User talk:Evolution and evolvability
Archives
|
Index |
Inspiration
I recently received a "thank you" notice from you for 998115350. This led me to look into you and eventually I stumbled upon and was inspired by your interview with Ainali. Perhaps I should become more involved with WJ. —Uzume (talk) 22:49, 5 January 2021 (UTC)
- @Uzume: You're definitely welcome to! There are a range of ways to get involved either sporadically or ongoing: from formatting & copyediting (many new articles created are by first-time wikimedians, so references often inserted as plaintext; example) through to submitting an article (created from scratch, or submitted from wikipedia; WP:JAN) through to joining the user group as an ongoing associate/board editor (example). Happy to give more info if you're interested. T.Shafee(Evo&Evo)talk 23:53, 5 January 2021 (UTC)
- @Evolution and evolvability: as a long time Wikimedia editor, I am interested. I also have some concerns.
- I have a background in Informatics, Computer and Systems sciences and engineering (applied sciences) so these might play into Wiki.J.Sci. and Wiki.J.Pre. I might start off in WP:JAN as that is not so far from editing Wikipedia content but I can also see myself perhaps becoming an editor and/or making submissions (but obviously not on the same submitted materials as that would be a conflict of interest). Making "review" submissions with heavy Wikipedia content is interesting but I think eventually "original research" submissions would prove more interesting to me. I also like bibliographic information sciences content and have been working on Wikidata and SDC.
- I read somewhere that submitters and editors might have to divulge legal names and I would likely want my legal name credited with published works authored or edited by me anyway, however, I would prefer to not have my legal name associated with this account (providing some anonymity). I would not mind making another "public" account for such but that probably runs awry with sockpuppety unless I publicly link them and that defeats the purpose of making such to begin with. Can submissions be made without an WP:SUL? How would that work? I envision emailing content to a submission email address or similar. Can someone be an editor without an WP:SUL? I imagine there is no issue with using this account for WP:JAN duties (do copy editors get credited?). —Uzume (talk) 00:45, 6 January 2021 (UTC)
- @Uzume: At the moment, we've done almost zero advertising, so probably 50% of submissions come from people with an existing interest from the wikipedia side of things. I suspect that as the journals mature, original research articles will make up an increasing proportion as a fee-free OA publishing option. As well as the mixture of reviews and original research. Really good questions on the universal login question. We've had people send submissions in by email previously, so could easily receive a wikimarkup file (previously ppl have sent in latex and docx files, which we've later had to ask them to convert or convert for them). Conceivably, it's possible that a user could create a valid second account (WP:VALIDALT) and notify a checkuser (WP:ALTACCN) if they were to use that account only for the purpose of submission and editing of the article under their real name and keep it fully separate from any activities associated with their existing main pseudonymous account. T.Shafee(Evo&Evo)talk 05:15, 8 January 2021 (UTC)
Template error
Hi E&e: I see that you've regularly modified the {{Template:Academic peer reviewed}} template. Can you take a look and see if you can fix the error it's now throwing up? It shows on the documentation page too. Thanks! MeegsC (talk) 18:54, 12 January 2021 (UTC)
Editing news 2021 #1
Read this in another language • Subscription list for this newsletter
Reply tool
![Graph of Reply tool and full-page wikitext edit completion rates](http://upload.wikimedia.org/wikipedia/commons/thumb/2/27/Junior_Contributor_Reply_Tool_and_full_page_edit_completion_rate.png/300px-Junior_Contributor_Reply_Tool_and_full_page_edit_completion_rate.png)
The Reply tool is available at most other Wikipedias.
- The Reply tool has been deployed as an opt-out preference to all editors at the Arabic, Czech, and Hungarian Wikipedias.
- It is also available as a Beta Feature at almost all Wikipedias except for the English, Russian, and German-language Wikipedias. If it is not available at your wiki, you can request it by following these simple instructions.
Research notes:
- As of January 2021, more than 3,500 editors have used the Reply tool to post about 70,000 comments.
- There is preliminary data from the Arabic, Czech, and Hungarian Wikipedia on the Reply tool. Junior Contributors who use the Reply tool are more likely to publish the comments that they start writing than those who use full-page wikitext editing.[1]
- The Editing and Parsing teams have significantly reduced the number of edits that affect other parts of the page. About 0.3% of edits did this during the last month.[2] Some of the remaining changes are automatic corrections for Special:LintErrors.
A large A/B test will start soon.[3] This is part of the process to offer the Reply tool to everyone. During this test, half of all editors at 24 Wikipedias (not including the English Wikipedia) will have the Reply tool automatically enabled, and half will not. Editors at those Wikipeedias can still turn it on or off for their own accounts in Special:Preferences.
New discussion tool
![](http://upload.wikimedia.org/wikipedia/commons/thumb/b/b1/New_Discussion_Tool_v1.0.png/380px-New_Discussion_Tool_v1.0.png)
The new tool for starting new discussions (new sections) will join the Discussion tools in Special:Preferences#mw-prefsection-betafeatures at the end of January. You can try the tool for yourself.[4] You can leave feedback in this thread or on the talk page.
Next: Notifications
![](http://upload.wikimedia.org/wikipedia/commons/thumb/3/33/White_square_with_question_mark.png/60px-White_square_with_question_mark.png)
During Talk pages consultation 2019, editors said that it should be easier to know about new activity in conversations they are interested in. The Notifications project is just beginning. What would help you become aware of new comments? What's working with the current system? Which pages at your wiki should the team look at? Please post your advice at mw:Talk:Talk pages project/Notifications.
–Whatamidoing (WMF) (talk) 01:02, 23 January 2021 (UTC)
COVID questions
Hey Thomas, I just started reading Misinformation related to the COVID-19 pandemic by China, where I see for instance this study [5] listed as an example of misinformation spread by the Chinese government, based on these references [6][7][8][9]. First, does the Biosafety and Health article check out, in your view? And second, are the newspaper / industry critiques sufficient to classify this as misinformation? Sorry, I'm a little out of my depth here. -Darouet (talk) 21:12, 2 February 2021 (UTC)
- @Darouet: It's probably worth asking over at WT:WikiProject COVID-19. My initial impression is that it seems facts of the study aren't being particularly questioned, but it's interpretation and subsequent usage in decision-making. In that sense, the usage of those subsequent refs are probably reasonable (several seem to be citing a WHO report on the matter, which TBH would be the better ref). As for the first ref, It'd probably be better to include this one, which has a whole review section on 'Frozen food and cold chain transportation'. However it looks like there's been a lot of overall debate over content over that last week at its talkpage that might also be relevant. Hope that helps! T.Shafee(Evo&Evo)talk 03:43, 5 February 2021 (UTC)
Merchandise Giveaway Nomination – Successful
![A Wikimeida t-shirt!](http://upload.wikimedia.org/wikipedia/commons/thumb/6/69/BlueIEditShirt-plainBackground.jpeg/150px-BlueIEditShirt-plainBackground.jpeg)
Hey Evolution and evolvability,
You have been successfully nominated to receive a free t-shirt from the Wikimedia Foundation through our Merchandise Giveaway program. Congratulations and thank you for your hard work! Please email us at merchandisewikimedia.org and we will send you full details on how to accept your free shirt. Thanks!
On behalf of the Merchandise Giveaway program,
-- Vermont (talk) 00:24, 6 February 2021 (UTC)
Bio-like structures
Hi. I strongly apologise to bother you, but if you do not mind, I would like to ask you a favour. Recently, I have created a 'draft' of an article regarding structures described by the Soviet microbiologist V. O. Kalinenko. If you find some time, could you check it, please? Since you are an experienced Wikipedia user as well as an expert in the fields of biochemistry and evolutionary biology, I am really interested in your opinion. Also, please feel free to make some changes, additions and adjustments, if applicable. Thank you very much. --Pinoczet (talk) 13:30, 8 February 2021 (UTC)
- @Pinoczet: No problem at all! I've replied over on User talk:Mrjulesd, since I found an existing discussion there and it's probably sensible to centralise. T.Shafee(Evo&Evo)talk 02:48, 9 February 2021 (UTC)
- Thank you for the reply, I appreciate it. Some of the Russian papers are available online, see: Biopodobnyye struktury, — Можно ли сделать амебу?, — Нет, амебу сделать нельзя!. In fact, Kalinenko did not "observe" the structures in distilled water, but rather "obtained" them under the influence of electric current. To my knowledge, these statements were not called into question; the problem was what these structures truly are. As for "caudate rockets", after checking some sources, I am pretty sure it was meant to describe a shape resembling a "tailed" comet. I really felt all this information deserves a standalone Wikipedia article (two primary sources and four secondary sources), but now, it seems not to be the case. Therefore, I decided to give up. Anyway, thanks a lot once again. Kind regards, --Pinoczet (talk) 11:35, 9 February 2021 (UTC)
about this image
![](http://upload.wikimedia.org/wikipedia/commons/thumb/7/7d/CYP21Aevolution.png/600px-CYP21Aevolution.png)
Hi, Evolution and evolvability!
You have made so many pictures about genetics and genomics, so I would like to ask you to help improve this image.
I drew this picture using the drawing program of windows system. The motivation came from Fig. 1 of that review,[1] which mentioned that human and mouse inactivated CYP21A1 and CYP21A2 into pseudogenes respectively.
A few months later, I added STK19 and TNXB in the upstream and downstream, which doubled in the same tandem repeat event and then inactivated one copy.
I think there are at least two aspect to improve this picture:
- Color the genes and pseudogenes respectively.
- Add upstream and downstream genes not repeat in the MHC III, to indicate that this event occurred only in these four gene segments (~80kbp).
I have two other concerns:
- TNXA and STK19. Are these two pseudogenes inactivated in one event or twice? So I didn't mark inactived on these two pseudogenes.
- In NCBI rat gene Cyp21a1,[2] Genomic context, I can't find rat CYP21A2P, C4B or TNXB. Is this a gene loss event or a missing annotation?
In sum, I think this is a good example to explain genetic syntenic analysis.--Htmlzycq (talk) 08:15, 9 February 2021 (UTC)
References
- ^ Nebert, DW; Nelson, DR; Adesnik, M; Coon, MJ; Estabrook, RW; Gonzalez, FJ; Guengerich, FP; Gunsalus, IC; Johnson, EF; Kemper, B (January 1989). "The P450 superfamily: updated listing of all genes and recommended nomenclature for the chromosomal loci". DNA (Mary Ann Liebert, Inc.). 8 (1): 1–13. doi:10.1089/dna.1.1989.8.1. PMID 2651058.
- ^ "Cyp21a1 cytochrome P450, family 21, subfamily a, polypeptide 1 [Rattus norvegicus (Norway rat)] - Gene - NCBI". www.ncbi.nlm.nih.gov.
- @Htmlzycq: Thanks for brining this up! It'd be particularly useful for the Synteny article. A few suggestions:
- Colour usually helps these sorts of images. I recommend keeping it simple, so:
- Either, plain green for active genes, grey for inactive ones (emphasises the pseudogenisation aspect)
- Or, 4-colour for each set of genes (perhaps green, green-blue, blue, blue-purple as an aesthetic spectrum, since we're not trying to emphasise the individual genes, just the order); then a light version of that colour for the pseudogenes (also emphasised the duplication aspect)
- I'm ambivalent about including the upstream and downstream gene. In a way it could make the duplication clearer, but it also adds additional. If the flanking genes are included, it's probably work keeping them in line with the colour scheme of the in-between genes to emphasise, and maybe including "a" and "b" in the duplicated
- The vertical arrows should probably go from row 2->3 and row 2->4 (not 3->4) since a) both human and mouse evolved from the common ancestor will the full set of 8, rather than the human evolving from the mouse, and b) it's not clear in what order the pseudogenisation occurred.
- To know whether TNXA and STK19 were inactivated once or twice would probably need some phylogenetics ofa few other related species (to see in which ancestor the inactivation(s) took place), and to look at what the mutations were that inactivated each of them (e.g. if it's a premature stop codon in the same place, then it's more likely to have been a single event)
- As for the rat, it's hard to tell. You're right that it could just be missing annotations (I notice in this table, that there's a lot of variation on whether orthologs of cyp21a have been detected). The best thing would be to download the region's sequence and do some pairwise alignments to check, and maybe doing some more sensitive BLAST searches.
- It might be worth saving it as a .svg file so that it's more easily editable
- Colour usually helps these sorts of images. I recommend keeping it simple, so:
- So that's my thought process for suggestions. Hopefully these are interesting ideas! I'm happy to look at it again if you update it. T.Shafee(Evo&Evo)talk 08:44, 10 February 2021 (UTC)
- @Htmlzycq: Thanks for brining this up! It'd be particularly useful for the Synteny article. A few suggestions:
Thank you for your reply, my mother tongue is not English, so there may be some misunderstanding.
I just uploaded a test version of the gene with color, which adds a line between the ancestral genome and the descendants to reduce misunderstanding. Since I can't edit SVG images, I can't SVG them.
in pig there is only one STK/C4/CYP21/TNX copy flanked by DXO and ATF6B gene.
in cattle there are three C4-like gene and one CYP21-like pseudogene (LOC101904057).
This makes me wonder in which generation of common ancestor this tandem repeats took place, Euarchontoglires?--Htmlzycq (talk) 12:07, 10 February 2021 (UTC)
- After consulting more Euarchontoglires' CYP21 upstream and downstream genes, I pessimistically found that STK/C4/CYP21/TNX tandem repeats in mouse and human genomes may be two independent events, rather than from a common ancestor.
- In Rattus rattus (black rat), Peromyscus leucopus (white-footed mouse) and Oryctolagus cuniculus (rabbit), there is only one STK/C4/CYP21/TNX copy
- In Cricetulus griseus (Chinese hamster) there is one TNX copy downstream
- In some monkey genomes, there are some related pseudogenes, like CYP21A1P in green monkey and CYP21A1 in Rhesus monkey, while white-tufted-ear marmoset have one STK/C4/CYP21/TNX copy
It seems that there are two independent evolutionary events, one occurred in the common ancestor of Old World monkeys, and the other is a very recent mouse ancestor, while it's a coincidence that stk19b and tnxa, rather than stk19a and tnxb, became pseudogenes in both human and mouse.--Htmlzycq (talk) 09:57, 14 February 2021 (UTC)
Hi, Evolution and evolvability!
About the time that this gene duplication (STK/C4/CYP21/TNX) in the mouse genome. There is only one copy was found in the genome of Mus caroli, and two C4 gene (LOC110335909 and LOC115062505) in the genome of Mus pahari, with a gap in genome sequencing assembly between them. If these three genes (CYP21/TNX/STK19) can appear in this gap, can it be explained that this repeated event occurred in the common ancestor of Mus musculus and Mus pahari mice, rather than the common ancestor of all Mus genus including Mus caroli?
But to my dismay, this conjecture does not match the current taxonomy of Mus, Mus musculus and Mus caroli belong to subgenus Mus, Mus pahari belong to subgenus Coelomys. --Htmlzycq (talk) 04:20, 24 February 2021 (UTC)
Speedy deletion nomination of Category:WikiJournal of Psychology, Psychiatry and Behavioral Sciences
![](http://upload.wikimedia.org/wikipedia/en/thumb/1/15/Ambox_warning_pn.svg/48px-Ambox_warning_pn.svg.png)
A tag has been placed on Category:WikiJournal of Psychology, Psychiatry and Behavioral Sciences requesting that it be speedily deleted from Wikipedia. This has been done under section C1 of the criteria for speedy deletion, because the category has been empty for seven days or more and is not a disambiguation category, a category redirect, a featured topics category, under discussion at Categories for discussion, or a project category that by its nature may become empty on occasion.
If you think this page should not be deleted for this reason, you may contest the nomination by visiting the page and clicking the button labelled "Contest this speedy deletion". This will give you the opportunity to explain why you believe the page should not be deleted. However, be aware that once a page is tagged for speedy deletion, it may be deleted without delay. Please do not remove the speedy deletion tag from the page yourself, but do not hesitate to add information in line with Wikipedia's policies and guidelines. Liz Read! Talk! 16:14, 13 February 2021 (UTC)
- @Liz: No worries. It'll start to be filled next month, but I understand if it should only be created once an item is ready to be place in. T.Shafee(Evo&Evo)talk 01:49, 14 February 2021 (UTC)
Catalytic triad citation issues
Hi there! I have seen some citation needed tags in your well-edited Catalytic triad article added by an editor. Some tags may or may not be trivial but I have seen entire paragraphs get tagged. Because (I assume) you are an expert on the topic, it would be appreciated if you took care of this. I'm well aware that you could be busy, so take your time. Cheers! Wretchskull (talk) 21:09, 21 February 2021 (UTC)
- @Wretchskull: Thanks for pinging me - must've missed those on my watchlist. I'll have a go at working through them this week! T.Shafee(Evo&Evo)talk 23:59, 21 February 2021 (UTC)
Listeriabot
Hi, I saw your post on the Magnus talk page. If I understood correctly, do you want to learn easily and quickly about how to use the Wikidata and Listeriabot list? If so, I've been writing a help page for the Catalan wikipedia (well, I'm still working on it). I had the same problem, because the documentation on the wikidata list is horrible. The only problem ... it's in catalan. You can try reading or requesting translations from Mr Google (pretty good in Catalan-English). See ca:Ajuda:Llistes_automàtiques and ask me if anything is difficult to understand. I hope you find it useful. Salut ! --Amadalvarez (talk) 18:24, 23 February 2021 (UTC)
- @Amadalvarez: Gràcies for the message! Your summary is nicely organised (I particularly appreciate the diagram in Article on ubiquem la llista automàtica section. Unfortunately, I also need information on how to activate the listeriabot on a new wiki (e.g. if you place
{{Wikidata list}}
...{{Wikidata list end}}
on wikiversity, nothing happens because the bot isn't active there (example). T.Shafee(Evo&Evo)talk03:03, 24 February 2021 (UTC)- Ahhh. Technical set-up !. Sorry it's not my field. It sounds like the bots need to be authorised by an admin to run in a WP (I do not how). May be you'll have better response from a enwiki admin. I'll try to find someone in cawiki. Good luck !. --Amadalvarez (talk) 05:09, 24 February 2021 (UTC)
Sorry, are you admin in wikiversity ?Amadalvarez (talk) 05:32, 24 February 2021 (UTC)- NEWS: I changed invoke to Listeriabot, because it changed server a few months ago. See: wikiversity:special:diff/2262433, I also did a minor change in your SPARQL because left the WHERE. Now, ListeriaBot runs. However doesn't give results, as the query was wrong. I test it in cawiki and it runs well, but no in my wikiversity sandbox. We're closer to the solution.... Amadalvarez (talk) 06:59, 24 February 2021 (UTC)
- @Amadalvarez: Thanks for looking at this with me. I've also added a formal bot permission application on Wikiversity (link). I don't know whether the bot is not working on wikiversity due to it not yet having bot permissions, or if there is some file in the bot's code itself that needs to be edited. T.Shafee(Evo&Evo)talk 11:23, 24 February 2021 (UTC)
- NEWS: I changed invoke to Listeriabot, because it changed server a few months ago. See: wikiversity:special:diff/2262433, I also did a minor change in your SPARQL because left the WHERE. Now, ListeriaBot runs. However doesn't give results, as the query was wrong. I test it in cawiki and it runs well, but no in my wikiversity sandbox. We're closer to the solution.... Amadalvarez (talk) 06:59, 24 February 2021 (UTC)
Share your feedback on the OCR improvements!
![](http://upload.wikimedia.org/wikipedia/commons/thumb/f/f7/Magic_Wand_Icon_229981_Color_Flipped.svg/48px-Magic_Wand_Icon_229981_Color_Flipped.svg.png)
Hello! We (the team responsible for the Community Wishlist Survey) have launched the project for OCR improvements. With this project, we aim to improve the experience of using OCR tools on Wikisource. Please refer to our project page, which provides a full summary of the project and the main problem areas that we have identified.
We would love if you could answer the questions below. Your feedback is incredibly important to us and it will directly impact the choices we make. Thank you in advance, and we look forward to reading your feedback! SGrabarczuk (WMF) (talk) 03:33, 9 March 2021 (UTC)
Question about the rating of Dicke model
Hi User:Evolution and evolvability,
I was wondering how did you choose to rate the Dicke model page as "B" quality and "low" importance?
Best, Moroses (talk) 11:43, 18 March 2021 (UTC)
- @Moroses: No problem. Ratings are always tricky, but here was my thinking for the estimate:
- B-class is the highest quality rating possible without passing through Wikipedia's own internal review process to get GA or FA status. This article is clearly of the highest quality, so this is the effective cap for all PLOS topic pages even though it can seem misleadingly low.
- Low-importance was much harder to estimate. I checked Wikiproject Physics's guidelines and checked a few related pages. It seems that sub-concepts (e.g. two-state system and superradiant phase transition) are usually mid models (JCM and JCHM) are almost always classed as low. That being said, I'm no physicist so I'm happy to add a request at Wikipedia_talk:WikiProject Physics to ask for rating by a more informed opinion!
- T.Shafee(Evo&Evo)talk 00:07, 19 March 2021 (UTC)
Structured data across Wikimedia is starting!
Hello there, Thomas! I am writing to you because a new WMF project, Structured Data Across Wikimedia (SDAW), is about to start.
SDAW is a grant-funded programme that will explore ways to structure content on wikitext pages in a way that will be machine-recognizable and -relatable, in order to make reading, editing, and searching easier and more accessible across projects and on the Internet.
The reason why I am contacting you is because of your work across the Wikimedia projects, and your opinion would be of great interest for us to kickstart the discussion. We defined a series of questions we would like to have feedback on. If you want to ask a question on your own, or just want to share with us your ideas or opinions, please feel free to do so!
Also, if you know some other user(s) that can be interested, please let me know or invite them to join the discussion. The more, the better!
Hope to hear from you soon! -- Sannita (WMF) (talk) 14:43, 20 March 2021 (UTC)