Wikipedia talk:WikiProject Molecular Biology/Molecular and Cell Biology/Archive 4

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Amyloid beta, amyloid-beta, beta amyloid or beta-amyloid?

Wikipedia articles refer to an important peptide associated with Alzheimer's disease in a few different ways: amyloid beta, amyloid-beta, beta amyloid or beta-amyloid. The literature seems to use the two interchangeably between publications (though consistently within the same publication). Biological databases also refer to the molecule differently. Which version of the peptide name is best?

I'm inclined to say "beta-amyloid". This formulation matches protein names used in literature, e.g. alpha- and beta-adrenergic receptors, beta-arrestin, beta-secretase, beta-thromboglobulin, etc. The (Greek letter)-(protein name) pattern is also used consistently for protein names modified by alpha, beta or gamma in Lehninger Principles of Biochemistry, 4th ed..

I ask this here because I think having a consistent, systematic way to refer to this peptide and other such proteins would reduce potential confusion, help readers when searching within an article for an explicit string, and make automatic analysis easier. Emw (talk) 02:10, 16 October 2012 (UTC)

I also agree that "beta-amyloid" makes the most sense, and all the terms have just about the same amount of results on Google. I find it interesting that the beta amyloid article consistently uses the term "amyloid beta". • Jesse V.^(talk) 02:40, 16 October 2012 (UTC)

Agreed. Things like consitent naming are important.
—Sowlos (talk) 09:13, 16 October 2012 (UTC)

Unsure. We have amyloid alpha, amyloid beta, amyloid kappa, amyloid lambda, amyloid tau, etc.; some even write directly: amyloid β-protein, etc. [1]. Common abbreviations: Aβ (not βA) for amyloid beta, Aλ for amyloid lambda. I believe the issue merits more discussion and literature research - using e.g. PubMed rather than the imprecise Google search. kashmiri 08:09, 18 October 2012 (UTC)

Abbreviating this as Aβ seems to be the most common, if the ratio of 19,080 to 3,680 articles in Neuron is any guide. The results were more even when spelled out. It found 26,461 articles for: ALL("beta amyloid") vice finding 24,010 articles for: ALL("amyloid beta"). The spelled-out results include the variations with the unspelled letter and with the hyphen. (Neuron's search engine ignores "beta" vs "β" distinction, and also ignores the hyphen vs space.) LeadSongDog come howl! 14:42, 18 October 2012 (UTC)

We should have an article on necroptosis

This recently described type of programmed cell death is mentioned in a couple of our articles, but I think we should have at least a short article about it. Unfortunately I'm not capable of writing one. Looie496 (talk) 15:01, 24 October 2012 (UTC)

 Done I am probably not qualified either, but I was bold and nevertheless went ahead and created a stub. Boghog (talk) 19:58, 24 October 2012 (UTC)

Cool! That's a lot more than I could have done. Looie496 (talk) 22:01, 24 October 2012 (UTC)

I left a note at ...

... Talk:GTP_cyclohydrolase_I#A_note_from_the_article. -- Alan Liefting (talk - contribs) 05:08, 27 October 2012 (UTC)

scope of the medicine project

I see a conflict with the medicine project people, who prevent insertion of data regarding molecular effects on cells, with claims that the data is not from a review article, and if it is from a review, then they claim that the info is out of due weight, despite it being mainstream knowledge, or other excuses which I think are just excuses, where their goal is just to hide the information from the public. I read in the WP:MEDRS different rules than the medicine project people employ, including that their rules apply only to medicine texts, yet they prevent describing molecular effects. Since molecular biology and physics are not necessarily medical claims, I think they should not be allowed to remove text that describe that. Is there a way to limit their scope? Terry Georgew (talk) 13:18, 26 October 2012 (UTC)

If you're going to accuse other editors of participating in a conspiracy to suppress information, it would be helpful to identify a) the articles where these disputes have occurred; b) the specific content and sources that are being excluded; and c) the specific location(s) where you have engaged in calm, reasoned discussion with other editors about your proposed edits.

Since you seem to have created a new account to post your complaint here, it is difficult to follow up on or verify your concerns. I am not able to locate any obvious recent threads at WT:MED (or WP:RSN) where you have attempted to raise this issue before now. TenOfAllTrades(talk) 13:58, 26 October 2012 (UTC)

I think the issue raised by Terry is legitimate as I have also observed similar over zealous suppression of information. The critical question is whether the inserted material concerns medical claims or not. If it does, the WP:MEDRS applies. If not, then the less stringent WP:SCIRS applies. The problem is that some worry that readers might extrapolate from animal studies to possible human effects. As long as preclinical studies are placed in separate sections from human studies and no claims about possible implications to humans is made, in my opinion, there should not be a problem. In extreme cases, it might be necessary to split the article into two (see for example the insulin vs. insulin therapy articles). Boghog (talk) 14:06, 26 October 2012 (UTC)

I also just noticed that the first post in this thread is from an account without any prior history and hence there is a distinct risk of forum shopping. Boghog (talk) 14:17, 26 October 2012 (UTC)

Hello. In reply to Boghog (not the spa!), there are actually much wider concerns with relying on primary research to substantiate medical and other health-related claims. However, I don't think Medicine project regulars would insist on WP:MEDRS for descriptive, historical or social content. Having said that, my own feeling is that providing local guidance on how to identify and weight reliable sources on which to base content claims, per WP:SECONDARY, could be really useful in other fields characterized by lines of ongoing research, such as molecular biology and the social sciences. As I mentioned here, WP:SCIRS currently seems to lean more towards primary sources. Cheers, —MistyMorn (talk) 14:42, 26 October 2012 (UTC)

The big issue I see with relying on primarily sources is they often introduce undue wight. There is a huge amount of evidence on insulin with lot of good secondary sources. One does not need to use primary sources.

In my experience primary sources are often used for self promotion (ie it is the editor who wrote the primary paper). And that paper would not be used by an editor / Wikipedian who did not write it themselves. We see the same primary paper added all over the place often with the addition of no new content. Doc James (talk · contribs · email) (if I write on your page reply on mine) 15:23, 26 October 2012 (UTC)

(edit conflict) At the risk of stating the obvious, I'd add that primary studies generally require some degree of confirmation, and that high-quality reviews are better sources to capture the overall picture in its context (cf WP:SECONDARY: Wikipedia articles usually rely on material from reliable secondary sources.). —MistyMorn (talk) 15:34, 26 October 2012 (UTC)

As an aside, I think it's also worth bearing in mind that MEDRS – either its content or its application – isn't under the control of WP:MED. (Though obviously there will be overlap between editors with an interest in WP:MEDRS and WP:MED...and WikiProject Pharmacology, and WikiProject Molecular and Cellular Biology, and probably a whole bunch of others.) There isn't a shadowy WikiProject Medicine Cabal that meets to decide where WP:MEDRS applies; if discussion between editors on an article's talk page can't reach a consensus on how to apply MEDRS (or WP:SCIRS, for that matter) to a particular situation, those disputes are escalated to Wikipedia:Reliable sources/Noticeboard (WP:RSN) just like any other sourcing dispute.

Ultimately, every edit on Wikipedia is made by an individual person, not by a WikiProject or other group. There will naturally be cases where editors can have a good-faith disagreement about how and where to apply (or to modify!) Wikipedia's policies and guidelines, and there will be cases where both new and even experienced editors make honest mistakes about how best to build articles. TenOfAllTrades(talk) 15:26, 26 October 2012 (UTC)

It has been awhile since we have had a vigorous discussion on this talk page so thanks to everyone for weighing in with your observations :-) . In my view which I think is similar to SCIRS is that secondary sources are preferred, but high quality primary sources should be permitted for recent preclinical scientific findings for which there has not been sufficient time for review articles to have been published. Furthermore secondary sources are not automatically better than primary sources. There are many superficial review articles published in obscure journals that are not worth the paper that they are printed on. In these cases, a high quality primary source (i.e., a peer reviewed article in a high impact journal) trumps a low quality secondary source. I am also well aware of the problem of self citation which represents a conflict of interest and should be strongly discouraged. The proper course of action in these case is for the editor to make a suggestion on the talk page to be evaluated by other editors. Boghog (talk) 19:43, 26 October 2012 (UTC)

I certainly agree that a low-quality review article is not preferable to the content of a high-quality primary source. As someone tempted to join MCB (the Necroptosis addition triggered memories of copyediting articles on apoptosis in the early 1980s), can I say that I do feel that SCIRS can afford to have a more nuanced approach to primary sources, especially when no high-quality secondary source is currently available. Regards, —MistyMorn (talk) 20:27, 26 October 2012 (UTC)

If we are dealing with a major topic and a secondary source does not cover it we need to seriously consider if the content in question is of due weight. For minor topics yes. In medicine a single RCT does not typically change practice. For example we had a trial show that a 64 slice CT might be sufficient to rule out a subarachnoid if done within 8 hours. The guidelines do not reflect this yet / it is not yet standard of care. We are a cautious profession for good reason. Think CCSVI. If something new is supported it is not long before secondary sources appear. Doc James (talk · contribs · email) (if I write on your page reply on mine) 02:45, 27 October 2012 (UTC)

CCSVI clearly falls within the scope of WP:MED and I think everyone here would agree that secondary sources are required for such an article. This thread concerns topics that fall outside the scope of WP:MED. Boghog (talk) 08:15, 27 October 2012 (UTC)

What if there would be an animal study of CCSVI, where the blood flow would artificially be affected and the effects of it would be described to be similar to MS? I think it should be concidered to be in the scope of biology. By the way, the CCSVI article include a section that comes with a warning that it include primary sources. According to the WP:*RS a content can't be out of due weight if the content mention its own weight. Granted, with a good review there aren't any concerns regarding due weight. However, with primary sources the only concern should be that the content would mention its own weight, even according to medrs. Terry Georgew (talk) 11:46, 27 October 2012 (UTC)

Erm, I believe animal studies are considered within the scope of biology (though, per WP:MEDRS, findings from animal studies can't be used as a basis for clinical claims). —MistyMorn (talk) 11:53, 27 October 2012 (UTC)

To be honest, I think it's a mug's game to try to draw an artificially sharp distinction between different branches of biomedical (see what I did there?) research. TenOfAllTrades(talk) 17:22, 27 October 2012 (UTC)

Thanks for the advice, however, I do not think it would work. Take this discussion for example, it was already reported at the WP:MED talk page. Noticeboard cases and edit disputes are reported there in the same way, and then the medicine project people dictate the consensus at the noticeboard.Terry Georgew (talk) 15:47, 27 October 2012 (UTC)

It's not really helpful (or accurate) for you to treat "the medicine project people" as some sort of faceless, monolithic voting bloc. I have seen, and participated in, many vigorous discussions and disagreements with and among members of that project about how best to apply Wikipedia's policies on sourcing and due weight. Nor is it useful to try to insert some sort of us-versus-them wedge between WP:MED and WP:MCB; the reason why someone posted a notice on WT:MED about this discussion is because there are so many editors at WP:MED with an equal interest in molecular and cellular biology—many of whom already watch this space for topics of interest.

Among WP:MED's active contributors, I see a great deal of respect for the notion that WP:MEDRS (and Wikipedia's 'rules' in general) are and should remain flexible—policies and guidelines exist to serve the encyclopedia, and not the other way around. If you dig through the archives of WT:MEDRS, you'll find past discussions about whether or not it should be 'upgraded' from a guideline to a policy. One of the main concerns (supported, I might add, by a number of WP:MED members) was that slapping a {policy} tag on MEDRS would discourage further refinement of the guideline, and would encourage less-experienced editors to treat MEDRS' suggestions and rules of thumb as etched-in-stone commandments. The section of MEDRS offering guidance on use of sources isn't titled Rules, it's titled Basic advice; I don't think that's an accident.

Generally speaking, there's no possible way to formulate a policy or guideline that will precisely and unambiguously handle 100% of all sourcing questions; even if we did have such a magical policy, there's no way to guarantee that every editor would fully understand it and apply it correctly. We write documents like WP:MEDRS, WP:SCIRS, and WP:RS to provide a shorthand and a shortcut to handle most situations: a way to avoid having to go back and reinvent the "What do we mean by 'reliable source'?" wheel every time we edit an article. We accept that no guideline is 'complete' and that sometimes we'll hit gaps and soft spots in the written rules. We know that hard cases make bad law, and that spending a long time trying to hash out firm guidelines to handle a tiny minority of pathological cases is an exercise in futility, so we have specific outlets – WP:RSN – to address those instances that need extra care, attention, or review.

So I guess, after that long-winded message, I have a question (well, several related questions). There have been a couple of comments here about overzealous application of MEDRS, but all I'm seeing in this thread are general remarks. If we really want to know what the problem is that we're dealing with, I think some specific examples would help. Is the problem with MEDRS itself, or is it with inexperienced or overenthusiastic editors overreaching in its application, or is it systematic abuse by experienced editors (as Terry Georgew asserts), or what? Where are the trouble articles? What steps have editors taken to try to rectify the problems that they've seen? Is it the occasional one-versus-one revert war carried out through snippy edit summaries? Have editors made their cases on article talk pages? Have unresolved questions about sourcing been escalated to WP:RSN and discussed, or is there no followup? Are there individual editors misapplying MEDRS whose conduct should be addressed?

Before we let this discussion get framed as some sort of duelling guidelines battle royale, I think we should try to understand what problem we're trying to fix. TenOfAllTrades(talk) 20:43, 27 October 2012 (UTC)

While I have seen a few cases of over zealous application of MEDRS to articles that are outside the scope of WP:MED, I wanted to make clear that these cases have been isolated and for the most part from inexperienced editors or in a few cases from trolls. There has certainly not any systematic attempt by WP:MED members to impose MEDRS on topics that are outside the scope of MED. There are of course grey areas where MED and MCB overlap. For example, there is often a "clinical significance" section in Gene Wiki articles that may contain information on mutations of a gene that is associated with a disease or the possible application of the transcribed product of the gene as a drug target. However since these discoveries are often far from clinical application, these sections fall more within the scope of MCB than MED. In the middle of the spectrum might be an approved drug with which whose clinical trials have been reviewed by reliable secondary sources and thus conforms to MEDRS. In many cases, it may be impractical or unethical to preform certain mechanistic studies in humans, hence including animal studies may provide valuable insights into how a drug works. Animal studies that are consistent with the human results for the approved indications and in addition, shed additional light on the mechanism are fair to include. This is a grey area where it could be argued that either MEDRS or SCIRS applies. At the other end of the spectrum is an article like CCSVI. Actually there have been at least two animals studies (PMID 21385345 and PMID 22457780, both primary sources) that have come to opposite conclusions concerning possible links between CCSVI and MS. However since human patients have already treated based on this controversial theory, I think it is reasonable that MEDRS apply to the entire article, including sections dealing with animal studies. Boghog (talk) 09:43, 28 October 2012 (UTC)

Why is WP:SCIRS still an essay and not a guideline? (If there's a better forum to post this question, please boldly move it there.) --Anthonyhcole (talk) 08:38, 27 October 2012 (UTC)

A good question that should be posted to the essay's talk page. As can be seen on the talk page, there were several attempts made to promote this essay to a guideline, but apparently there was insufficient consensus to do so. Boghog (talk) 10:14, 27 October 2012 (UTC)

I've just read the talk page and the edit history. It was being developed 2 years ago, at the height of the Climate Change Wars. Two of the editors involved have been banned, one permanently, one for a year, one ridiculously pro-science and the other far too pro-woo in my opinion. The main sticking point was how to define appropriate use of popular press, monographs, patents, primary, secondary and tertiary scholarly sources, etc. but it certainly didn't seem insuperable. The protagonists were all acting in good faith, but the charged atmosphere due tho the CC issues had them suspicious of each other and defensive, talking past each other. --Anthonyhcole (talk) 17:28, 27 October 2012 (UTC)

Emerich Szörényi

Hello,

User:Alensha kindly translated some information about the biochemist Emerich Szörényi (see e.g. Arginine kinase) from the article here. The translation is on my talk page. I will try to add part of the information to the article about his son, the philologist Omry Ronen, but I think there is actually enough information for a stub about Emerich Szörényi (which I do not want to write due to my incompetence, but I would be glad to help if an expert would like to invest some time in this).

Best regards, Sasha (talk) 15:01, 8 November 2012 (UTC)

Missing images

Hepatitis B virus PRE alpha and Hepatitis B virus PRE beta have redlinked images. Cheers. -- Alan Liefting (talk - contribs) 04:44, 11 November 2012 (UTC)

fyi, Dutch hypothesis

Just a heads up about this new page, also briefly discussed here. —MistyMorn (talk) 11:22, 19 November 2012 (UTC)

File:Tert picture.jpg

found this File:Tert picture.jpg , if you need it, please fill in the fair use rationales. -- 70.24.250.26 (talk) 07:46, 21 November 2012 (UTC)

Modulating stress responses by the UPRosome: A matter of life and death

Comment welcome at this AfD on a new article. It shares a title with this 2011 Trends Biochem Sci. paper and may be copied from it - does anyone have access to the text of the paper? JohnCD (talk) 10:42, 22 November 2012 (UTC)

Someone found it here and the article was indeed too closely taken from it. JohnCD (talk) 13:52, 22 November 2012 (UTC)

Gene and protein article titles

Why are so many protein and gene article titles in the abbreviated rather than full form? This seems to go against WP:TITLEFORMAT: "Abbreviations and acronyms are generally avoided unless the subject is almost exclusively known by its abbreviation". For example, Triadin is titled TRDN, and I had to get a redirect made at WP:AfC/R so that a search for the full name would result in the reader being brought to the correct article. Would it not make more sense for these articles to be titled in the full form, and make the abbreviated form a redirect? On a separate issue, in many cases, the full name is not a redirect to the proper article, a quick poll of Category:Chromosome 15 gene stubs, which the above article is in, reveals that this is the case for almost all of them. 137.43.188.209 (talk) 17:06, 3 December 2012 (UTC)

That's a good question. I don't know the answer, but I'm mostly involved with WikiProject Medicine. Hopefully someone will give you a good reply. Or maybe you're just the person to fix the problem you perceive, since you noticed and you're working on it at the moment. =) Best. Biosthmors (talk) 17:19, 3 December 2012 (UTC)

Well it's a bit of a pain filing a WP:RM for each of these, seeing as there are probably thousands of these. It would probably not qualify as a non-controversial move either, since there appears to be an informal convention that these articles be titled by the abbreviation. Filing thousands of controversial RMs would overwhelm those working there, and I'm not a fan of bundled noms. What I was hoping for was a consensus as to which form is preferable, possibly leading to a formal naming convention similar to Wikipedia:Naming conventions (astronomical objects). Regards, 137.43.188.209 (talk) 17:31, 3 December 2012 (UTC)

Most of these articles were created by a bot which used the gene name for convience. Some of these articles have been renamed manually by human editor, but as you point out, most have not. Some proteins have unwieldily long names, and in these cases, naming the article after the gene symbol is arguably better. I suppose a bot could go through the ~10,000 Gene Wiki articles are rename each, but this would likely create a huge number of double redirects that would take forever to cleanup. Typing in the protein name in the search box may not lead one directly to the article, but it will likely be among the top search results. This change would require a lot of work with little practical benefit. Realistically there are simply not enough editors with enough energy left to do this. More practical is to leave the titles the way they are and provide appropriate redirects. A bot could do this (similar to this proposal). Boghog (talk) 17:35, 3 December 2012 (UTC)

I don't think huge numbers of double redirects matter, as there are multiple bots that fix them automatically (Wikipedia:Double_redirects#Double_redirects_and_bots). Adrian J. Hunter^{(talk•contribs)} 23:41, 3 December 2012 (UTC)

A naming convention for Gene Wiki articles has been proposed here. Boghog (talk) 17:38, 3 December 2012 (UTC)

If this bot is still active, could we get it to at least create redirects from the official full name on http://www.ncbi.nlm.nih.gov/gene, as these are reasonable search terms. I still think that articles like TRDN, which have a short full name, should be moved. A quick search on google scholar reveals that the long name is used in articles much more often. 137.43.188.209 (talk) 17:47, 3 December 2012 (UTC)

In my understanding and experience in scientific community, at least most of the genes and most of the proteins are addressed by the acronyms. The original verbose title, the acronym was derived from, is memorized only sometimes and merely as inspiration for the gene's actual acronymous three-leter "name". That said, the short one would not be probably the official name. Still, the gene/protein had become to be almost exclusively called by the abbreviation. Then again, this custom might be different in different sub-field of molecular biology or biology in general. I am working in plant_molecular_biology/plant_physiology and the genes are referred almost exclusively by the shortest version possible. --Reo ⁺ 18:28, 3 December 2012 (UTC)

One also should keep in mind that these articles are not only about the protein, but the gene encoding that protein. Furthermore in the field of genetics, it is very common to use the gene symbol in preference to the gene name. The optimal article name I think needs to be determined on a case by case basis. I agree in the case of a short distinctive name like triadin, the article should be named triadin. As a side note, the recommended protein names should be taken from UniProt while the official gene symbols is the responsibility of HUGO. Boghog (talk) 19:54, 3 December 2012 (UTC)

I think the key question is whether the gene/protein is "almost exclusively known by its abbreviation", I agree that that's probably the case for many of them, and that a case-by-case approach is best. 137.43.188.209 (talk) 20:13, 3 December 2012 (UTC)

One should probably do Google Scholar search (or look in Science Citation Index) to establish most common name per WP:COMMON NAME, but this is time consuming... My very best wishes (talk) 02:09, 6 December 2012 (UTC)

Invitation to review course project articles

Back in August, I mentioned here that a JHU professor and I are doing a Wikipedia project having students make improvements to Wikipedia articles. There are now six days left in the semester. Apologies, in that I should have thought of this earlier, but here is a last-minute invitation to anyone who would like, to review and make suggestions on those articles. If you'd like to, then please:

• Do it as soon as possible. The final day of the semester is next Saturday, Dec. 5.
• Please make suggestions on the article's talk pages, and please refrain from editing the articles themselves, at least until next week. This will make our evaluations easier, if we don't have to filter out outside edits.
• Please make concrete, specific suggestions, that it would be reasonable to expect could be acted on in a couple of days.

Here are the lists of articles: Section 81 articles, Section 83 articles.

Klortho (talk) 17:16, 9 December 2012 (UTC)

Help desk question related to project.

What should be done in the case of Wikipedia:Help_desk#Article_with_.CE.91_.28Alpha.29_rather_than_A_.28Latin.29, please help with the name of the article.Naraht (talk) 21:36, 28 December 2012 (UTC)

Currently at Alpha-2-HS-glycoprotein and lowercase. But is lowercase right? Biosthmors (talk) 22:09, 28 December 2012 (UTC)

Xenobiotic metabolism

Hi folks, I just found two mutually redundant pages, Drug metabolism and Xenobiotic metabolism, which have been known to be in need of merging since '09. I am busy writing a new article (Enzyme promiscuity) despite having "retired" from editing wikipedia some years back, so I don't have the time. In light of the cobwebs on the two pages, I reckon the guidelines on merger proposals can be defenestrated and a merger can be performed without delay. Anyone want to detoxify these two pages? Cheers --Squidonius (talk) 22:17, 28 December 2012 (UTC)

I will take a crack at it over the weekend. Boghog (talk) 22:32, 28 December 2012 (UTC)

 Done I have merged Xenobiotic metabolism into Drug metabolism and edited the merged article to minimize redundancy, however more work is needed. Boghog (talk) 13:00, 29 December 2012 (UTC)

Spam?

I'm not feeling up to properly assessing the article on blockmir, but it definitely feels like spam. Can someone more trained in the field have a look to assess whether this term is actually in use by anyone who doesn't have a financial interest in it? Thanks. DS (talk) 18:18, 29 December 2012 (UTC)

A more neutral heading for this section might have been better. I have not seen that term used except by that company. I've not looked at every one of the sources cited, but looking through many sources I don't see evidence of this term by independent, reliable sources. Looks like spam. -- Scray (talk) 19:35, 29 December 2012 (UTC)

Agreed. • Jesse V.^(talk) 19:46, 29 December 2012 (UTC)

This is a proprietary technology and does not appear to be widely used. Furthermore it reads like an advertisement. I would suggest merging the useful parts into Antisense RNA. Boghog (talk) 20:50, 29 December 2012 (UTC) Even better, merge into Antagomir. Boghog (talk) 16:41, 30 December 2012 (UTC)

ABC proteins - merge

I would like to bring to Your attention the following merge proposal:
Talk:ATP-binding_cassette_transporter#Merge_proposal_-_Merge.7CATP-binding_cassette_family
... some rewriting is probably also needed Reo ⁺ 02:54, 30 December 2012 (UTC)

Blockmir

The above article has been nominated for deletion. Your input is welcome. Boghog (talk) 12:40, 1 January 2013 (UTC)

WikiProject Cell Signaling and a Spring 2013 course in signal transduction

Comments at Wikipedia_talk:WikiProject_Cell_Signaling#Wikipedia_Education_Project_in_a_Signal_Transduction_Class:_Advice_requested, FYI. If anyone has a preference that the class occasionally communicate here instead of there, please say so. I figured that through my help, the professors' interest, and the classroom edits, we'd let the semi-active project "reactivate" for Spring 2013 at least. Thanks. Biosthmors (talk) 20:42, 9 January 2013 (UTC)

If the class is looking for feedback from the Wikipedia community, posting here is more likely to generate a response than there. Otherwise I don't think it matters if it is posted here or in the signal tranduction daughter proejct. Cheers. Boghog (talk) 21:01, 9 January 2013 (UTC)

Requested move at Talk:Haplogroup R1b (Y-DNA)

Greetings! I have recently relisted a requested move discussion at Talk:Haplogroup R1b (Y-DNA)#Suggested move, regarding a page relating to this WikiProject. Discussion and opinions are invited. Thanks, Tyrol5 [Talk] 00:48, 14 January 2013 (UTC)

Bioluminescence reference

Hi I'm working on a thesis on Bioluminescence. I saw that there were no sources or references on: http://en.wikipedia.org/wiki/Bioluminescence#Characteristics

Where does the information in this section come from, please?

Thanks /Patrick — Preceding unsigned comment added by 193.242.103.48 (talk) 15:01, 15 January 2013 (UTC)

Biochemistry class at Stanford looking for some support

Hi! A Biochemistry class at Stanford will be editing Wikipedia as a brief classroom assignment this quarter. The professor is working with the Wikipedia Education Program, where Wikipedia Ambassadors work with students online and in-person to help them through their class edits. I'm wondering if anyone who is a member of this WikiProject is interested in becoming a Campus Ambassador and hosting some in-person training sessions with the students in this class. I can probably find somebody in the Bay Area, but I'd love for somebody with an interest in the topic to work with these new users, so we can hopefully work to transition them into regular editors. If anyone is interested, please let me know on my talk page, and I can connect you with the prof. Thanks! JMathewson (WMF) (talk) 21:06, 24 January 2013 (UTC)

Interesting. I'd be happy to help answer any questions posted on my Talk page, but being an ambassador looks pretty serious and I don't really have the time right now for that sort of commitment. I'm also in Utah, which isn't exactly close. Speaking of biochemistry, I've already got Folding@home to FA class, and it's one thing Stanford is famous for. It's quite likely that they know Vijay Pande... :) • Jesse V.^(talk) 21:15, 24 January 2013 (UTC)

Thanks, Jesse! I will definitely give the professor your username to direct his students to ask you any content-specific questions, should they arise. Being an Ambassador isn't so bad :). JMathewson (WMF) (talk) 21:28, 24 January 2013 (UTC)

"DNA computing (2013)"

FYI, there's a note at WT:MED about the title for DNA computing (2013) -- 76.65.128.43 (talk) 09:38, 25 January 2013 (UTC)

Portal:Viruses

Portal: Viruses has been nominated for deletion -- 70.24.246.233 (talk) 06:43, 26 January 2013 (UTC)

Charles Tanford (Cross-posted to WT:MCB and WT:Chemistry)

Looks like this article has been somewhat neglected. I happened to notice it was tagged with a "ref improve" tag, so I turned to the most logical source for citations.. the Protein Science "In Memoriam" article from 2009. Unfortunately, it appears that much of the current page is copied verbatim from the "In Memoriam" article. Tanford's a pretty significant figure in protein chemistry, so it would probably be worth expanding the article beyond just being a carbon copy of the obituary. Does anyone have time to work on such an expansion? Thanks. (+)H₃N-Protein\Chemist-CO₂(-) 18:33, 10 February 2013 (UTC)

Essential molecules for living systems and importance

I just made thiamine diphosphate top importance because I assume it would be, although maybe that's more strictly in terms of biochemistry. Biosthmors (talk) 21:00, 12 February 2013 (UTC)

MCB at wikidata

Please come help sort out the structured side of knowledge in Wikipedia at the new MediaWiki sponsored, WikiData initiative http://www.wikidata.org/wiki/Wikidata:Molecular_Biology_task_force We are currently soliciting proposals for properties to capture about genes and proteins. — Preceding unsigned comment added by Genewiki123 (talk • contribs) 00:09, 20 February 2013 (UTC)

Retinal precursor cells

Hello. Please, could anyone with some knowledge in this area check this new article? It was nominated for speedy deletion as a {{db-hoax}} shortly after creation. --Vejvančický (talk / contribs) 07:36, 28 February 2013 (UTC)

request a reassessment?

I have had trouble finding a place to request a re-assessment of an article (Branched-chain alpha-keto acid dehydrogenase complex). I am more familiar with WP:MED which has WP:MEDA to request an assessment/reassessment, but i see no similar place to do so here, other than Peer Review (which, to my mind is more for GA/FA). I noted a new user has brought this article up from stub to at least start, if not C/B, in the last 12 houts or so, and i wanted to encourage them to continue. -- [UseTheCommandLine ~/talk] #_ 00:43, 4 March 2013 (UTC)

Adding links from sequenced species to Ensembl Genomes?

Hi,

Ensembl Genomes (EG) provides a genome browser for around 110 publicly available genome sequence (excluding vertebrates and bacterial genomes). Where a corresponding article exists, would it be OK to add a link to the genome browser in EG?

Cheers, --Dan Bolser (talk) 15:41, 12 March 2013 (UTC)

Lua protein figure maker

I've been working up a Lua script to take an NCBI protein record and turn it into a figure for Wikipedia. It isn't yet ready for prime time but far along enough that I could ask for reactions.

See Module_talk:ImportProtein for a sample run with Src (gene). Wnt (talk) 23:47, 18 March 2013 (UTC)

Interesting! PDBHandler, a MediaWiki extension that enables interactive 3D models for PDB files, may also be of interest: http://pdbhandler.wmflabs.org. It's intended for deployment for Wikipedia and currently undergoing code review. Emw (talk) 02:57, 19 March 2013 (UTC)

Merge?

Wouldn't merging glutathione S-transferase, C-terminal domain and bacterial glutathione transferase into the parent article glutathione S-transferase be a reasonable approach, given the lengths of the articles? Biosthmors (talk) 05:15, 19 March 2013 (UTC)

I agree that it would be appropriate to merge bacterial glutathione transferase into glutathione S-transferase (same EC number), however I think glutathione S-transferase, C-terminal domain should not be merged. The later article is a about a protein domain that is found not only in glutathione S-transferase, but also functionally unrelated proteins (see this list). Boghog (talk) 22:08, 21 March 2013 (UTC)

Merging HGSNAT gene and its product?

Shouldn't HGSNAT and Heparan-alpha-glucosaminide N-acetyltransferase be merged? kashmiri 22:19, 21 March 2013 (UTC)

There is a only one gene in the human genome (HGSNAT) that encodes an enzyme with this activity (see EC 2.3.1.78), hence I support merging of these two articles. Boghog (talk) 22:27, 21 March 2013 (UTC)

 Done. kashmiri 23:37, 21 March 2013 (UTC)

questions regarding the meanings of something on laminates

On the page regarding "Laminins" it refers to "Laminins are trimeric proteins that contain an α-chain, a β-chain," and " Thus, laminin-511 contains α5, β1, and γ1 chains" What is the chain they're talking about? Is it B-chain or 31 chain? what is that little line in front of the 3? It's confusing! Please help! Thanks!184.1.8.151 (talk) 19:56, 21 March 2013 (UTC)

Each protein has three parts - an α-chain, a β-chain, and a γ-chain (those are the greek letters alpha, beta and gamma). There are several types of each chain too though - five α-chains, four β-chains, and three γ-chains. The proteins are named according to which types are found in the protein - lamanin-511 contains the 5th α-chain and the 1st β-chain and γ-chain. Complicated yes, but according to many scientists this is a "simplified nomenclature" to the previous way of naming them. If you click that link and scroll down, you'll be able to see some diagrams that might help. SmartSE (talk) 20:26, 21 March 2013 (UTC)

Wow, I didn't know anyone with modern education wouldn't recognise at least the first four letters of the Greek alphabet. Note that the IP user is asking about "laminates". SmartSE, I am afraid your explanation might be slightly too advanced... (Sorry couldn't stop myself from commenting). kashmiri 14:40, 22 March 2013 (UTC)

Article needing an image

Can anybody draw a scheme like this [2] for the Permeability section of the Cell membrane article? Thanks Zorahia (talk) 23:10, 22 March 2013 (UTC)

Infobox for metabolic and signalling pathways

Hi all,

I have just been looking at a couple of articles like Glycolysis and TCA cycle. There are a number of databases about these pathways and it would seem to make sense to me to have an infobox for these. Some examples of databases are Wikipathways, Kegg and Reactome. Has this been discussed previously? Any other thoughts about what would go in such a infobox. Thanks Alexbateman (talk) 15:21, 9 April 2013 (UTC)

{{Infobox metabolic pathway
| Symbol = 
| Name = TCA cycle VII (mammalian)
| image = 
| width = 
| caption = 
| MetaCyc = PWY66-398
| KEGG = map00020
}}

Interesting idea. This could get somewhat messy however since for something as simple as the TCA, there are many variants. Anyway, I started to create a mockup for what such an infobox might look like (see {{infobox metabolic pathway}} and the example to the right). Please feel free to experiment further with the mockup. Boghog (talk) 16:59, 9 April 2013 (UTC)

Here is a list of databases: Metabolic Pathways Databases. Boghog (talk) 17:13, 9 April 2013 (UTC)

Peer review article for SR Proteins

Hi all,

I was hoping some volunteers could check out the peer review article on SR proteins that I have been editing. It is an assignment for this graduate-level course and we were asked to try and get feedback from other reviewers. Thanks much. MChapman5 (talk) 23:50, 20 April 2013 (UTC)

Edit war

We have an edit war ongoing at African admixture in Europe - could we get a few experienced editors to look over this edit - see what is going on here,Moxy (talk) 19:49, 26 April 2013 (UTC)

See the complaint at WP:AN3#User:Daufer reported by User:GreekPost (Result: ), which is about this article. EdJohnston (talk) 20:11, 26 April 2013 (UTC)

Leukoplakia#Medications ... cell growth suppressor proteins?

Hi, I'm reworking the above article. A source mentions cell growth suppressor proteins, where could I wikilink this term to please? Am I also ok with my layperson descriptions of carotenes and retinoids, or are they inaccurate? Thank you, Lesion (talk) 17:55, 5 May 2013 (UTC)

Your descriptions of carotene and retinoid are reasonably accurate. I am not certain what is meant by "cell growth suppressor proteins", but tumor suppressor gene (that encode tumor suppressor proteins) may come close. Boghog (talk) 18:27, 5 May 2013 (UTC)

Thanks for verifying those descriptions. I've already wikilinked to p53 and tumor suppressor genes...the context of the source suggests that cell growth suppressor proteins are something that can be eaten/added to the diet. I wasn't sure for this reason if wikilinking to tumor supressor genes is appropriate...but then I ran some google searches and p53 is indeed listed as an example of a "cell growth suppressor protein", so sounds like you are correct, thanks. Lesion (talk) 18:41, 5 May 2013 (UTC)

Europeans share common ancestors who lived 1,000 years ago

Pls see Talk:Genetic history of Europe#Europeans share common ancestors who lived 1,000 years ago -- Moxy (talk) 02:32, 8 May 2013 (UTC)

Hoyle's fallacy

Hello, there are two ongoing discussions at Talk:Hoyle's fallacy which have relevance to this project, one move request and one content suggestion. --Cerebellum (talk) 16:08, 14 May 2013 (UTC)

AfC

Hello there! Got another submission for you people. I suspect these articles all belong to an educational project, given we've had quite an influx of late. The reason why I show you this particular one is that it carries a bit of original research. I think it's as simple as getting in touch with the editor and advising him or her on the appropriate policies and Wikipedia's ways. They're certainly making great contributions. Thanks for the help! FoCuSandLeArN (talk) 19:37, 17 May 2013 (UTC)

Thanks for the heads up. I am also concerned with the amount original research contained in these articles (e.g., using bioinformatics software to make predictions about the properties of these proteins). In addition, as the function of some of these proteins is unknown, several of these articles may have notability concerns. I have made several attempts to contact the instructor through the students, but so far have not succeeded. Boghog (talk) 09:21, 18 May 2013 (UTC)

Wikipedia talk:Articles for creation/Carbomycin

Dear biochemists:

You may wish to take a look at: Wikipedia talk:Articles for creation/Carbomycin

—Anne Delong (talk) 21:02, 19 May 2013 (UTC)

Need a little help

I was editing the page for the Tenascin C protein, and I noticed that Tenascin C is currently listed in the fibrous proteins template, when it is actually a conjugated protein. I'm fairly certain Tnc plays no structural roles like a fibrous protein, but I'll make a lit search to be sure. In the event that it doesn't, I don't know how to remove it from the template. Also, Tnc might be an article to consider making a part of the Molecular and Cellular Biology wikiproject. (I'm not sure what that process is.) Serotonick (talk) 05:44, 20 May 2013 (UTC)

It appears that if anything, tenascin C is an anti-adhesive/antifibrotic protein. Hence I agree that it probably should not be included in the {{Fibrous proteins}} template. The same applies to tenascin X. Unless others disagree, I will go ahead and remove both from the template. Finally I note that tenascin C is already designated as part of the MCB project on the article's talk page. Boghog (talk) 06:17, 20 May 2013 (UTC)

Comments requested Talk:Vitamin_U#Merger

There is a discussion about the vitamin U article, which used to be a redirect to S-methylmethionine. So far 3 reliable secondary sources describe vitamin U as a synonym of this single chemical, or alternatively Methylmethionine sulfonium chloride. I feel the editor created the new stand alone vitamin U page with mostly primary sources, to state that it is not the above, but a term that refers to several chemicals. Primary sources are being used to over-ride mainstream definitions found in secondary sources. The article has already been nominated for merging back to Methylmethionine sulfonium chloride and tagged with notability issues. A previous consensus of 3 vs 1 (mainly using WP:COMMONNAME as an argument) failed to merge the page. I feel that this article has WP:OR, WP:COI, WP:CHERRY issues and needs attention. I have requested that the editor remove the primary sources and provide reliable secondary sources to support the content they have created, and so far this has not happened. Comments requested here please, thanks Lesion (talk) 15:42, 26 May 2013 (UTC)

Another submission coming your way

AfC: Wikipedia talk:Articles for creation/GeneTalk. FoCuSandLeArN (talk) 14:34, 29 May 2013 (UTC)

Wikipedia:Article Incubator/Crocodillin

Wikipedia:Article Incubator/Crocodillin has been nominated for deletion -- 65.94.76.126 (talk) 07:00, 31 May 2013 (UTC)

Dopaquinone article needed

I'm not sure this is the right WikiProject, but what the hell. We need an article about dopaquinone (also known as dopamine-quinone), a precursor of melanin. I could create a two-sentence stub, but I'm helpless with chemistry and wouldn't be able to do an infobox or any of the other standard stuff. Looie496 (talk) 14:28, 5 June 2013 (UTC)

•  Done Boghog (talk) 15:11, 5 June 2013 (UTC)

Thanks, that was quick! Looie496 (talk) 16:28, 5 June 2013 (UTC)

Articles about electrophoresis

Hi there, I was trying recently to clean up mess in my home wiki (czech) in articles about electrophoresis (but don't worry, I made some edits here as well in the process). So I came here for inspiration how to organize such articles, however local ones have similar problems with duplicity and redundancy. I would like to ask if there is any consensus how to organize such articles. My main issue (in both wikipedias) is (in three permutations):

• where should links to different electrophoretic methods in articles lead? Like in: "this stuff is usually studied using electrophoretic method xy" should there be, like "SDS-PAGE" (the most common, but not only one); polyacrylamide gel electrophoresis/ polyacrylamide gel electrophoresis; or link to some general protein methods?
• some type of gels are often used for one type of analysis (agarose for nucleic acid or polyacrylamide for proteins), but there are some exceptions (SDS-PAGE for sequenation of DNA, or worse, polyacrylamide gel for humic acids), is it correct to link to article about the most common term, or it is better to link to the general one?
• what about types of gels and their polymers? should article that mentions some usage of agarose gel lead to agar(like now?)/agarose/agarose gel/agarose gel electrophoresis?

Thanks, --Faskal (talk) 16:55, 4 June 2013 (UTC)

Currently there is a hierarchy of articles (and sections of articles) from the most general to the most specific: electrophoresis → gel electrophoresis → Gel_electrophoresis#Agarose + Gel_electrophoresis#Polyacrylamide + Gel_electrophoresis#Starch. There is also a separate article about SDS-PAGE. Links to these articles (or sections of articles) should be made on the basis of context. Is the discussion containing the link general or specific? Other than SDS-PAGE, there does not appear to be specific articles for specific applications of these gels. If the context is specifically about DNA sequencing, a link to SDS-PAGE may be appropriate, otherwise a link to one of the other articles is more appropriate. Finally sections of the gel electrophoresis article already mention the three most common type of polymers used for electrophoresis. Boghog (talk) 17:31, 4 June 2013 (UTC)

Thank you. This question is specific for this category of electrophoresis, in other cases I don't usually have problem to distinguish general and specific; and it seems that I am not the only one. I've checked gel electrophoresis article and there are more that sixty direct links to some form of "agarose gel electrophoresis" (and much more, that leads to "gel electrophoresis" but are specifically about "agarose gel electrophoresis"), but there are only few sentences about "agarose gel electrophoresis" itself and informations about this topic are dispersed through other articles. I think there should be standalone article about "agarose gel electrophoresis", and most of the links should go there. It seems however that original article was not specific enough and it was merged with gel electrophoresis. To a lesser degree it applies for other articles about this topic as well. I think that articles about molecular biology are really great on en.wiki, but electrophoretic ones need some improvement. --Faskal (talk) 18:40, 4 June 2013 (UTC)

Agarose gel electrophoresis is a redirect that links to Gel_electrophoresis#Agarose. As a fairly short section, it is appropriate that "agarose gel electrophoresis" is currently part of the "gel electrophoresis" article. If and when this section grows, it would be appropriate to split this section out of the parent article and create a new article. You mention that information about this topic is dispersed through other articles. My suggestion is that you merge this information into the Gel_electrophoresis#Agarose section. If there is sufficient material after the merger, then again, it would be appropriate to split out this material as a new article leaving behind a {{main}} template in the parent article. Boghog (talk) 18:57, 4 June 2013 (UTC)

Well, I would say that Gel_electrophoresis is actually an article about Agarose electrophoresis with some bonus. Agarose electrophoresis used to be separate article (see history), but it was merged, but quite poorly, with more general article and that's the reason why it is linked in such unfortunate way. If you compare new article with the old one, you can see, that only beginning, "separation" and "type of the gel" is relevant for gel electrophoresis itself. "Gel condition" refers only to SDS-PAGE (it lacks details about denaturing RNA electrophoresis), "buffers" is clearly only about agarose, "visualization" and "analysis" as well. That's enough information to make a new article specifically about agarose gel electrophoresis (or to resurrect the old one), that could be properly expanded in future. I suggest that "gel electrophoresis" should contain only general informations that are common for all types of gel electrophoresis and disambiguation of terms; now it is misleading, as it is only describing specific conditions for each type of gel without proper specification what is being described. Frankly, I don't want to do it myself (alone), as it is work for a group of people and not for one guy with poor grammar.--Faskal (talk) 21:36, 4 June 2013 (UTC)

I was the one who merged the articles a year and a half ago. Most of the information in the current article is relevant to both agarose and polyacrylamide gels, including the "Gel conditions", "Buffers", and "Visualization" sections. I agree with Boghog's suggestion; it would be fine to create a new Agarose gel electrophoresis article if there is enough information that pertains to agarose gels specifically and not to all types of gel electrophoresis, but the truth is that the way they work and the methods to handle and process them are mostly the same.

I'd also like to point out that we do have daughter articles Gel electrophoresis of nucleic acids and Gel electrophoresis of proteins, since the methodology and analysis tends to differ between analytes more than between types of gel. Antony–22 (^talk⁄_contribs) 02:56, 5 June 2013 (UTC)

I would like to thank both of you for response. I would argue that sections "Gel conditions", "Buffers", and "Visualization" are relevant for both articles. Well, definitely, they should be there, but current content is: gel condition: variations of SDS-PAGE, but not a word about agarose gel electrophoresis or other types of gels; buffer: only discussion about TAE/TBE; visualization is currently only about EtBr. This is my main problem - it is clearly conglomerate of two articles and it is not clear which section corresponds to general topic and which to special features of subtypes. Reader without knowledge about this topic will be probably unable to recognize what is common for gel electrophoresis and what is some specificity.

My original question was if it is better to expand the general article and link it from most articles that mention some kind of electrophoresis or to truncate general article, keep only really general stuff and put specific information to specific articles (lets say into agarose gel electrophoresis and/or gel electrophoresis of NA/proteins). Gel electrophoresis of nucleic acids could serve as general article for different topics about analysis of nucleic acids and genetic engineering (sequencing, isolation from gel,...) Gel electrophoresis can be more physical. As you can see, I respect your decision about merging and I don't plan any guerilla edits and revert wars, I just think there is really big opportunity to improve en.wiki. I think that Sheehan's Physical biochemistry has quite nice outline:

• Principles of Electrophoresis (this is great candidate for electrophoresis and part of gel electrophoresis article)
  • Physical Basis
  • Historical Development of Electrophoresis
  • Gel Electrophoresis
• Nondenaturing Electrophoresis (this could be part of some kind of polyacrylamide gel electrophoresis, mentioned in gel electrophoresis, in distant future even standalone article)
  • Polyacrylamide Nondenaturing Electrophoresis
  • Protein Mass Determination by Nondenaturing Electrophoresis
  • Activity Staining
  • Zymograms
• Denaturing Electrophoresis (already nicely covered by SDS-PAGE)
  • SDS Polyacrylamide Gel Electrophoresis
  • SDS Polyacrylamide Gel Electrophoresisin Reducing Conditions
  • Chemical Crosslinking of Proteins – Quaternary Structure
  • Urea Electrophoresis
• Electrophoresis in DNA Sequencing (well, this is actually not about electrophoresis)
  • Sanger Dideoxynucleotide Sequencing of DNA
  • Sequencing of DNA
  • Footprinting of DNA
  • Single Strand Conformation Polymorphism Analysis
• Isoelectric Focusing (IEF) (already done to some degree in Isoelectric focusing)
  • Ampholyte Structure
  • Isoelectric Focusing
  • Titration Curve Analysis
  • Chromatofocusing
• Immunoelectrophoresis (I know next to nothing about this topic)
  • Dot Blotting and Immunodiffusion Tests with Antibodies
  • Zone Electrophoresis/Immunodiffusion Immunoelectrophoresis
  • Rocket Immunoelectrophoresis
  • Counter Immunoelectrophoresis
  • Crossed Immunoelectrophoresis (CIE)
• Agarose Gel Electrophoresis of Nucleic Acids (this should be definitely standalone article, as it is the most relevant article for general public)
  • Formation of an Agarose Gel
  • Equipment for Agarose Gel Electrophoresis
  • Agarose Gel Electrophoresis of DNA and RNA
  • Detection of DNA and RNA in Gels
• Pulsed Field Gel Electrophoresis (this could be in agarose gel electrophoresis)
  • Physical Basis of Pulsed Field Gel Electrophoresis
  • Equipment Used for Pulsed Field Gel Electrophoresis
  • Applications of Pulsed Field Gel Electrophoresis
• Capillary Electrophoresis (and more, articles in wikipedia are quite OK, I quess)
• Electroblotting Procedures (western blotting has nice article already)

Sorry for long post, but I thing that current state of articles about electrophoresis is not clear enough for high-school-class-level-reader and above is my suggestion how to improve them. I would be glad to help.--Faskal (talk) 08:02, 5 June 2013 (UTC)

No worries, I'm glad to see someone thinking deeply about how to improve this article. I agree that it's not very coherent at the moment and is clearly an amalgamation of people's mostly-unreferenced brain dumps over the years. The tricky part is that it's possible to choose any combination of gel material (agarose/polyacrylamide), conditions (native/denaturing), analyte (protein/nucleic acid), and visualization method, so these all need to be discussed in their own sections. (For example, SDS-PAGE is a protein-specific denaturing method, but it's possible to do denaturing gels for nucleic acids in both polyacrylamide and agarose gels. It's also possible to run native nucleic acid gels with both these gel types.) The text currently doesn't do a good job of explaining all the aspects of each of these and which combinations are more common.

I too prefer that this article focus on the physical basis, with the applications summarized here and discussed in detail in subarticles such as Gel electrophoresis of nucleic acids. Another good source is Bloomfield et al. (ISBN 0935702490). I think the best way to proceed would be to expand this article, and then worry about splitting off new articles later if this article ends up being too long. Antony–22 (^talk⁄_contribs) 19:49, 6 June 2013 (UTC)

So I messed a little bit with the overall layout of the gel electrophoresis article and now every previously ambiguous paragraph should be categorised into protein/nucleic acid and my main objection vanished. The cost was increased redundancy in electrophoresis articles, but at least it is more clear. As a plan for the future I would like to suggest to take most of the content of some sections (mainly buffers and visualization) and put them elsewhere, to gel electrophoresis of proteins or gel electrophoresis of nucleic acids, or some specific article (now non-existent agarose gel electrophoresis, for example). Also, I would like to thank all of you for recent extensions and rewritings of gel electrophoresis article, especially to Antony. --Faskal (talk) 17:09, 10 June 2013 (UTC)

Great! Let's continue discussions at Talk:Gel electrophoresis. Antony–22 (^talk⁄_contribs) 01:11, 12 June 2013 (UTC)

Some of the protein structures in wikipedia are inaccurate..

..in that the structure is really of a fragment of the protein bound to another larger protein (usually an antibody). Tau protein is an example. This appears to be particularly a problem for intinsicaly disordered proteins and other hard to crystallize proteins. Are the strucures currently added by bots or humans? If by bots can some protein boxes be locked? --Biophysik (talk) 20:20, 8 June 2013 (UTC)

Thanks for editing the figure caption in that structure. I would characterize the display of the structure in the tau protein article as more misleading than inaccurate. I believe that most of the structures and captions were added by one time bot run and are not routinely maintained so there is no need to lock the protein boxes. Manual changes to the captions and graphics will not be overwritten by a bot. Since there are a very large number of Gene Wiki articles (~10,000), the best solution may be to replace the bot added captions with the PDB structure titles that are more descriptive. We might convince a bot owner to do this. Boghog (talk) 21:03, 8 June 2013 (UTC)

Wikipedia talk:Articles for creation/Skin immunity

Please could someone have a look at Wikipedia talk:Articles for creation/Skin immunity. Not really sure what to make of this one. By my reasoning it needs merging into an existing article, if anything? But not sure if Skin is appropriate. Anybody got any suggestions? Pol430 talk to me 15:19, 10 June 2013 (UTC)

It is not clear to me what to do with this either. I am leaning toward a stand alone article after some cleanup. I will work on editing this submission a bit more. Boghog (talk) 20:05, 10 June 2013 (UTC)

Thank you. I'll leave the submission in reviewing 'mode'. Please feel free to move it to mainspace when you think it's ready. Or you can ping me and I'll move it. Pol430 talk to me 18:57, 12 June 2013 (UTC)

File:C1orf123 Protein Predicted Secondary Structure.png

File:C1orf123 Protein Predicted Secondary Structure.png has been nominated for deletion. -- 65.94.79.6 (talk) 02:29, 30 June 2013 (UTC)

Guidelines needed for our articles on human genetics

Please comment on Wikipedia talk:WikiProject Human Genetic History#Guidelines desperately needed. Thanks. Dougweller (talk) 13:38, 2 July 2013 (UTC)

(RS)-1-benzyl-1,2,3,4-tetrahydroisoquinoline N-methyltransferase

I stumbled on (RS)-1-benzyl-1,2,3,4-tetrahydroisoquinoline N-methyltransferase, and found it lacking in the basic introductory and non-specialist context required by WP:ARTICLE and WP:NOTJOURNAL. I then sampled a dozen articles in its category, and they all seem to have that problem. They are written in a style that gives the impression that they are machine-generated. The article history suggests that's a possibility.

As the article stands right now, I think it violates the WP:NOTJOURNAL policy, and should undergo the WP:PROD process on that basis.

And then I read this on your wikiproject page:

A primary goal of this project is to collect and organize the totality of this information and make it accessible to researchers and laypeople alike by providing an entry point to the wealth of biological data that is currently hidden in obscure databases and journal articles.

It says "providing an entry point"—that makes me wonder if your project members see (RS)-1-benzyl-1,2,3,4-tetrahydroisoquinoline N-methyltransferase as a page that belongs in Wikipedia as a stub, but not an article stub. Wikipedia has lists, it has disambig pages, it has other kinds of pages that don't qualify as articles. Perhaps (RS)-1-benzyl-1,2,3,4-tetrahydroisoquinoline N-methyltransferase is one of these non-article pages, and shouldn't be held to article standards of WP:GNG. Perhaps the most trivial of enzymes is by definition notable, so even if the average lay person's eye would glaze over trying to make sense of the description, an encyclopedic goal is served by having such pages.

If so, to avoid WP:NOTJOURNAL policy challenges to a bunch of pages in your domain of interest, I am wondering if what is really needed is acknowledgement that "entry points" are a legitimate type of page. They could be flagged with a template of some sort, perhaps at the bottom:

or perhaps at the top:

Thanks in advance. 72.244.204.201 (talk) 23:15, 8 July 2013 (UTC)

Thanks the heads up. I have made some basic edits to the article which hopefully makes it clearer.

Six years ago, several thousand similar enzyme stubs were created by a script assisted editor with the full knowledge and support of this project (see this this and this discussion). Each one contains the introductory sentence: "In enzymology, a XXX is an enzyme that catalyzes the chemical reaction" which provide a very basic introduction to the subject. Hence these stubs meet the basic criteria for a Wikipedia article and on that basis avoids WP:NOTJOURNAL. Even if they didn't, per WP:SURMOUNTABLE, an inaccessible lead is not in itself a valid reason for justifying its deletion. Also, just to be clear, these stubs are Wikipedia articles and not another type of entry point. Keeping in mind WP:NORUSH, the intention of these enzyme stubs and the related Gene Wiki articles is that they will be later be expanded upon by human editors. Nevertheless, I was considering running a bot to cleanup these stubs further (e.g, breaking out a separate nomenclature section, removing dated structural studies section that is made redundant by the PBD links in the {{infobox enzyme}} templates, etc.) Boghog (talk) 12:12, 10 July 2013 (UTC)

File:Tertiary structure 2.PNG

File:Tertiary structure 2.PNG has been nominated for deletion -- 76.65.128.222 (talk) 04:51, 10 July 2013 (UTC)

Human genome

I have been involved in a content dispute involving human genome over how to describe what the term represents. Additional eyes would be helpful. Agricolae (talk) 19:13, 18 July 2013 (UTC)

My missing topics pages

I have updated Missing topics about Metabolism - Skysmith (talk) 11:05, 29 August 2013 (UTC)

Phosphoribosylanthranilate isomerase Structure.png

image:Phosphoribosylanthranilate isomerase Structure.png has been nominated for deletion -- 65.92.181.39 (talk) 04:10, 30 September 2013 (UTC)

NCBI traffic data

If you have ideas or suggestions as to which data NCBI should make available about traffic they get from Wikimedia servers, please list them here. Thanks! -- Daniel Mietchen (talk) 21:22, 25 October 2013 (UTC)

Wikipedia talk:Articles for creation/Phosphomimetics

Hello biochemists! This article which has been submitted at Afc may be of interest. Would anyone like to review it? —Anne Delong (talk) 09:22, 27 October 2013 (UTC)

It's in the encyclopedia now. Thanks! —Anne Delong (talk) 13:36, 6 November 2013 (UTC)

And this one too. Thanks, FoCuSandLeArN (talk) 22:30, 30 October 2013 (UTC)

Cytoplasmic streaming

Cytoplasmic streaming recently had an anon completely rewrite it. I merged their version with that which preceded it as best I could, but it's now a mess. Sorry about that. See ya! Josh Parris 11:01, 7 November 2013 (UTC)

FNDC5

Could I have some more eyes over at FNDC5? It's quite a controversial protein, given that it was reported last year to produce a peptide hormone that turns white fat into brown fat and there is some debate around whether this is really true in humans. I rewrote it a few days ago, but it looks as if scientists from either side of the debate are editing it, so more neutral eyes would be very helpful. I'm not sure how to balance the sides at the moment, but considering WP:MEDRS, I would prefer to be overly cautious. Cheers SmartSE (talk) 12:46, 10 November 2013 (UTC)

Two issues with Pluripotent Stem Cell

This new article contains a few instances of close paraphrasing from http://cdn.preterhuman.net/texts/other/crystalinks/stemcells.html Duplication Detector Report. It is not so prevalent as to constitute a copyright violation, but this needs to be addressed. The article should also be checked to ensure there are no further instances of close paraphrasing/copying from other texts listed in the references.

The title capitalisation also needs to be changed. However, Pluripotent stem cell currently exists as a redirect to Cell potency#Pluripotency and needs an admin to move it over the redirect. Not being a specialist in this area, I am unclear as to whether this should exist as a separate article or should be merged into Cell potency#Pluripotency. - Voceditenore (talk) 11:16, 16 November 2013 (UTC)

Help with Talk:Epstein-Barr virus naming controversy

I have been trying to normalize the naming of Epstein–Barr virus related pages on Wikipedia: Talk:Epstein–Barr virus. Any input would be greatly appreciated. Thank you! Walternmoss (talk) 12:59, 17 November 2013 (UTC)

As a scientist, I think your points are well taken, but as a WP editor I am worried by your tone. All of us on WP are "amateur"s (volunteers, actually), so that word seems out of place and off-putting. Your use of "arguing" might be misinterpreted to suggest a battleground mentality, which is to be avoided assiduously. I will go over to that Talk page. -- Scray (talk) 15:42, 17 November 2013 (UTC)

Agreed and thank you for these good points. Walternmoss (talk) 23:13, 18 November 2013 (UTC)

By editing your original post (which I know you did in good faith, given your comments here and on my talk page) you've changed the context of mine, which now seems to be a non sequitur. I'll strike mine, but please read WP:REDACT for other alternatives for a situation like this one. -- Scray (talk) 00:30, 19 November 2013 (UTC)

Thank you again Walternmoss (talk) 01:54, 19 November 2013 (UTC)

Where should KPC-Oxa 48 redirect to?

Seems to be important enough to even be stubbed (mentioned in [3]), but Wikipedia doesn't seem to have anything significantly related, at least as far as the non-expert (me) can tell. --_{Piotr Konieczny aka Prokonsul Piotrus| reply here} 04:58, 21 November 2013 (UTC)

KPC-Oxa 48 appears to be a strain of multi-drug resistant enterobacteriaceae that carries the bla_KPC and bla_OXA-48 carbapenem hydrolyzing β-lactamase genes (see Class D OXA-48 Carbapenemase in Multidrug-Resistant Enterobacteria, Senegal). The most specific target for the redirect is probably Carbapenem resistant enterobacteriaceae. Cheers. Boghog (talk) 05:44, 21 November 2013 (UTC)

Significant change of meaning at Tricyclic antidepressant

[4] An editor has been averaging the K_i values found at http://pdsp.med.unc.edu/pdsp.php

I've asked the editor to explain but his/her answer is out of my depth. Do we have anyone who can review these edits and the calculations the editor did to arrive at these values, anyone with biochemistry expertise who can check for WP:OR, WP:NPOV, etc.? --Anthonyhcole (talk · contribs · email) 11:28, 4 December 2013 (UTC)

Self published source widely used in articles

I've just noticed that a source published by Nova Science Publishers that is not peer reviewed is used in many important articles relevant to this WikiProject (cell, bacteria etc.) From the articles I have checked, the source has been added by Bernstein0275 (talk · contribs) who it would appear is the author of the source. They have added other seemingly good content by other authors to articles as well, but I'm concerned that they are propagating a fringe view that may not be accepted by other academics. There is also the potential that they are using Wikipedia to promote their own work, although I will assume good faith for now. Could someone with more expertise take a look at the content? Unless there is a strong reason not to, I would suggest that we remove the references and any material cited to it. SmartSE (talk) 15:47, 7 December 2013 (UTC)

The ideas presented in the Nova article have been reported extensively in the peer reviewed literature. See these references as a partial list. I referred to the Nova article because it was recently published, includes up-to-date information and is accessible. I will be glad to replace this article by an appropriate substitute from the peer reviewed literature. Bernstein0275 (talk) 17:33, 7 December 2013 (UTC)

Extended content

Thanks for those references. Most of them are written by you though, so there is still a problem that you have added information about your own theory to many important articles without there being clear evidence that it is widely acknowledged by other academics. The paper in Science has been widely cited, but your most recent (?) publication has only been cited by 2 other authors (one of them several times) since 2010, which to me suggests that this it isn't widely accepted and therefore Wikipedia should not make it appear more accepted than it is (WP:WEIGHT). I'm no expert on this, which is why I posted here to get more people to take a look. SmartSE (talk) 17:48, 7 December 2013 (UTC)

Could anybody help review some articles over the weekend?

A few of us have been OA-ing for two sections of a molecular biology class, and they are almost over. We'd like to do some final reviews of the students' articles this weekend, after which the students will have one more week to complete their edits. (The final day is December 12). If anyone here could help out with that, it would be appreciated. Any feedback/advice you can give would be helpful. The criteria we've given the students to use to review each other are listed here. If you feel up to it, it's good to check for plagiarism or too-close paraphrasing.

The list of articles is here. I know it's short notice, but even if you can only do one article, and only cursorily, it would be a big help.

Thanks! Klortho (talk) 04:03, 7 December 2013 (UTC)

I've commented on a few of the pages. Well done on a great way to get undergrads enthused about wikipedia editing as well as putting the high quality essay work to good use rather than just sitting in some dusty draw. I might try to do the same things with any student I end up supervising. T. Shafee (Evo&Evo) (talk) 12:58, 8 December 2013 (UTC)

Protein style standardisation

The link on the portal's main page includes the sentence:

'Please also see our discussion about how to standardize the depiction of proteins.'

It simply links to the proposals section of the wikiproject which isn't really the relevant page. Perhaps it would be better to link directly to here, the diagram guide page?

Additionally, that diagram guide page needs to make some sort of definitive comment on how to represent protein structures which is discussed here (original discussion in this page's archives), here (a vote on which rendering program to use) and here (discussion on digaram guide's talk page) but without firm conclusions. Shall we try to distil a final set up recommendations out of the discussion? I'm happy to help, but I feel that more experienced editors and admins may be better suited. T. Shafee (Evo&Evo) (talk) 00:44, 9 December 2013 (UTC)

Thanks for highlighting the problem. I am afraid that those discussion out died a long time ago. IMHO, PyMOL is probably the best choice for creating graphics of protein structures (or at least it is the one that I use). The program is still being actively maintained and improved. Also an open source version is still available. As far as standards, I think protein graphic structures should use (1) a white back ground, (2) protein cartoon, (3) "chainbow" colored (N-terminus blue, C-terminus red), and (4) ray tracing. Protein backbone and side chains should not normally be displayed unless the protein is small (i.e., a peptide) or there is some reason to highlight certain protein side chains (i.e., catalytic residues, binding site residues, etc.). It would probably be a good idea included a couple of example PyMol scripts and the rendered image each produces. Thoughts? Boghog (talk) 06:10, 9 December 2013 (UTC)

I agree that Pymol is probably the best platform. The only area where I disagree is chainbows. I've never really found them to be helpful in seeing the structure, sometimes I think they even obscure it. That's why I'd favour white simply because it allows you to see the perspective better. Also then some sort of colour scheme could be set for for substrates, cofactors, inhibitors and active site residues and specific features to be highlighted. For example TEV protease (note, I made the page so I'm pretty biassed). A sample gallery and how-to/script would definitely be a good idea. T. Shafee (Evo&Evo) (talk) 08:12, 9 December 2013 (UTC)

#hide repeated chains in crystal
as cartoon
set cartoon_color, white
bg white
set ray_trace_mode, 1
set antialias, 2
ray

I agree that chainbows are not appropriate in all cases. This is particularly true for protein complexes where coloring each subunit a different color is probably clearer (e.g., File:PR DBD 2C7A.png). On the other hand, chainbows are useful in helping the viewer follow the primary sequence (N-terminus → C-terminus) within the tertiary structure (e.g., File:1BMC.png and File:MDR3 3g5u.png). For the style guide, I would also add (1) zoom the size of the structure as much as possible to make best use of the screen (I have seen too many student produced graphics where a tiny protein structure is surround by an enormous empty space) (2) the PyMOL orient command often produces a better view that again make best use of screen real estate, and (3) properly document the structure by at least specifying the PBD accession number, and ideally include the PBD code directly in the file name. Boghog (talk) 19:15, 9 December 2013 (UTC)

Proposal to rename "Epigenetics in psychology" article

A request for comment has been made at the above link. Your input is welcome. Boghog (talk) 19:42, 9 December 2013 (UTC)

Merging several redundant articles

I would like to propose the following article mergers:

• MT-CO1 with Cytochrome c oxidase subunit I
• MT-CO2 with Cytochrome c oxidase subunit II
• MT-CO3 with Cytochrome c oxidase subunit III

Each of these pairs of articles cover the exact same gene/protein, just under a different name. MT-XXX is the abbreviation most commonly used when discussing the gene in humans, but the MT-XXX articles do not seem limited to human contexts, nor should they be, IMO. I would prefer that the articles live at the "Cytochrome c oxidase subunit X" titles as these are more descriptive and more commonly used overall (especially outside of medical lit). Kaldari (talk) 17:24, 26 December 2013 (UTC)

• Concur. Gene/gene product articles can usually be merged. JFW | T@lk 18:12, 26 December 2013 (UTC)
• Agree – the scope of Gene Wiki articles is both the human protein and the gene encoding that protein as well as orthologs in other species. I have been bold and went ahead with the mergers. Boghog (talk) 02:00, 28 December 2013 (UTC)

  Thank you! Kaldari (talk) 07:54, 4 January 2014 (UTC)

Proteases and MEROPS

Since MEROPS is the dominant repository for protease classification and information, is there a way that the enzyme infobox could be updated to include a link to the MEROPS page for each enzyme? I don't have the technical know-how to go about it. Any strong opinions? T. Shafee (Evo&Evo) (talk) 16:39, 30 October 2013 (UTC)

One immediate problem I see is that there is not a clean mapping between genes/proteins, EC and MEROPS numbers. Existing enzyme Wikipedia articles are based on gene/proteins (GeneWiki; {{GNF_Protein_box}}) and EC numbers ({{Infobox enzyme}}). Hence it may not be obvious which article a given MEROPS number would be appropriate for. However I can add this if you like. Is the following format OK (for serine carboxypeptidase A):

• MEROPS: S10.002

Boghog (talk) 17:51, 30 October 2013 (UTC)

Good point Boghog. I see what you mean about the mapping of MEROPS to EC numbers. I'm not really sure ho to tackle that but despite the possible ambiguity it'd probably better to show something rather than nothing. I think it'd therefore probably still be worth having the template that you've shown above. T. Shafee (Evo&Evo) (talk) 12:52, 8 December 2013 (UTC)

I would think it would be good to include MEROPS numbers in the protein infoboxes. I'm not sure about the implementation but I think it should be achievable. EC numbers for proteases are not well structured. This is because EC is based around the substrates of reactions. But peptidases have complex protein substrates so the EC system really falls down. The lack of an EC number shouldn't stop MEROPS data being included. Although it might actually make it rather difficult. I'll talk to Neil Rawlings and ask him to comment. Alexbateman (talk) 09:38, 14 January 2014 (UTC)

Help request for an article

Hi, I'm hoping someone here can assist me in getting an article into wikipedia.

The article is here:https://en.wikipedia.org/wiki/Wikipedia_talk:Articles_for_creation/Identifiers.org

Over the past year or so, this article has been rejected 4 times, and I am becoming increasingly frustrated.

The first rejection was due to providing 'insufficient context'. I addressed this by significantly expanding the section on URI schemes.

The second rejection then stated that 'the subject of this article already exists', referring to it being a URI scheme! I commented that there were already articles on other URI schemes, and hence did not accept this as a valid criticism. (Words to that effect anyway).

The next rejection suggested we 'improve the submission's referencing', which I responded to by adding more references, and resubmitting.

The final rejection (to date), states that 'All of the references provided for this subject have been produced by closely connected authors'.

I could add some more references, for example to articles written by us in book chapters, or to conference proceedings, but again these are authored by us.

Any help would be gratefully received!

Nsjuty (talk) 13:48, 16 January 2014 (UTC)

This is unlikely to be accepted without independent, third party reliable sources. Also the tone of the article is not encylopedic; there is no background or context. A lay reader would not be able to understand it. Graham Colm (talk) 14:21, 16 January 2014 (UTC)