Furthermore most individual EC nodes have not changed since they were first introduced. The system as a whole is relatively stable. Wikipedia conforms to the long tail with a hierarchy of articles from the most general (e.g., enzyme) that would be of interest to a wide audience to very specific ones like glucan 1,4-beta-glucosidase that would likely be of interest only to specialists. The only requirement for creation of a Wikipedia article is if there are sufficient reliable sources to establish the notability of the subject, not how wide of interest a subject may be. There are sufficient reliable sources to establish the notability of most if not all EC nodes.

not every substance that readers may look up in Wikipedia and is supported by reliable publications has a number in the Chemical Abstracts database – False. CAS and Beilstein work diligently in registering and indexing chemicals that are described in the chemical, patent, and related literature. If a chemical does not have a CAS or Beilstein number, it probably is not notable.

Wikipedia aims to provide "the sum of all human knowledge". The types of reactions that are catalyzed by enzymes as reflected in the EC nomenclature system is part of that knowledge hence having a series of Wikipedia articles that capture that knowledge is appropriate. Boghog (talk) 08:48, 6 July 2014 (UTC)

One additional point. As illustrated in {{Infobox enzyme}}, links to IntEnz, BRENDA, ExPASy, KEGG, PRIAM, PDB, and PubMed are all based on the EC number. The EC number is not only used by the Enzyme Commission database, but these other seven databases as well. One cannot have a comprehensive article about an enzyme without mentioning its EC number. Boghog (talk) 18:20, 7 July 2014 (UTC)

Nagalase

Nagalase previously linked to the Alpha-N-acetylgalactosaminidase article, which contained substantial amounts of uncited material, and what appeared to be a three-paragraph copyvio from an abstract. Given the recent controversy regarding nagalase research (for example, this article retraction, we should be very careful about ensuring all statements on this subject are both adequately cited, and that a retraction search has been performed on the cited papers. -- The Anome (talk) 16:29, 27 July 2014 (UTC)

image feedback - addiction cascade

The addiction diagram; collapsed by Seppi333

Signaling cascade in the nucleus accumbens that results in psychostimulant addiction Note: colored text contains article links. Nuclear pore Nuclear membrane Plasma membrane Cav1.2 NMDAR AMPAR DRD1 DRD5 DRD2 DRD3 DRD4 Gs Gi/o AC cAMP cAMP PKA CaM CaMKII DARPP-32 PP1 PP2B CREB ΔFosB JunD c-Fos SIRT1 HDAC1 This diagram depicts the signaling events in the brain's reward center that are induced by chronic high-dose exposure to psychostimulants that increase the concentration of synaptic dopamine, like amphetamine, methamphetamine, and phenethylamine. Following presynaptic dopamine and glutamate co-release by such psychostimulants, postsynaptic receptors for these neurotransmitters trigger internal signaling events through a cAMP-dependent pathway and a calcium-dependent pathway that ultimately result in increased CREB phosphorylation. Phosphorylated CREB increases levels of ΔFosB, which in turn represses the c-Fos gene with the help of corepressors; c-Fos repression acts as a molecular switch that enables the accumulation of ΔFosB in the neuron. A highly stable (phosphorylated) form of ΔFosB, one that persists in neurons for 1–2 months, slowly accumulates following repeated high-dose exposure to stimulants through this process. ΔFosB functions as "one of the master control proteins" that produces addiction-related structural changes in the brain, and upon sufficient accumulation, with the help of its downstream targets (e.g., nuclear factor kappa B), it induces an addictive state. References

I'm still undecided on whether or not to use this image outside ΔFosB, but if anyone has any feedback - technical, cosmetic or otherwise - for improving this, I'd appreciate it. This is probably the most apt wikiproject to ask for technical feedback, so chime in if you have any. Seppi333 (Insert 2¢ | Maintained) 06:24, 20 July 2014 (UTC)

Featured picture nominations for technical diagrams

Cross-posted on WT:MED, WT:PHARM, WT:MCB, and WT:NEURO

I nominated two technical diagrams (the signaling cascade involved in psychostimulant addiction and amphetamine pharmacodynamics in dopamine neurons) for featured picture.
I spent about 30 hours making the ΔFosB diagram alone, so I'd really appreciate it if anyone is willing to contribute an image review!

Regards, Seppi333 (Insert 2¢ | Maintained) 21:28, 21 August 2014 (UTC)

Anybody reviewing Medgirl131's edits?

Cross-posting Wikipedia_talk:WikiProject_Pharmacology#Anybody_reviewing_Medgirl131.27s_edits.3F FYA. Thanks. Samsara (FA • FP) 10:27, 30 August 2014 (UTC)

LAK Cells - own article or separate?

Hello, I came across a draft today about Cytokine-induced killer cells, but I was unsure of whether it was notable enough to have its own topic or should be added as a section in the Lymphocyte article (or something related). Thoughts on how to proceed would be much appreciated. Thanks! Primefac (talk) 19:56, 29 September 2014 (UTC)

There is already an article Lymphokine-activated killer cell that looks very similar to the draft. Best to probably delete the draft and have a merge discussion at the article's talk page. --Mark viking (talk) 20:23, 29 September 2014 (UTC)

Comment on the WikiProject X proposal

Hello there! As you may already know, most WikiProjects here on Wikipedia struggle to stay active after they've been founded. I believe there is a lot of potential for WikiProjects to facilitate collaboration across subject areas, so I have submitted a grant proposal with the Wikimedia Foundation for the "WikiProject X" project. WikiProject X will study what makes WikiProjects succeed in retaining editors and then design a prototype WikiProject system that will recruit contributors to WikiProjects and help them run effectively. Please review the proposal here and leave feedback. If you have any questions, you can ask on the proposal page or leave a message on my talk page. Thank you for your time! (Also, sorry about the posting mistake earlier. If someone already moved my message to the talk page, feel free to remove this posting.) Harej (talk) 22:47, 1 October 2014 (UTC)

Expert needed on Morphogen

Is there anyone here who could bring Morphogen up to date? It has been flagged for years as poorly cited, and is clearly far out of date in a changing field. Chiswick Chap (talk) 08:28, 3 October 2014 (UTC)

Parahuman

See Talk:Parahuman#Requested move. Isn't this article relevant to this project? Dougweller (talk) 10:37, 10 October 2014 (UTC)

Requested move

Input requested at Talk:Serotonin N-acetyltransferase. Dekimasuよ! 00:10, 10 November 2014 (UTC)

What is actually needed in enzyme articles?

I've been hoping to expand some articles under this project, but I have no idea what you'd write. There are a million variations on enzymes. Is there anything fun to say? Or at least expand on? What would you write? Panyd^{The muffin is not subtle} 18:28, 12 November 2014 (UTC)

Hi Panyd. Welcome to the MCB project! We don't have a style guide specifically for enzymes, but the sections section of the gene/protein style guide can give you some ideas. Also some of the more well developed enzyme articles (e.g., alcohol dehydrogenase) might serve as templates. As far as fun things to say, enzyme articles tend to be pretty dry, but you occasionally run into odd things like this.

Also it is important to realize that specific enzyme as defined by an Enzyme Commission (EC) number are strictly speaking the chemical reaction catalyzed by an enzymatic protein and not the protein itself. Structurally unrelated proteins may catalyze the same reaction and hence are assigned the same EC number (many to one relationship) If there is a single human protein that corresponds to an EC number (one to one relationship), then we usually have a single article that covers both the protein and the reaction catalyzed by that protein. I hope this helps. If you have any additional questions, don't hesitate to ask. Cheers. Boghog (talk) 20:29, 12 November 2014 (UTC)

Hi Panyd. One thing that's often missing in enzyme pages is links to other, related enzymes. There are relatively few pages for enzyme superfamilies currently (e.g. Alpha/beta hydrolase fold), but linking related enzymes with different activities would be useful to give readers a sense of the evolution of these superfamilies. Have fun editing! T. Shafee (Evo&Evo) (talk) 23:03, 12 November 2014 (UTC)

You guys rock. Thank you! Panyd^{The muffin is not subtle} 23:34, 12 November 2014 (UTC)

Energy systems

The article energy systems is proposed to be renamed, for the discussion, see talk:energy systems ; it appears to be an ATP metabolism article

-- 67.70.35.44 (talk) 06:22, 7 December 2014 (UTC)

Launch of WikiProject Wikidata for research

Hi, this is to let you know that we've launched WikiProject Wikidata for research in order to stimulate a closer interaction between Wikidata and research, both on a technical and a community level. As a first activity, we are drafting a research proposal on the matter (cf. blog post). Your thoughts on and contributions to that would be most welcome! Thanks, -- Daniel Mietchen (talk) 02:15, 9 December 2014 (UTC)

Protein articles titles - Name or Gene?

Hey all, Quick question from someone with little experience editing protein pages. As we're all aware gene names and protein names can differ. In glancing at some pages about proteins, I've been a little curious about the fact that the titles for those pages appear to be gene names (see POLR2A, ABO (gene)). This strikes me as confusing. Is there an accepted practice/policy for dealing with this? NickCT (talk) 18:48, 11 December 2014 (UTC)

There relevant guideline is here. The vast majority of Gene Wiki articles are about both the protein and the gene that encodes that protein. Because the gene and protein are so interrelated, it makes sense to discuss both in the same article. Unfortunately this causes an unavoidable ambiguity as to what to call the article. The guideline suggests to use use the UniProt protein name if relatively short or the HUGO gene symbol if the protein name is unwieldy.

In the two examples you cite (POLR2A and ABO (gene)), the protein names are rather long. Hence the current article titles are consistent with the guideline.

Also concering the lead sentence in Gene Wiki articles, as discussed here and here, we have tried to make clear that these articles are not only about the human gene/protein, but also orthologs that exist in other species. The wording that was reached through consensus is perhaps a little awkward, but it is both accurate and concise:

• <recommended UniProt name> is a protein that in humans is encoded by the <approved HUGO gene symbol> gene.

The "that" in the above sentence is non-limiting implying that the protein (and gene) exists in other species besides human. Boghog (talk) 19:46, 11 December 2014 (UTC)

@Boghog: - Thanks for the explanation Boghog. I have to say though, using the gene name or protein name interchangeably based on something potentially arbitrary like how "verbose" the protein name is, strikes me as a little confusing. Giving an article the name of gene, then having the first line of an article read "X is a protein" seems like is might confuse folks not familiar with the subtleties involved.

Hard to know the best strategy here. Perhaps this is a discussion to have on the policy page. NickCT (talk) 23:50, 11 December 2014 (UTC)

@NickCT: Likewise, I am not sure what the best policy here is either. I agree with you that there is a conflict between the suggested lead sentence and using the gene name as the title of the article and this has caused some confusion and controversy on occasions (e.g., editors modifying the lead sentence so that it starts with the gene name). Further complicating maters is that some gene/protein paris like BRCA1 are much better known by their gene symbols than protein names while others like insulin the reverse is true. So even if we established a more specific guideline, there would always be exceptions. Boghog (talk) 15:35, 13 December 2014 (UTC)

Using space-filling diagrams for articles describing molecules

As a student with a biotechnology certificate, it seems to me that articles on specific molecules should include space-filling models as the primary diagram for the top of the article page. I'm sure this has been discussed at some point, so if someone could point me toward that discussion, I would be interested in joining. Thanks for any guidance or consideration this has required on your part.

Regards,

Rrossmith (talk) 16:50, 13 December 2014 (UTC)rrossmith

It is often difficult if not impossible to tell exactly what the structure is from a space-filling model. Therefore I think this type of representation is not the best choice for the primary diagram. For small molecules, the primary diagram should be a 2D depiction (see for example chemistry structures and pharmacology structure diagrams). For biopolymers such as proteins, a cartoon or ribbon diagram is probably most appropriate (see recommended representations). Boghog (talk) 17:35, 13 December 2014 (UTC)

I guess I agree. The largest difficulty with the space-filling model would be to choose it's most suitable viewing angle. Without a system to view it from multiple angles, or zooming capacity, that seems difficult. I still have difficulty seeing the value of the ribbon diagrams, but maybe that's just where I am with my knowledge. Thanks for the response!

Rrossmith (talk) 18:26, 13 December 2014 (UTC) Rrossmith

The advantage of the ribbon diagram is that it is easy to trace the primary structure through the protein (especially if it is rainbow colored, for example N-terminus blue, C-terminus red) as well as illustrate the secondary structure (e.g., α-helices are shown as coiled ribbons or thick tubes, β-strands as arrows, and lines or thin tubes for non-repetitive coils or loops). Boghog (talk) 18:55, 13 December 2014 (UTC)

There was a discussion to allow rotation of structures with Jmol, however as far as I know, this was never implemented. Jmol allows 3D rotation of structures as well as toggling between different display modes including space filling. However even with 3D rotation, I still think a ribbon diagram is more informative. Boghog (talk) 19:02, 13 December 2014 (UTC)

The space-filling model could be the most 'realistic' for showing the electron structure and the steric hindrances, if any. But for most practical purposes getting a clear view of the backbone is more useful. Though Rrossmith didn't mention any specific article, the use of diagrams in Luciferin seems about right. One space-filling model and several conventional 2D diagrams. As I skipped through some visual pigment articles quickly, I noticed a lack of *any* diagrams, something that could surely be rectified. EdJohnston (talk) 19:08, 13 December 2014 (UTC)

Free 'RSC Gold' accounts

I am pleased to announce, as Wikimedian in Residence at the Royal Society of Chemistry, the donation of 100 "RSC Gold" accounts, for use by Wikipedia editors wishing to use RSC journal content to expand articles on chemistry-related topics. Please visit Wikipedia:RSC Gold for details, to check your eligibility, and to request an account. Andy Mabbett (Pigsonthewing); Talk to Andy; Andy's edits 09:16, 14 January 2015 (UTC)

WikiProject X is live!

Hello everyone!

You may have received a message from me earlier asking you to comment on my WikiProject X proposal. The good news is that WikiProject X is now live! In our first phase, we are focusing on research. At this time, we are looking for people to share their experiences with WikiProjects: good, bad, or neutral. We are also looking for WikiProjects that may be interested in trying out new tools and layouts that will make participating easier and projects easier to maintain. If you or your WikiProject are interested, check us out! Note that this is an opt-in program; no WikiProject will be required to change anything against its wishes. Please let me know if you have any questions. Thank you!

Note: To receive additional notifications about WikiProject X on this talk page, please add this page to Wikipedia:WikiProject X/Newsletter. Otherwise, this will be the last notification sent about WikiProject X.

Harej (talk) 16:57, 14 January 2015 (UTC)

Substrates and products merge

Just a quick post to both WP:MCB and WP:Chem. There are duplicate stub pages for substrate and product. Since in each case one copy just repeats the other I propose that they're merged into substrate_(chemistry) and product_(chemistry) with the biochem-specific parts just as a section.

• Substrate: Substrate (chemistry) and Enzyme substrate (biology)
• Product: Product (chemistry) and Product (biology)

Any opinions? T.Shafee(Evo﹠Evo)^talk 09:30, 20 January 2015 (UTC)

• Merge – The disambiguation "biology" is not appropriate to begin with ("products" of biology are offspring ;-) If not merged, the disambiguation "biochemistry" would be more appropriate. Since all four articles deal with chemicals, merging Enzyme substrate (biology) into Substrate (chemistry) and Product (biology) into Product (chemistry) IMHO is appropriate. Boghog (talk) 14:01, 24 January 2015 (UTC)

For reference, I've performed the merge and expanded the articles a bit. Anyone interested in further improving them would be very welcome! T.Shafee(Evo﹠Evo)^talk 03:51, 10 February 2015 (UTC)

Create the Category 'Biochemistry databases'

Hi, here's a link to the category talk page, all the best, --Ghilt (talk) 10:08, 19 February 2015 (UTC)

FAR

I have nominated Enzyme for a featured article review here. Please join the discussion on whether this article meets featured article criteria. Articles are typically reviewed for two weeks. If substantial concerns are not addressed during the review period, the article will be moved to the Featured Article Removal Candidates list for a further period, where editors may declare "Keep" or "Delist" the article's featured status. The instructions for the review process are here.--Jarodalien (talk) 07:02, 13 February 2015 (UTC)

I've recently nominated the reviewed enzyme article to be featured on the front page since it's gone though so many changes since 2006. T.Shafee(Evo﹠Evo)^talk 01:17, 8 March 2015 (UTC)

Never mind, apparently we don't re-run articles after they've gone though FAR. I suppose it is reasonable to prioritise newly promoted FAs. T.Shafee(Evo﹠Evo)^talk 00:08, 9 March 2015 (UTC)

Proteomic code

To me, a 'lay' reader, the subject (a broad solution to the protein folding problem) seems to be a fringe view, hardly discussed by any sources but its originator, who, coincidentally, seems to have written the Wikipedia article as well (technically a copyvio of his own journal article).

I am prodding it for now; if anyone with knowledge of the subject (or otherwise) disagrees, please de-prod.

הסרפד (call me Hasirpad) 17:17, 24 March 2015 (UTC)

If we place copyivio and conflict of interest aside, I think it could be salvaged if the title and the first sentence of the article specify that it is a [rejected?] hypothesis. BatteryIncluded (talk) 18:59, 24 March 2015 (UTC)

The idea is mentioned briefly in Genetic code#Origin, which could probably be expanded a bit. I don't think this guy's theories in particular have been taken very seriously, though. Most of the author's papers give the appearance of being fairly well-cited, but he self-cites a lot and the rest are mostly "So, this theory exists [1]. Aaaaanyway,..." The author now seems to spend his time writing articles about the Jewish conspiracy to claim more than their share of Nobel Prizes. Opabinia regalis (talk) 03:57, 25 March 2015 (UTC)

In that case, Proteomic code could be merged to Genetic code#Origin as a brief paragraph, then delete the 'Proteomic code' article. BatteryIncluded (talk) 16:47, 25 March 2015 (UTC)

BatteryIncluded: I'm not sure a merge is a good ides. Opabinia regalis: in what way is Biro's theory—which he, alone apparently, does not think is a rejected hypothesis—related to theories of the origins of the genetic code? Biro describes what he thinks is happening in modern cells, where DNA or RNA (I didn't get it straight) preforms a "chaperone" function. (Perhaps I should desist, so as not to lend credence to the belief in said conspiracy. As it happens, I was not given this assignment at the most recent conference of the Elders.) הסרפד (call me Hasirpad) 17:49, 29 March 2015 (UTC)

@הסרפד:I have no strong feelings at all for keeping or deleting the article. My thought is that if someone heard rumors of this "code" or "conspiracy theories", they could rest in peace after reading here that it is an incorrect/rejected hypothesis. Truly your call. Cheers, BatteryIncluded (talk) 17:55, 29 March 2015 (UTC)

@BatteryIncluded: @הסרפד: Sorry, didn't mean to cause confusion; I agree there's nothing meaningful to merge from the existing article. The connection I meant is: the idea underlying Biro's 'hypothesis' is a relationship between the physical properties of amino acids and their corresponding codons, which is also an idea floated in the 50s as an explanation for the origin of the genetic code. That idea was certainly never referred to as the "proteomic code", which is a term that never seems to come up outside of Biro's work or references to it. Sure, that's what they all say... Opabinia regalis (talk) 19:28, 29 March 2015 (UTC)

Chromatophore FAR

I have nominated Chromatophore for a featured article review here. Please join the discussion on whether this article meets featured article criteria. Articles are typically reviewed for two weeks. If substantial concerns are not addressed during the review period, the article will be moved to the Featured Article Removal Candidates list for a further period, where editors may declare "Keep" or "Delist" the article's featured status. The instructions for the review process are here. SandyGeorgia (Talk) 18:44, 4 April 2015 (UTC)

requesting help with info box

I'm editing the epsin article for a class and would like to add an info box. Can someone help me with this? I have the crystal structure downloaded on my computer, but have not yet uploaded to WP. Lnbond92 (talk) 17:44, 14 April 2015 (UTC)

Hi, welcome to the MCB page. You'll need to go to the Template:Infobox_protein page which explains how to insert the protein infobox. Basically copy-paste the template below and fill in as many of the parameters as possible:

Protein infobox template to copy-paste in
{{Infobox protein | name = | image = | width = | caption = | Symbol = | AltSymbols = | IUPHAR_id = | ATC_prefix = | ATC_suffix = | ATC_supplemental = | CAS_number = | CAS_supplemental = | DrugBank = | EntrezGene = | HGNCid = | OMIM = | PDB = | RefSeq = | UniProt = | ECnumber = | Chromosome = | Arm = | Band = | LocusSupplementaryData = }}

Have you made the protein image yet and need help uploading, or do you need help converting the .pdb file into an image? Feel free to ask more questions if you need more help. T.Shafee(Evo﹠Evo)^talk 23:41, 14 April 2015 (UTC)

Likewise, welcome to the MCB project. Epsin is not one protein, but a family of proteins with four paralogs in humans and orthologs in many other species. Hence it is not clear if a {{infobox protein}} or {{infobox nonhuman protein}} template is appropriate. Also family members contain at least two pram domains, hence a {{infobox protein family}} is not really appropriate either. Hence it may be better just to insert the the graphic with a caption: [[File:Name|Thumb|Caption]] Boghog (talk) 04:27, 15 April 2015 (UTC)

Good point Boghog, a [[File:Name|Thumb|Caption]] with a descriptive caption is probably the best option. T.Shafee(Evo﹠Evo)^talk 04:36, 15 April 2015 (UTC)

Great! Thank you so much. The best full length crystal structure I could find on rcsb is of Rat Epsin1 so I will use the non human protein box. If I run into any trouble putting it together I'll post again. Lnbond92 (talk) 02:04, 16 April 2015 (UTC)

Annotated image policy

If anyone has an interest in interactive annotated images, I've made a post on WP:IUP to discuss when wikilinked image annotation is appropriate. T.Shafee(Evo﹠Evo)^talk 02:23, 19 April 2015 (UTC)

Draft:CDP-choline pathway

Hello, biochemists. This old AfC submission appears to be related to this project. It will shortly be deleted because it is unsourced and abandoned. Last chance for someone to take an interest in it.—Anne Delong (talk) 14:35, 17 April 2015 (UTC)

@Anne Delong: Thanks for the heads-up. Topic is keep-worthy for sure. I haven't checked the whole article but nothing stands out as obviously wrong. There are references available in abundance for the topic. (The history seems a little unfortunate - I don't see any evidence that the author, who evidently has some knowledge of the topic, ever got anything but a template on their talk page, and if they'd created it in mainspace it certainly wouldn't have been deleted.) Running out of time now but I'll deal with it tomorrow hopefully. Opabinia regalis (talk) 07:07, 19 April 2015 (UTC)

Thanks, Opabinia regalis; I have postponed its deletion to give you time to do something with it. It's not surprising that the article wasn't accepted, because it has no references at all. It wasn't deleted at AfC, either; the author was just asked to add references. Most people who have studied biology, even in high school, understand the importance of citing sources, so I am presuming that this person either never came back to check on the draft, or was just too busy to comply. That's why the drafts are being checked over when they've been "abandoned" for six months. It would likely be a good idea to check them sooner, but there is a shortage of willing editors working in this area. If you are able to add some verification in the form of sources, we can move it into mainspace.—Anne Delong (talk) 11:59, 19 April 2015 (UTC)

I agree with Opabinia regalis that the draft is worth keeping and just lacks sources. PMID 20503434 is a recent review that should be sufficient to source most things currently in the draft. I have started working on this. Boghog (talk) 12:46, 19 April 2015 (UTC)

The article has three sources now plus two editors here who have agreed that the content is suitable, so I have moved it to mainspace. Thanks to Opabinia regalis, Boghog and Ppgardne for taking time to check this out.—Anne Delong (talk) 03:05, 20 April 2015 (UTC)

Peptidase 1 (mite) article revision

I have been currently working on a revision of the peptidase 1 (mite) page in my sandbox, since I noticed that this article was heavily lacking in information. I left a message on the article's talk page, but because the said talk page seems to be completely dead, I figured that I'd also post this message to this project's talk page since that article is part of this project. It's still a work-in-progress (I'd like to include more info on Der f 1's function in promoting allergic immune responses, and I still have general clean-up of links, citation order, redundancies, etc. reserved for the end), though I hope to have it finished by tomorrow afternoon (EST). If anyone has any suggestions for improvement, please let me know - I'd appreciate the help! --PeabodySam (talk) 19:19, 11 April 2015 (UTC)

I'd like to quickly thank Boghog for contributing infoboxes to the article for each allergen. However, where each allergen has its own subsection under both "Structure" and "Biological Function" (with the former currently placed before the latter), would these infoboxes be better placed in the "Structure" subsections (which come first) or the "Biological Function" subsections (where Boghog has added them)? Unfortunately, considering that the infoboxes are currently larger than the subsections themselves, having four in a row causes a bit of "pile-up"... this could be addressed by a {{clear}} template or something similar, but then we end up with garish gaps in the article.

Also, just as a quick question that I forgot to ask earlier: how sophisticated should the scientific language be in this article? Some of my peers expressed concern that my sanbdox's terminology was a little too complicated for an online encyclopedia intended for public use by anybody, even with links to other articles for clarification. Do you agree? And, if so, do you have any suggestions for how I could make the wording easier for a general audience to understand? --PeabodySam (talk) 22:08, 11 April 2015 (UTC)

Thanks for expanding the peptidase 1 (mite) page. I have moved the infoboxes closer to where the respective proteins are first mentioned and removed the EC link which is redundant (links already supplied in the enzyme infobox). Removing this link slightly reduces the size of the infoboxes. Concerning the level of language, it is important that at least the lead is accessible to a wide audience. The rest of the article I would worry less about. We have a hierarchy of articles. The most general, like enzyme are written in a way so that it can be understood by a wide audience. It is understood that more specialized articles like peptidase 1 (mite) are inherently technical and less likely to be read beginning to end by non-specialists. Boghog (talk) 22:25, 11 April 2015 (UTC)

If it's alright with you guys, I'm going ahead and adding the content from my sandbox to the mainspace article. Feel free to undo or edit anything you don't like. --PeabodySam (talk) 22:28, 22 April 2015 (UTC)

Draft:CXorf67

I've copied the following post that might be of interest over from WT:BIOL. T.Shafee(Evo﹠Evo)^talk 10:27, 12 May 2015 (UTC)

Please could someone with knowledge in biology/proteins look at this draft article- due to my lack of subject knowledge, I cannot determine if it's notable enough for Wikipedia or not. Joseph2302 (talk) 15:50, 11 May 2015 (UTC)

Also Draft:PRP36. Cheers, FoCuSandLeArN (talk) 00:35, 14 May 2015 (UTC)

Disamb. needed?

Do you reckon Extrinsic pathway could use a disambiguation page? It's too vague a term in my opinion. Let me know your thoughts and ping me if possible. It came to my attention when reading Prothrombin time and noticing the wikilinks in the lede had nothing to do with coagulation. Regards, FoCuSandLeArN (talk) 21:50, 19 May 2015 (UTC)

Wikipedia talk:Articles for creation/De novo protein synthesis theory of memory formation

Hello, biochemists. I found this old draft, but I am not sure if this the correct venue to report it. Is this a notable topic? Are the references appropriate?—Anne Delong (talk) 16:33, 5 May 2015 (UTC)

@Anne Delong: Thanks, this is a good place for it. The idea that protein synthesis is involved in memory formation is true enough, but this looks like (pretty good) classwork, with the expected tinge of OR and essay style. Maybe a selective merge to memory consolidation, which already covers the topic briefly. Some of the PKMzeta stuff could go to Protein kinase C zeta type - this hypothesis is still very much up in the air (eg PMID 24076105). Opabinia regalis (talk) 01:37, 6 May 2015 (UTC)

Thanks, Opabinia regalis. It's been edited now, so it will hang around for six months of so in case someone here wants to work on it or merge sections as you suggest. I can't do it myself, not having studied biology.—Anne Delong (talk) 06:56, 28 May 2015 (UTC)

OK, I'll put it on the to-do list. Thanks! Opabinia regalis (talk) 07:10, 28 May 2015 (UTC)

what can Wiki Education Foundation do to help WikiProject MCB?

Hi WikiProject MCB,

The Wiki Education Foundation wants to know what it can do to empower editors who work on science-related content on Wikipedia.

If you're familiar with Wiki Ed, it's likely by way of our classroom program, which grew out of the Wikipedia Education Program and through which we provide support for instructors and students who work on Wikipedia as part of a class assignment. This post is about something different, though. We'll be continuing to develop that program, of course, but we also want to start working on ways to help the existing Wikipedia community directly.

In 2016, Wiki Ed will be running a campaign tentatively titled, "Wikipedia Year of Science". The goal, generally stated, will be to improve the content and coverage of science-related content on Wikipedia ("science" interpreted loosely). Whereas our classroom program, as with many other extra-organizational initiatives, is premised on attracting and/or training new users, my aim is to figure out the sorts of things we can do to help the editors who are already engaged in the improvement of science content. The question is indeed wide open, but think about it this way: we have staff and a lot of institutional connections; how can we use our resources and relationships to support you? For example, is there a special collection of photos we should try to get on Commons? What about a document archive? Databases or specific journals? Organizationally, is there software that could be built that would help people working on these topics? What kinds of research could we conduct or help to organize that would help you to work more effectively? What are ways we can connect you with other human resources -- experts, for example (though, again, this is not intended to be an outreach program)? How could we motivate people to contribute, whether it be adding content, improving content, conducting reviews, adding images, improving sourcing, or any other part of the process? How can we get more biology-related articles to FA/GA? How could we help you to spend more of your time working on things you find fun and interesting and less time on process, organization, and functionary duties?

These questions are really just intended to get the ball rolling as this really is a nascent idea. So all ideas are welcome: big, small, obvious, obscure, ambitious, simple, technical, organizational.... I want to be clear that this is not just some survey -- the feedback I get will help to give shape to the "Year of Science" campaign.

I should also mention that this community engagement program we're starting isn't limited to the Year of Science campaign. Researching and planning it is high on my priority list right now, but we can also talk about shorter- or longer-term projects you may have in mind, too.

Apologies for the long message and thanks for your time. Looking forward to hearing what you think. --Ryan (Wiki Ed) (talk) 04:09, 28 May 2015 (UTC) (volunteer account: User:Rhododendrites)

@Ryan (Wiki Ed): This is kind of a brain dump, in no particular order. For what it's worth, I'm in biophysics/computational biology and I think the field has done pretty well by academic standards - the Biophysical Society, ISCB, and PLoS Comp Bio have all engaged here at one point or another.

1. Technical solution to citation bloat: One of the most annoying things about editing science articles right now is the giant sticky boogers of cite template wikimarkup snot everywhere. They're impenetrable to new users, are a totally non-transferable skill, generate no end of pointless formatting arguments, take up a ton of space in the edit window, and are impossible to deal with on mobile. The problem is especially acute for science articles because they tend to be densely cited to a large number of different sources (and because the subfield equivalents of "the sky is blue" tend to attract drive-by citation-taggers). I actually really like Citoid, but the Visual Editor introduces frustrations of its own. I keep seeing comments that Wikidata will solve this problem, but haven't seen much progress. This is an issue where some technical leadership would go a long way.
2. Open access/free knowledge/etc: I'd really like to see the project to mark OA sources in reference lists take off. (Granted I've done nothing to push this forward myself.) Links to PMC are nice, but I'd like to see a more prominent highlight of sources under OA licenses. On the topic of finding OA sources to include in wiki articles, I've poked a little at the idea of getting Google Scholar to offer an "open access only" search parameter, but that hasn't really gone anywhere. Maybe a case where institutional initiative could help.
3. Getting academic "credit" for Wikipedia writing: This is sort of a perennial proposal. Over at WT:MED there was an idea floated a few weeks ago about starting a peer-reviewed journal that would republish modified versions of wiki articles, among other things; it's an interesting idea but, I think, not a natural fit for my field, and where there is a fit the niche is already occupied by PLoS Comp Bio. I'd be interested in seeing some thinking on how to let people - especially early-career researchers - present Wikipedia editorship as science writing and public outreach experience in a consistent and recognizable way. Assign DOIs to specific revisions? Have a structured fellowship program? Some kind of GLAM-like arrangement with a scientific society, or one of the OA publishers that already engages this population? (e.g. the PLoS student blog or the F1000 specialists program) Academia being what it is, a way to turn existing editing practices into a recognizable line or two on a CV may well get more people involved.
4. System for reviewing Wikipedia articles: Another perennial proposal, and one I'm less excited about than some; this is usually formulated as "get a recognized Big Name expert to put their name on a reviewed version of an article", but I want to see the scientific world invest less in trading on the personal reputation of a few prominent individuals (which has all kinds of problems with systemic bias). One idea might be to engage with the Publons people to make relatively lightweight article reviews (done independently, or maybe as part of peer review or FAC/FAR?) count as review credits. This could also result in early-career scientists being able to accumulate a reputation as good or prolific reviewers under the publons system. This would rely on some kind of identity authentication, though.
5. Mechanism for recognizing women and minority editors in STEM: I haven't thought of a good way to do this yet without tripping over gender-gap drama or attracting trolls, but science on Wikipedia is two intersecting white-male-enriched environments and it would be nice to have some way of recognizing people who push back on that trend. This is another matter of presentation, I think; you can imagine someone listing on the "outreach" section of their CV something like "Wiki[pedia/media/edu?] Community Diversity Advocate, 2014-15" or "Some Notable Sponsor Award for Excellence in Science Writing, awarded to the top contributors of Wikipedia content on women and minority scientists" or some such, but most of the existing internal Wikipedia mechanisms for recognizing contributors and content are too inside-baseball. (I've actually seen a CV listing Featured Article authorship, but that's a tough bet. What if the person reading the CV goes to check out the article and it's been vandalized or filled up with cruft while you weren't looking? You need a way to point to explicit recognition by a real-world entity.)

Opabinia regalis (talk) 20:50, 29 May 2015 (UTC)

Category renaming proposed

Category renaming proposed at here. About 25 categories included in this category, renaming from, for example, Category:Genes on chromosome 1 → Category:Genes on human chromosome 1 is proposed (adding "human" to category name). Although I think there are no need to explain the reason of renaming to the members of this project, chromosome number which contains certain gene varies in species-to-species. So we need to specify species. --Was a bee (talk) 17:27, 30 May 2015 (UTC)

Wikipedia:Articles for deletion/Differential DVH

Members of this project are invited to comment. --Kudpung กุดผึ้ง (talk) 02:00, 10 June 2015 (UTC)

Definition of a Gene

As the Gene article is about to be GA reviewed, it might be useful to check that there is consensus on the definitions (Talk:Gene#Definitions). T.Shafee(Evo﹠Evo)^talk 01:15, 14 June 2015 (UTC)

Updating the WP:MCB project page

What do people think of a bit of a refresh of the WP:MCB page? We have a lot of subpages that have been inactive for a long time and it might be worthwhile consolidating into fewer pages (so that the project isn't as labyrinthine). For example, both the project and talk pages prominently display a link to the defunct Collaboration of the month page. We could put together a page more focussed on the active project areas (like this talk page). What do people think? T.Shafee(Evo﹠Evo)^talk 11:21, 26 May 2015 (UTC)

Yes, I agree that the project subpages should be consolidated. Given the relatively low traffic on the discussion subpages, they should probably all be merged into the main talk page. The "Tasks that need attention" subpages should be retained for historical reference, but the links to these pages from the main page could be removed. The Worklist could be converted into a "resource". Boghog (talk) 05:12, 28 May 2015 (UTC)

Also agree, thanks for looking into this. There is definitely a lot of old cruft around here. Opabinia regalis (talk) 07:06, 28 May 2015 (UTC)

Initial plans

So currently I plan to:

1. Collect defunct subpages into a list that we can keep a link to on the main page for history - WP:MCB/Historical
2. Refocus link attention to this page as the main hub of activity
3. Update the visual style to be a bit more modern

Long term possibilities:

• A public watchlist of articles?
• Clean-up (& consolidation) of the editing advice pages?
• Any ideas about the members list?
• Is our worklist still automatically updated?

Anyone is welcome to help out. I'm relatively new to extensive use of templates and I've no idea about bots. I'll also try to keep an eye on the tools and design ideas that Wikiproject X is developing. T.Shafee(Evo﹠Evo)^talk 02:54, 29 May 2015 (UTC)

The worklist does not appear to be automatically updated, but User:WP 1.0 bot/Tables/Project/MCB is. The Grading part of the work list could be converted into a resource. There has been no significant update to the Categories section of the work list since 2009. Hence I think the Categories section should be retired/archived. Boghog (talk) 03:36, 29 May 2015 (UTC)

Sounds like a good plan. I suspect most of the editing advice pages are even more out of date than the rest, and ignored anyway. Members list I guess could be filtered so anyone who hasn't edited in a year or so gets moved to an 'inactive members' list, though I doubt too many people read those lists either. Personally I think all the grading/assessment criteria other than FA are useless and chronically outdated, but it still might be worth switching the project talk page banner to the full quality scale, which includes drafts. Opabinia regalis (talk) 05:35, 29 May 2015 (UTC)

I've put together the pages that I think are inactive as well as the other non-main discussion pages (WP:MCB/Historical). There are also a few pages that'll need to be updated:

• Directory
• Advice
• References
• Style guidelines
• Style guide (gene and protein articles)
• Diagram guide
• PyMol tutorial
• Related projects and resources
• Worklist
• MCB articles by quality log

I think that's all the subpages accounted for. some of these can probably be combined or retired as well. T.Shafee(Evo﹠Evo)^talk 04:45, 30 May 2015 (UTC)

Thanks for starting the cleanup. The participants list was recently edited to remove inactive editors and few new editors have been added in 2015. Hence I think this list should still be considered active. I agree that it is appropriate to retire the rest of the pages in the WP:MCB/Historical list. Boghog (talk) 06:00, 30 May 2015 (UTC)

Seconding the thanks to Evo & Evo. Just a heads-up that the way things are currently transcluded, I see "This MCB project subpage is no longer in use..." within the to-do list at the top of this page, making it appear (at a glance) as though this page is inactive. I guess we just need the whole to-do list to no longer be transcluded, but I'll leave it to Evo & Evo or whoever to find the best solution. Adrian J. Hunter^{(talk•contribs)} 06:42, 30 May 2015 (UTC)

I've updated the WP:MCB page so that it can render properly on mobile devices. I've left it in the same uninspiring beige for now, but might attempt to make it look a little less dated once the content is sorted. I'm planning to make an updated navigation bar. It's currently the following 4 sections which I think seem to me the most active areas:

• Main
• Discussion (to encompass help queries, article requests, review requests, notifications)
• Advice & resources (a collection of style guidelines and help pages)
• Alerts & statistics (automatically updated quality stats and article alerts)

Also, thanks Adrian J. Hunter, well spotted. We had the same problem with members list on the main page. I've moved the <noinclude> to encompass the warning header. T.Shafee(Evo﹠Evo)^talk 02:03, 31 May 2015 (UTC)

@Evolution and evolvability: Huge improvement! This cleanup was long over due and you have done an excellent job. Thanks for taking the initiative. Boghog (talk) 19:38, 31 May 2015 (UTC)

Agreed, nice job!

BTW, I tweaked the article tag {{WikiProject MCB}} to use the full quality scale (so new drafts of interest can be tagged by the AfC people and will show up in our project categories) but excluded files and project pages. Feel free to change if you think there's any use in tagging all the (active?) projectspace talk pages with the project class, but I thought that seemed unnecessary. Opabinia regalis (talk) 23:06, 31 May 2015 (UTC)

Let me know if I'm being too trigger happy with {{MCB historical}}. T.Shafee(Evo﹠Evo)^talk 13:05, 3 June 2015 (UTC)

Alerts and stats section

I've finished updating the Alerts and Statistics section (WP:MCB/S) to contain the relevant automatically-updated information. T.Shafee(Evo﹠Evo)^talk 08:52, 14 June 2015 (UTC)

Non-protease catalytic triads

Hi, I'm hoping to nominate Catalytic triad to be reviewed for GA status soon. It's currently quite protease-heavy. If anyone has knowledge of examples from non-protease catalytic triads, it could help make sure the article is more thorough. Thanks in advance for any help! T.Shafee(Evo﹠Evo)^talk 12:24, 24 June 2015 (UTC)

Images are excellent as always! Posting here to remind myself to take a look this weekend :) Been doing too much meta nonsense lately. Opabinia regalis (talk) 08:01, 26 June 2015 (UTC)

Signpost interview

For those interested, there was an interview in the Signpost about this wikiproject recently. T.Shafee(Evo﹠Evo)^talk 11:32, 29 June 2015 (UTC)