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THOMAS SHAFEE
Catalytic triad of TEV protease
THOMAS SHAFEE
Evolution and Evolvability




Welcome!

Hi, Evolution and evolvability. Welcome to Wikipedia! Thank you for your contributions. I hope you like the place and decide to stay. Our intro page contains a lot of helpful material for new users—please check it out! If you need help, visit Wikipedia:Questions, ask me on my talk page, or place {{helpme}} on this page, followed by your question, and someone will show up shortly to answer your questions. jonkerz ♠talk 15:59, 19 October 2013 (UTC)

A barnstar for you!

The Original Barnstar
Thanks for your excellent article on the PA clan and many other contributions to Protein and RNA families! Alexbateman (talk) 11:15, 15 January 2014 (UTC)
@Alexbateman: I just realised that I never thanked you for this. I'm glad that the PA clan article and Protein superfamily are useful. Hopefully more of the well-defined superfamilies and folds will get pages over time. T.Shafee(Evo﹠Evo)talk 11:07, 11 June 2015 (UTC)

If you get bored of enzymes, I have a suggestion...

The gene article still contains this aesthetically unpleasant low-res image File:Rna-codons-protein.png that some idiot edited and uploaded ages ago :) Opabinia regalis (talk) 09:53, 6 March 2015 (UTC)

@Opabinia regalis: Ha, thanks for pointing me in its direction. I'll definitely have a stab at it, and maybe a couple of other images in at now that I've had a look. Being part of the Enzyme FAR has made me more comfortable with the idea of editing bigger articles. T.Shafee(Evo﹠Evo)talk 10:31, 6 March 2015 (UTC)
Thanks! That image is annoying because it's my only remaining one that hasn't been moved to commons, and now it's stranded because it's so old the NIH doesn't use it anymore, and the fact that it's still hosted on their server somewhere is good enough evidence for PD here but not on commons.
I don't have it on hand right now but there's evidence somewhere around here that the bigger/broader wikipedia articles are systematically crappier. So I say go for as big an article as you have the patience for :) Opabinia regalis (talk) 20:21, 7 March 2015 (UTC)

Image lifecycle

Hey, I really like your question about image lifecycle. Nobody has looked into image halflife. I would agree with your conclusion: images are there for a very long time regardless of content. I have seen typos on images that have persisted for years and there are a lot of unclear and unrelated images in articles —I have shied away from deleting many. Unfortunately I don't have the space and time to download and parse the wikimedia commons dump right now —next week?. My guess is like your, namely they are pretty immutable; but the distribution may be surprising as quality would influence half-life. Although, I should do that in a dozen years as your images will probably smash all records given their quality! Matteo--Squidonius (talk) 21:59, 9 March 2015 (UTC)

Idea for glycolysis

A summary pathway diagram of glycolysis, showing the multi-step conversion of glucose to pyruvate. Each step in the pathway is catalysed by a unique enzyme.
The image above contains clickable links
The metabolic pathway of glycolysis converts glucose to pyruvate via a series of intermediate metabolites.    Each chemical modification is performed by a different enzyme.    Steps 1 and 3 consume ATP and    steps 7 and 10 produce ATP. Since steps 6–10 occur twice per glucose molecule, this leads to a net production of ATP.


Just a thought - your glycolysis diagram is much superior to the images already in the glycolysis article (File:Glycolysis2.svg and especially File:Glycolysis.jpg), but doesn't show the names of the enzymes associated with each step. If you numbered the arrows, as usually suggested on commons for text labels - and maybe colored the arrows for steps that consume/produce ATP? - your image would be a great substitute for the existing ones in the article, which get the job done but are very busy and cluttered-looking. Opabinia regalis (talk) 04:39, 23 March 2015 (UTC)

@Opabinia regalis: Thanks! I know what you mean, an article as important as glycolysis probably needs a little better than File:Glycolysis.jpg. I was thinking of doing a second version with more information. I like your coloured arrows idea for ATP production/use. May have to do something for NADH and H2O in reactions too. Not sure yet how to get enzyme and metabolite names in without cluttering but it should be ok. What do you reckon? T.Shafee(Evo﹠Evo)talk 11:08, 23 March 2015 (UTC)
Of course I can't think of an example now, but IIRC commons often recommends using numbers instead of text labels so that the image can be reused in non-English projects. I don't know that enzyme names change that much, but numbers would be easier to fit into the image. Highlighting the NADH and H2O in the reactions is a good idea. Thinking out loud, I'm imagining a second image containing the (color-coded?) enzyme names, presented in the article in a frameless table so that it looks like one continuous image. But that probably sounds too complicated; there's a reason I'm not a graphic designer :) Opabinia regalis (talk) 04:49, 24 March 2015 (UTC)
That sounds great. When it's easy, the usual thing to do is to produce a version with English labels and a separate file with numbers. In a well-ordered .svg file, it's often possible for knowledgeable people (i.e., not me) to change the labels to whatever language they want.
If it sounds like fun, there's also an image map system at Commons. When you hover, you get more (text) information. I don't know much about it, but I could probably find someone who did. Just ping me if you want to know more about that. WhatamIdoing (talk) 16:57, 25 March 2015 (UTC)
@WhatamIdoing:I was thinking of using wikilinkable image annotations (something like this). The main thing that I don't like is how when you then open the full-sized image the text isn't there. T.Shafee(Evo﹠Evo)talk 03:04, 26 March 2015 (UTC)
Do you think that commons:Help:Gadget-ImageAnnotator would do what you want? WhatamIdoing (talk) 00:24, 27 March 2015 (UTC)

@Opabinia regalis, WhatamIdoing, and Seppi333: Thank you for all your help so far. Here is my first attempt at using image annotations: Template:Glycolysis summary. I've transcluded it into the Glycolysis article. Any thoughts? T.Shafee(Evo﹠Evo)talk 12:49, 27 March 2015 (UTC)

Wow, this is great, nice work!! The annotation template is a really good idea; I didn't even know it existed. I have one ridiculously picky comment - it might just be my browser, but the 'split' in the bottom arrow (which is a really clever idea) appears in the full view to be solid white, not transparent. Opabinia regalis (talk) 06:30, 28 March 2015 (UTC)
@Opabinia regalis: Hah, good point! I always forget to check waht I've made transparent, and what I've made white! The main down-side of both image annotator and image map is that neither works properly with the mobile phone interface! T.Shafee(Evo﹠Evo)talk 11:04, 28 March 2015 (UTC)
That looks great. Thanks for doing that! WhatamIdoing (talk) 15:28, 28 March 2015 (UTC)
I normally think the mobile interface is embarrassingly terrible, but I just checked this on my phone and the image and annotations display OK to me. The only problem is that the image is too wide for the vertical orientation, but it displays as expected horizontally.
Is there such a thing as a featured template? :) Opabinia regalis (talk) 19:50, 28 March 2015 (UTC)

Your GA nomination of Gene

Hi there, I'm pleased to inform you that I've begun reviewing the article Gene you nominated for GA-status according to the criteria. This process may take up to 7 days. Feel free to contact me with any questions or comments you might have during this period. Message delivered by Legobot, on behalf of Cerebellum -- Cerebellum (talk) 01:40, 10 April 2015 (UTC)

The article Gene you nominated as a good article has been placed on hold . The article is close to meeting the good article criteria, but there are some minor changes or clarifications needing to be addressed. If these are fixed within 7 days, the article will pass; otherwise it may fail. See Talk:Gene for things which need to be addressed. Message delivered by Legobot, on behalf of Cerebellum -- Cerebellum (talk) 17:20, 11 April 2015 (UTC)

The article Gene you nominated as a good article has failed ; see Talk:Gene for reasons why the nomination failed. If or when these points have been taken care of, you may apply for a new nomination of the article. Message delivered by Legobot, on behalf of Cerebellum -- Cerebellum (talk) 03:41, 19 April 2015 (UTC)

@Cerebellum: Thanks for acting as reviewer. You're definitely right that the citations are below par. Will try to address that and resubmit soon. T.Shafee(Evo﹠Evo)talk 04:09, 19 April 2015 (UTC)
@Evolution and evolvability: Great, let me know when you resubmit and I'll be happy to review again. --Cerebellum (talk) 11:29, 20 April 2015 (UTC)

Interview for The Signpost

This is being sent to you as a member of WikiProject Molecular and Cellular Biology The WikiProject Report would like to focus on WikiProject Molecular and Cellular Biology for a Signpost article. This is an excellent opportunity to draw attention to your efforts and attract new members to the project. Would you be willing to participate in an interview? If so, here are the questions for the interview. Just add your response below each question and feel free to skip any questions that you don't feel comfortable answering. Multiple editors will have an opportunity to respond to the interview questions, so be sure to sign your answers. If you know anyone else who would like to participate in the interview, please share this with them. Thanks, Rcsprinter123 (express) @ 16:23, 9 May 2015 (UTC)

Have been meaning to do this for weeks...

The Graphic Designer's Barnstar
Awarded to Evolution and evolvability for contributing many outstanding images to Wikipedia, including this highly informative and unique overview of gene structure. Adrian J. Hunter(talk•contribs) 04:24, 10 June 2015 (UTC)
Seconded! It's really nice to see wiki articles illustrated with professional and modern-looking images, and those annotated templates are great. Opabinia regalis (talk) 21:09, 10 June 2015 (UTC)
@Adrian J. Hunter and Opabinia regalis: Thank you both! I've really enjoyed making some updated images for wikipedia and it's good to know that they're clear to others as well! T.Shafee(Evo﹠Evo)talk 11:07, 11 June 2015 (UTC)

Thank you

Thank you for thanking me for the edits to the "glycolysis" article. Cruithne9 (talk) 05:20, 20 July 2015 (UTC)

Your GA nomination of Gene

The article Gene you nominated as a good article has passed ; see Talk:Gene for comments about the article. Well done! If the article has not already been on the main page as an "In the news" or "Did you know" item, you can nominate it to appear in Did you know. Message delivered by Legobot, on behalf of Cerebellum -- Cerebellum (talk) 17:41, 25 July 2015 (UTC)

Congratulations! :) Opabinia regalis (talk) 18:09, 25 July 2015 (UTC)

Your GA nomination of Catalytic triad

Hi there, I'm pleased to inform you that I've begun reviewing the article Catalytic triad you nominated for GA-status according to the criteria. This process may take up to 7 days. Feel free to contact me with any questions or comments you might have during this period. Message delivered by Legobot, on behalf of Stigmatella aurantiaca -- Stigmatella aurantiaca (talk) 22:40, 10 August 2015 (UTC)

Your GA nomination of Catalytic triad

The article Catalytic triad you nominated as a good article has passed ; see Talk:Catalytic triad for comments about the article. Well done! If the article has not already been on the main page as an "In the news" or "Did you know" item, you can nominate it to appear in Did you know. Message delivered by Legobot, on behalf of Stigmatella aurantiaca -- Stigmatella aurantiaca (talk) 16:01, 19 August 2015 (UTC)

Congratulations again! Really excellent work on this article. You could put some biochemistry on the main page now for DYK.... :) Opabinia regalis (talk) 07:53, 21 August 2015 (UTC)

Catalytic triad

Hi,

Thanks for the great work on the Catalytic triad article. I have asked Neil Rawlings (down the corridor) to comment on the article, but he is a bit busy at the moment. But if you can wait a few weeks I'm sure he'll give you some great feedback. Alexbateman (talk) 11:02, 24 August 2015 (UTC)

@Alexbateman: That's absolutely fine. There's no rush, and I'm always particularly happy to get input from people who don't typically wikipede. T.Shafee(Evo﹠Evo)talk 12:00, 24 August 2015 (UTC)

Half-life of protein backbone

I see that you have given the half-life of a protein backbone as being 500 years in the article Proteolysis, I wonder if you have a source for it. I'm just slightly puzzle because I have seen widely different figures given for peptide bonds, from 7 years here to over a hundred years here. I would assume the high figure of 500 has something to do with the exposure to water (or rather the lack thereof) in the folded interior of a protein, but I'm not sure because parts of most proteins would be exposed to solvent. Hzh (talk) 00:41, 1 September 2015 (UTC)

@Hzh: Thank you for reminding me. I'd meant to go back and pull out the reference for it:
:Radzicka, Anna; Wolfenden, Richard (January 1996). "Rates of Uncatalyzed Peptide Bond Hydrolysis in Neutral Solution and the Transition State Affinities of Proteases". Journal of the American Chemical Society. 118 (26): 6105–6109. doi:10.1021/ja954077c.
It's actually for dipeptides, so the effect of solvent exclusion for a folded protein is ignored. The other references you have could be interesting for comparison. T.Shafee(Evo﹠Evo)talk 00:57, 1 September 2015 (UTC)
Many thanks. I would assume the side-chain group has a strong effect on the rate of hydrolysis, maybe bulky groups side chains are less stable than gly-gly. The book might explain it more but only parts of it can be read. Hzh (talk) 01:09, 1 September 2015 (UTC)

WP:INTREF

There are a bajillion links that go to WP:INTREF, which is now a double-redirect (along with the links to the other pages). I think we should keep Help:Introduction to referencing/1 as-is, then have Help:Introduction to referencing (VE)/1. That OK? Otherwise thank you very much for creating the VE section, it was much needed. FYI you can transclude the verifiability and reliable sources sections in the VE pages, since they will be the same. — MusikAnimal talk 16:47, 13 November 2015 (UTC)

I've bold done both. So we'll keep Help:Introduction to referencing/1, etc, for the wikimarkup, just because that's the long-standing home and there's a lot of cleanup involved to get the redirects right. This is a highly visible page (link in the protection reasons, etc), so double-redirects are no good =P I also refactored the reliable sources to Help:Introduction to referencing/Reliable sources. It is now sourced in the VE pages. Thanks again for making this happen. Cheers — MusikAnimal talk 17:49, 13 November 2015 (UTC)
@MusikAnimal: Thanks for helping out! I'd not appreciated how much or a problem the double-redirects were. Is it possible to just change WP:INTREF to redirect to the ...(WM) version? I guess it's not the biggest deal in the world, but I feel the consistency could be useful. Good idea with transcluding to ensure that the info remains synchronised! I'm a big fan of trying to make sure that pages can be more easily maintained (hence the {{intro to}} template). If you've the time and inclination, it'd be great if you could have a quick look over the new Help:Introduction to referencing (VE) pages. T.Shafee(Evo﹠Evo)talk 09:23, 15 November 2015 (UTC)
Looks great! I guess I did not take the time to check how many redirects we are working with, and turns out there aren't many. Sorry about that, we can go back to ...(WM) naming scheme. I can handle that and the redirects, and will do so shortly.
But the big question remains... which referencing guide do we link to as the default? E.g. {{refimprove}} along with similar templates are atop millions of articles. Changing the "citations" link to the new VE pages will have a profound effect, I think. And honestly, in most cases it's SO much easier with VisualEditor, so I'm in favour of sending our users there, but we should seek broader consensus first. I can open up a discussion at WP:VPP, how does that sound?
Another thing, I have concerns Book:Wikipedia: The Missing Manual might be a little too much information for the users we're targeting on Help pages. How about linking to Help:Wiki markup instead? It's fairly comprehensive and not a long read. — MusikAnimal talk 19:29, 15 November 2015 (UTC)
@MusikAnimal: All very good points. Thanks for handling the behind-the-scenes redirects. For default referencing recommendations, I agree that it's reached a point where a WP:VPP is appropriate, and making sure that the relevant groups that might be interested are directed towards it. I've no experience in these matters, so I'm happy for you to put the proposal up!
My plan for the two base links is one for switching between WM/VE editing methods and two get to the fullest information repository. At the moment, I envisage that the WP:VisualEditor/User guide link will be at the base of all intro_to...(VE) pages. So similarly, I think it'd be good to have a consistent, equivalent link to put at the bottom of all intro_to...(WM) pages (including talk pages, tables, images etc). Now that I look at it, H:MARKUP does actually cover all that so is probably the closest equivalent of the WP:VE/UG. I suspect most readers will take the tutorials as self-contained modules, with the minimum necessary instruction to achieve basic editing proficiency. T.Shafee(Evo﹠Evo)talk 02:05, 16 November 2015 (UTC)
Ah, I realized we can't change all the links to the VE guide just yet. Anonymous users still don't have access to VisualEditor! Such a shame. It's only a matter of time before this happens, and when it does we'll revisit the proposal. For now we'll stick with what we have.
Did you say you were okay with changing the "full manual" link to H:MARKUP? The other issue with the book is that it goes well beyond wikimarkup, also documenting general Wikipedia best practices. I also worry if it is outdated, as much of the Book namespace seems to be. The idea behind Help pages should be to keep it really simple and brief, so I think H:MARKUP is fitting in this case. I have a long term goal of dumbing down all the other help pages, such as Wikipedia:Your first article. Out of all of the help pages I think WP:INTREF is the best example of how we should approach them. Brevity, easy navigation, illustrations, friendly wording, etc. — MusikAnimal talk 02:49, 16 November 2015 (UTC)


{{Intro to}}

Thanks for all the work you've done on this template and the related pages. One puzzle, for me: the template appears to force all paragraphs to be fully justified. That's not at all the norm for Wikipedia help pages. How would you feel about changing the alignment to left justification, which is the norm? -- John Broughton (♫♫) 21:49, 25 November 2015 (UTC)

@John Broughton:You're right that it's not the norm. I've not got particularly strong views.Justified text looks slightly neater to me, but then I can imagine it more easily misformatting on narrow screens. T.Shafee(Evo﹠Evo)talk 22:22, 25 November 2015 (UTC)
My personal philosophy with regard to readers is avoid surprises. Fully justified text is surprising because it's not used elsewhere. (I also personally don't like it - I find the odd spacing of words to be off-putting - but that's just a personal opinion.)
Since you don't have particularly strong views on this, and I do, would you mind if I changed the justification? (If you do mind, then the next step is to get some other opinions, of course.) -- John Broughton (♫♫) 17:44, 26 November 2015 (UTC)
@John Broughton:Changing the template's text alignment is fine by me. It can always be turned back if there's a sudden swell of support for a justified format! T.Shafee(Evo﹠Evo)talk 08:52, 27 November 2015 (UTC)
Thanks. -- John Broughton (♫♫) 19:55, 27 November 2015 (UTC)

Maybe

If you're interested in getting access to review articles for biomedical topics, then you might look at this new opportunity: Wikipedia:Annual Reviews. The usual rules seem to apply: you need to have made 500+ edits, to have been around for six months or more, and not have access to this particular source through work or school. Assuming you don't already have access elsewhere, then you easily meet the requirements. WhatamIdoing (talk) 17:32, 16 December 2015 (UTC)

More FP

So, which of your protein illustrations do you like best? Catalytic triad? I feel like we should nominate a couple at FP to set the standard for what a good, professional-quality protein image looks like, because crappy renders from 2006 sure aren't it. Opabinia regalis (talk) 00:00, 18 December 2015 (UTC)

Hi, I had a quick look through my archive for just a 'standard' ribbon cartoon as an illustrative example and realised that I'm almost always doing something extra. My favourites are probably:

I'm open to suggestion, of course, if you have opinions as to which. As always, I'm very happy to know that my images are useful! I might also do a bit of an update on the MCB diagram guide (although it's not exactly high-traffic). T.Shafee(Evo﹠Evo)talk 11:54, 19 December 2015 (UTC)

Ooh, I like all of these! I think the catalytic triad or the serpin would be my picks in terms of 'simple enough to explain to laypeople but complex enough to look impressive' :) Seems that FPC has lots of self-noms - do you want to do the honors or should I?
More updates on the diagram guide would be great - maybe it will get more traffic if there's more meat on the bones there. Opabinia regalis (talk) 05:35, 21 December 2015 (UTC)
Also, is File:Galactosidase enzyme.png galactosidase (in the filename) or glucosidase (in the caption and PDB description) or does that enzyme do both? Opabinia regalis (talk) 05:41, 21 December 2015 (UTC)
I would love you to nominate them! Somehow I still feel awkward self-nominating, even though there's little functional difference! Well spotted that File:Galactosidase enzyme.png is misnamed. I think I was planning on doing a different enzyme and changed half-way through the upload. I'll rename it on commons! T.Shafee(Evo﹠Evo)talk 05:50, 21 December 2015 (UTC)
I just took a look at the FP criteria and it appears there are Rules about image pixel size which these fall slightly short of. (So does the DNA clamp, but, well, 2006.) Any chance of re-rendering the tried at a larger size? (Apparently 1500px is the preferred minimum.)
Sorry, one other minor point: now that I've looked at the serpin on my phone, it's hard to distinguish the dark gray and light gray/white. That phone is old and crappy and has a cracked screen and is getting replaced soon, so take that for what it's worth :) Opabinia regalis (talk) 20:26, 21 December 2015 (UTC)
I'll fix the resolutions tonight. Should be easy enough. I'll also increase the tone difference between ther serpin and its target protease. You're right that it's actually too subtle when I use an outlined render. The ideal is an image that is as easily interpretable as possible. T.Shafee(Evo﹠Evo)talk 00:54, 22 December 2015 (UTC)

Ok, I've updated all the images to be at least 1500px wide. Also, File:Galactosidase enzyme.png → File:Glucosidase enzyme.png renaming complete. I actually took the opportunity to save an original vector version to the commons (File:Hexokinase induced fit.svg). I might actually go though enzyme and replace the images with .svg versions, since vectors are pretty good for web browsers. Either way, I think the images on the bullet-point list are good to go. T.Shafee(Evo﹠Evo)talk 10:19, 22 December 2015 (UTC)

Great, thanks! I am off to the airport for cattle call holiday travel and may not get to this till after Christmas, but on the other hand if plane wifi doesn't suck for once, I might do it tonight :) Happy holidays in either case! Opabinia regalis (talk) 00:30, 23 December 2015 (UTC)
Done, finally. Hope you had a good Christmas! Opabinia regalis (talk) 21:46, 26 December 2015 (UTC)
Thanks Opabinia regalis! I'm still getting used to the Australian Summer-Christmas. Hope you've had a good holiday too, despite the travel! T.Shafee(Evo﹠Evo)talk 01:21, 27 December 2015 (UTC)

Evolutionary algorithms

Hi, I just wonder what makes you worrying about the content of my userpage (is it appearing in some lists?), spend your time on Wikipedia at all? Btw, I'm currently studying NEAT algorithms. Neuroevolution of augmenting topologies — Preceding unsigned comment added by Ilyadorosh (talk) 11:26, 27 December 2015 (UTC)

@Ilyadorosh: Hi the level of duplicated content just made me a little uncomfortable. I realise you weren't trying to impersonate me, but the page ended up being misleading (e.g. listing my images and barnstars as yours and giving my email address as your contact details). I look forward to your contributions to the evolutionary algorithm articles! T.Shafee(Evo﹠Evo)talk 03:44, 5 January 2016 (UTC)

Mutation of PRNP

Hi, I wanted to know, what is the name of the highly resistant glycoprotein particles formed due to mutation in gene PRNP. Help me please. Ankit2299 (talk) 19:15, 4 January 2016 (UTC)

@Ankit2299: To my understanding the PRNP gene encodes a protein that is usually called prion protein (PrP). Its alternatively sometimes "cluster of differentiation 230" based on what we know of its native function. This naming is because the protein was first identified for its prion disease and its native function is actually still pretty poorly characterised. It's typically called PrPC when in its cellular isoform, performing whatever its native function is. It's called PrCPr once it converts to a prion isoform. There are a great many different mutations that increase the likelihood of conversion PrCC→PrCPr, and each of them is typically named X#Y (where native amino acid "X" at sequence position "#" is mutated to amino acid "Y", e.g. "D178N"). I hope that helps a little! The PRNP article has more info but for details on specific mutations you'd probably need to do a Google Scholar search. T.Shafee(Evo﹠Evo)talk 03:44, 5 January 2016 (UTC)
Thanks for your help. But I think you could still help me. Actually, I am solving a biology crossword puzzle, so the clue to this glycoprotein is, it is a 6 letter long word. ending with letter S, its seceond letter is R and fourth one O. Hope this time you come up with a specific answer. Thank you. Ankit2299 (talk) 06:32, 5 January 2016 (UTC)
@Ankit2299: Ah, well in that case the I suspect your crossword puzzle is looking for the generic term for those proteins, which is "prions". Just a note, you might want to state in your original question that you're asking about a crossword clue (as opposed to e.g. help with an exam question, or writing an essay). T.Shafee(Evo﹠Evo)talk 09:35, 5 January 2016 (UTC)
Yeah of course it ought to be the right answer. Thank you very much. Well the question states : "The highly resistant gycoprotein particles formed due to mutation in gene PRNP.(6)" Ankit2299 (talk) 11:47, 5 January 2016 (UTC)

Serpin/sandbox

Hello! I've moved Serpin/sandbox from main article space to User:Evolution and evolvability/Serpin/sandbox for now, as the main space WP:Subpages feature has been disabled in English Wikipedia. Thanks, NeemNarduni2 (talk) 01:56, 30 January 2016 (UTC)

@NeemNarduni2: Ah, thanks for letting me know. I'd not seen the WP:Subpages policy. Thanks for fixing. Do oldIDs still point to the same page versions at their new locations? T.Shafee(Evo﹠Evo)talk 02:09, 30 January 2016 (UTC)
That's a good question about oldIDs, but I'm afraid I don't know. Perhaps you could add an intro, and retitle it in mainspace to "List of...(something about serpin here)", then link it to the article, if you don't want to merge it into Serpin? Please let me know if I can help with any WP bits on that, although sadly I'll not be of much help on the protein chemistry content. :-) NeemNarduni2 (talk) 02:13, 30 January 2016 (UTC)
@NeemNarduni2: Thanks anyway! They are just some alternative versions of the table that I made for a discussion on the article's FA nomination. I've done some tests and the old ids for the original page now point to the correct, equivalent versions on the target page. Clever. T.Shafee(Evo﹠Evo)talk 02:22, 30 January 2016 (UTC)

Draft:Sandbox

Hi, that page actually suggests going elsewhere to try the visual editor. Wikipedia:VisualEditor/Feedback also redirects to mw.org (it's ok if we want to give a local target, but let's pick one and use that everywhere :) ). Finally, please format the link so that it actually invokes the visual editor for IP editors as well, as that's the entire point of pointing to a sandbox in a visual editor-enabled namespace :) TY! --Elitre (WMF) (talk) 13:00, 5 February 2016 (UTC)

@Elitre (WMF): You're quite right! I've updated the link to be target to the "veaction=edit" page. I've left it targetting Draft:sandbox for the moment, since I'm aiming to make that the default VE sandbox on Wikipedia for the moment (since User:sandbox is a less logical namespace for a sandbox, and displays a message about changing your username to 'sandbox' which is confusing to new editors. T.Shafee(Evo﹠Evo)talk 23:54, 5 February 2016 (UTC)

VisualEditor News #1—2016

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The formula editor has two options: you can choose "Quick edit" to see and change only the LaTeX code, or "Edit" to use the full tool. The full tool offers immediate preview and an extensive list of symbols.

Future changes

The single edit tab project will combine the "Edit" and "Edit source" tabs into a single "Edit" tab. This is similar to the system already used on the mobile website. (T102398) Initially, the "Edit" tab will open whichever editing environment you used last time. Your last editing choice will be stored as an account preference for logged-in editors, and as a cookie for logged-out users. Logged-in editors will have these options in the Editing tab of Special:Preferences:

  • Remember my last editor,
  • Always give me the visual editor if possible,
  • Always give me the source editor, and
  • Show me both editor tabs.  (This is the state for people using the visual editor now.)

The visual editor uses the same search engine as Special:Search to find links and files. This search will get better at detecting typos and spelling mistakes soon. These improvements to search will appear in the visual editor as well.

The visual editor will be offered to all editors at most "Phase 6" Wikipedias during the next few months. The developers would like to know how well the visual editor works in your language. They particularly want to know whether typing in your language feels natural in the visual editor. Please post your comments and the language(s) that you tested at the feedback thread on mediawiki.org. This will affect the following languages: Japanese, Korean, Urdu, Persian, Arabic, Tamil, Marathi, Malayalam, Hindi, Bengali, Assamese, Thai, Aramaic and others.

Let's work together

If you aren't reading this in your favorite language, then please help us with translations! Subscribe to the Translators mailing list or contact us directly, so that we can notify you when the next issue is ready. Thanks!

– Whatamidoing (WMF) 17:46, 25 February 2016 (UTC)

Hi again, a note about this edit. On Oct 7th we just confirmed that the VE preference switched from the Beta to the Editing tab, while the rollout to newbies was completed around Sep 1st. Have a nice weekend! --Elitre (WMF) (talk) 15:19, 26 February 2016 (UTC)
@Elitre (WMF): Thanks! I've now update the VisualEditor article. T.Shafee(Evo﹠Evo)talk 13:15, 9 March 2016 (UTC)

Thanks for the edit at Tac Promoter

I wondered a little more, could you help me a little, Sir? Please contact me on: aks23121990@gmail.com if you wish to listen my story. Atul Kaushal 13:13, 11 March 2016 (UTC)

Congrats on the Serpin FA promotion

The Science Barnstar
I know how much of a pain in the ass it can be to get an article promoted to FA. It's a big accomplishment, so congrats! Seppi333 (Insert 2¢) 01:15, 13 March 2016 (UTC)
Thanks! Getting a complicated article up to FA was an interesting experience, and I think will improve my general editing habits. Either way, it's a pretty satisfying milestone accomplishment, and feels like a solid contribution to the science sections of the encyclopaedia. T.Shafee(Evo﹠Evo)talk 09:47, 13 March 2016 (UTC)

Protein expression

Hello, the changes you made to Protein expression led to a lot of links that are now pointing to the disambiguation page. There are two ways to fix this. Either it is decided that one of the articles can be considered to be the primary topic, as protein production was before, or the links need to be redirected to either of both articles. Since you were the one who has made this change, could you please figure out what would be the best solution here? Since the topic is very specific, ordinary editors won't be able to do it. Thanks, --Midas02 (talk) 02:24, 29 March 2016 (UTC)

Thanks Midas02, I've gone through the pages. It was probably a useful opportunity to disambiguate the language used in them anyway. T.Shafee(Evo﹠Evo)talk 09:41, 29 March 2016 (UTC)
Great, thanks! --Midas02 (talk) 15:51, 29 March 2016 (UTC)

Precious

science made visible

Thank you for quality articles such as serpins, sharing your scientific expertise on evolution and evolvability ("experimental protein evolution"), for making it accessible by fascinating illustrations, for more accessibility by meaningful redirects, for a clear and informative user page, - Thomas, you are an awesome Wikipedian!

--Gerda Arendt (talk) 05:52, 2 April 2016 (UTC)

Thank you Gerda! I very flattered, and glad that the contributions I've made so far are helping! T.Shafee(Evo﹠Evo)talk 11:55, 2 April 2016 (UTC)
Good choice, Gerda, I agree ;) Opabinia regalis (talk) 04:58, 3 April 2016 (UTC)

A year ago, you were recipient no. 1359 of Precious, a prize of QAI! --Gerda Arendt (talk) 06:55, 2 April 2017 (UTC)

Two years now! --Gerda Arendt (talk) 07:12, 2 April 2018 (UTC)

@Gerda Arendt: - Great memories. I'm proud of how Wikipedia has continued to grow since then. T.Shafee(Evo&Evo)talk 07:16, 2 April 2018 (UTC)

Punning in scientific illustration

Hello, I came across your illustration

and it immediately looked familiar, a well-known Toulouse-Lautrec pastel of a woman with a hat wearing a corset or striped blouse? I can't find the exact prototype, but it's something like this one. So I'm not quite sure how much of the illustration actually shows some scientific property (why the kinks in the dark-blue line?, why the waist-like compression of the parallel blue arrows?) and how much it's just having fun. --Macrakis (talk) 20:28, 2 April 2016 (UTC)

Thanks Macrakis! I'd never viewed it like that, but I see what you mean. The likeness is simply a surprise coincidence! Indeed, just as the pastel image is merely a snapshot of the woman, the illustration is a snapshot of the dynamic serpin (the blue and white portion). The serpin's function is that the kinked dark blue section (which is highly flexible) whips downwards into the blue arrows (which are stressed a bit like a spring). This breaks the protease (the grey hat), which is why the serpin acts as a protease inhibitor! The image is directly based on experimental data gathered by firing X-rays through crystals of the protein and measuring their diffraction. When generating the protein image, I merely decided on the viewing angle, colouring and rendering! T.Shafee(Evo﹠Evo)talk 04:53, 3 April 2016 (UTC)

Signpost polar wikibomb

Hi! I was wondering if I could interview you for the Signpost about your work and the polar women wikibomb. Please ping me! Megalibrarygirl (talk) 14:13, 10 June 2016 (UTC)

@Megalibrarygirl: Hi! I'd love to. I'd also suggest talking to user:Janstrugnell as the originator of the idea! I'm happy to chat on or off-wiki (I also made a note on the Special_desk). T.Shafee(Evo﹠Evo)talk 03:57, 11 June 2016 (UTC)
Awesome! I'll shoot both you and Janstrugnell an email shortly. :) Megalibrarygirl (talk) 15:51, 11 June 2016 (UTC)
I'd also be very happy to chat more about this. Some pages accepted today, some not :( I have much to learn about wikipedia! :) Janstrugnell (talk) 02:02, 15 June 2016 (UTC)
@Megalibrarygirl: I've put together a draft signpost article. If you have a moment, it'd be good to have an outside's view into whether it's a good focus, or whether we should highlight other elements. Is it a bit dry? T.Shafee(Evo&Evo)talk 07:43, 12 August 2016 (UTC)
Evolution and evolvability, hi! Am I too late? I've been on vacation till today. Megalibrarygirl (talk) 17:19, 15 August 2016 (UTC)
@Megalibrarygirl: Not at all. You can see what I was sort of thinking of saying on the draft signpost article. I'd be very interested to hear your thoughts. If you'd like to convert it to a an interview format I'd be happy to answer questions too! I'm hoping to be ready for the 28th of August issue. T.Shafee(Evo&Evo)talk 02:26, 16 August 2016 (UTC)
Hi! I went ahead and took a look and made only a minor copyedit. I think it's really good. Have you thought about talking about the responses you've gotten from participants in the event? I know that learning how to edit Wiki isn't always easy. BTW, do any Antarctic women drafts need looking at right now? I can help with that too. :) Megalibrarygirl (talk) 16:36, 16 August 2016 (UTC)
@Megalibrarygirl: Thanks! Great plan getting a couple of quotes from the volunteer writers and got some lovely responses! I'll get back to you this afternoon with a little list of drafts I'd love you to take a look at. T.Shafee(Evo&Evo)talk 01:59, 18 August 2016 (UTC)

I saw the excellent timeline graphic in Signpost and just wanted to thank you for creating it. – Brianhe (talk) 16:54, 18 August 2016 (UTC)

@Brianhe: Thank you - I enjoy making diagrams, so it was no bother! T.Shafee(Evo&Evo)talk 09:22, 19 August 2016 (UTC)

THANK YOU!

The first image of yours that I admired, was the one in directed evolution. As more as I started to read about evolution, I was thinking: Oh wow, great artwork for the whole topic! Soon I realized it was all yours. Thank yo for putting in the effort and those wonderful graphics. And especially of allowing to use them. They have found a way into my teaching slides :)

A lecturer — Preceding unsigned comment added by 137.248.151.39 (talk) 11:42, 1 July 2016 (UTC)

Thank you! I'm very touched, and extremely glad that my images have been so useful. I've been really happy at their uptake! T.Shafee(Evo﹠Evo)talk 23:52, 1 July 2016 (UTC)

DYK for Elizabeth Truswell

On 4 July 2016, Did you know was updated with a fact from the article Elizabeth Truswell, which you recently created, substantially expanded, or brought to good article status. The fact was ... that Elizabeth Truswell used ancient pollen to show that plants existed in Antarctica before the ice cap formed? The nomination discussion and review may be seen at Template:Did you know nominations/Elizabeth Truswell. You are welcome to check how many page hits the article got while on the front page (here's how, Elizabeth Truswell), and it may be added to the statistics page if the total is over 5,000. Finally, if you know of an interesting fact from another recently created article, then please feel free to suggest it on the Did you know talk page.

Graeme Bartlett (talk) 22:18, 4 July 2016 (UTC)

DYK for Lois Jones (scientist)

 — Chris Woodrich (talk) 03:19, 6 July 2016 (UTC)

Your submission at Articles for creation: Justine Shaw has been accepted

Justine Shaw, which you submitted to Articles for creation, has been created.
The article has been assessed as Start-Class, which is recorded on the article's talk page. You may like to take a look at the grading scheme to see how you can improve the article.

You are more than welcome to continue making quality contributions to Wikipedia. Note that because you are a logged-in user, you can create articles yourself, and don't have to post a request. However, you may continue submitting work to Articles for Creation if you prefer.

Thank you for helping improve Wikipedia!

SwisterTwister talk 06:20, 10 July 2016 (UTC)

DYK for Ingrid Christensen

On 13 July 2016, Did you know was updated with a fact from the article Ingrid Christensen, which you recently created, substantially expanded, or brought to good article status. The fact was ... that in 1937 Ingrid Christensen became the first woman to set foot on mainland Antarctica? The nomination discussion and review may be seen at Template:Did you know nominations/Ingrid Christensen. You are welcome to check how many page hits the article got while on the front page (here's how, Ingrid Christensen), and it may be added to the statistics page if the total is over 5,000. Finally, if you know of an interesting fact from another recently created article, then please feel free to suggest it on the Did you know talk page.

The DYK project (nominate) 12:02, 13 July 2016 (UTC)

File:Glycolysis metabolic pathway 3 annotated.svg

Hello. If it's not too difficult for you, can you change the properties of the inscription "Glycolysis" in the image so that the link can be inserted on top of it? I'm translating Template:Glycolysis summary in Ukrainian. In any case, thank you. --Dctrzl (talk) 12:22, 30 July 2016 (UTC)

@Dctrzl: Thanks for bringing this to my attention - I'd left it in by accident, so I'm happy to have corrected the image. File:Glycolysis metabolic pathway 3 annotated.svg Should now have no annotations. I'm thrilled to know that it's finding uses in other languages! T.Shafee(Evo﹠Evo)talk 00:39, 31 July 2016 (UTC)

Thanks!

Thanks for your work on revolutionizing our help pages, they have become way much friendlier and easy to browse for newbies. Nice work. Moushira!! —Preceding undated comment added 09:06, 17 August 2016 (UTC)

@Melamrawy (WMF): I'm really glad to have made a difference! I'm hoping to eventually replace the current and horrible WP:Introduction with the newer Help:Introduction. T.Shafee(Evo&Evo)talk 12:37, 17 August 2016 (UTC)

Reference errors on 27 August

Hello, I'm ReferenceBot. I have automatically detected that an edit performed by you may have introduced errors in referencing. It is as follows:

Please check this page and fix the errors highlighted. If you think this is a false positive, you can report it to my operator. Thanks, ReferenceBot (talk) 00:22, 28 August 2016 (UTC)

A barnstar for you!

The Special Barnstar
Thanks for all your tireless work on the Antarctic Women Wikibomb. Without your help we would have managed about 10 pages I reckon. Thanks so much for guiding us through the process. You are a legend. Janstrugnell (talk) 07:06, 28 August 2016 (UTC)
The Special Barnstar
Thomas, you are our hero! Thank you for making the Antarctic women wikibomb a roaring success! NGWilson (talk) 08:03, 28 August 2016 (UTC)
The Original Barnstar
Thomas - for all the work you did making the Wiki Bomb go with a bang - despite it being out side your area of science interest - you put up with all the dumb questions... you've made a good thing happen! WavyGeek (talk) 15:40, 28 August 2016 (UTC)
The Tireless Contributor Barnstar
Thank you so much for helping to inspire thousands of budding young female scientists from about the world - and for teaching us more about Wikipedia than we ever thought we would know! Baeseman (talk) 08:29, 6 September 2016 (UTC)
The Barnstar of Diligence
Thomas - your contribution to showcasing the role of women scientists in Antarctic research has been outstanding. Thank you so much for your efforts!! Shawjustine (talk) 06:47, 7 September 2016 (UTC)
@Janstrugnell, Ngwilson, WavyGeek, Baeseman, and Shawjustine: Thank you all! It's been a pleasure to be a part of this project, and I'm thrilled that it went so well! I'm proud of what we accomplished and I feel like I was present at an important moment in history. T.Shafee(Evo&Evo)talk 07:14, 7 September 2016 (UTC)
May I add my own congratulations to all the above. It certainly has been a successful exercise but it seems to me that it's an ongoing story. There still seem to be quite a number of eminent female scientists, researchers and administrators associated with Antarctica, not to mention several explorers and adventurers mentioned in the literature, who are still not specifically covered in Wikipedia. I also have a feeling that more careful searches in some of the other languages, e.g. French, German, Norwegian, Russian and Spanish, would reveal names which have not yet been covered in English. I for one would be happy to spend at least another couple of weeks on the job. Are there any members of your team who are still interested? If so, we could continue our collaboration. In any case, there are still quite a few drafts which could be enhanced and moved into the mainspace.--Ipigott (talk) 16:14, 7 September 2016 (UTC)
@Ipigott: I plan to send an email around to our volunteer group this week, and do another round of from-scratch recruitment in the antarctic community, now that we've shown them what the project is capable of. The group Polar Educators International was very keen on helping out too, and I'm hopeful that there'll be a good group of writers. Hopefully this will all happen next week. I'm hopeful that the Antarctic sections of Wikipedia will become an example of one of the most thoroughly covered fields. T.Shafee(Evo&Evo)talk 00:23, 8 September 2016 (UTC)
That's excellent news. When you have more details, please keep us informed on the WiR talk page. In the meantime, we can continue adding biographies anyway.--Ipigott (talk) 07:20, 8 September 2016 (UTC)
@Ipigott: Absolutely - Just let me know if I start to spam the talk page too much! T.Shafee(Evo&Evo)talk 08:10, 8 September 2016 (UTC)

A barnstar for you!

The Technical Barnstar
Thanks for the improvements to the "pubmed indexed" template. Doc James (talk · contribs · email) 11:08, 6 September 2016 (UTC)
Thank you! Hopefully it'll become increasingly useful as more articles are subjected to peer review by various routes. T.Shafee(Evo&Evo)talk 11:41, 6 September 2016 (UTC)

rkishony video

External videos
video icon The Evolution of Bacteria on a “Mega-Plate” Petri Dish, Harvard Medical School[1]

Hi,

I'm the guy who put this external video into the Evolution and Antimicrobial resistance articles. I've put them back in, but I'm not trying to edit war here. User:Rkishony at Commons uploaded a copy of the original video to Commons, and you replaced my external video with the newly uploaded video. That video was then deleted at commons, leaving nothing in the articles. I'll try to contact Rkishony and explain the situation to him. IMHO opinion the video shouldn't have been deleted as we usually accept uploads from the author in good faith, and he appears to be the author. Nevertheless, I probably understand why the folks at Commons deleted it - it was his first (and only) upload, the video is a pretty prominent work, and it's even conceivable that somebody other than Rkishony owns the copyright (HMS? Science?). I'll try to contact him directly, but he has no e-mail link on his user page.

A couple of minor points:

  • though an uploaded file is generally better (we have it "permanently"), often the video quality is better via an external link
  • I noticed you make diagrams. Could you make a diagram similar to the tree of life I added. The one I added is too tall and too abstract. I'd like the aspect to be more like a TV screen. And the perfect "tree" would be very similar to the one at the end of the Kishony video - very realistic (time 1:45, maybe rotate 90 degree clockwise and just take the bottom half as a model). Of course the new diagram shouldn't be a copyright violation!

Thanks for any help.

Smallbones(smalltalk) 14:17, 3 October 2016 (UTC)

@Smallbones: Thanks for the message! I'm already in touch with Kishony (I suggested to upload in the first place), so can let him know about the current situ. I'll send him an OTRS copyright form to fill in. I'm currently a bit swamped over at the WikiJournal of Medicine, but I'll try to put together a phylogeny diagram in the next couple of weeks. All the best! T.Shafee(Evo&Evo)talk 22:32, 3 October 2016 (UTC)
  1. ^ "The Evolution of Bacteria on a "Mega-Plate" Petri Dish". Harvard Medical School. September 9, 2016. Retrieved September 12, 2016.
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