User talk:Opabinia regalis/Archive 5

Cladistics article
I really think this article needs pretty much entirely rewritten to remain a FA. There is just too much wrong with it, imo, to improve it. I keep looking at it, and I just don't see it improving much in its basic form. I will be glad to review it over the days and add comments if you have time to repair it, but I don't have time until after the first week in January. I will try to watch your talk page. I have finally gotten used to the Wikipedia, I write there, they answer on my talk page threading of converations when I run across whole messes of folks who do it the more sensible way. KP Botany 03:08, 27 December 2006 (UTC)
 * I agree that the article needs more than just referencing; as Aranae pointed out in more depth, it's rather muddled on the details, and not especially comprehensive. I've waffled a bit on this and ultimately decided there's no way I can keep it an FA working alone, even with comments/suggestions from others - cladistics is really well outside my field, and I don't trust myself to adequately and representatively cover differences of opinion within the discipline in a total rewrite, particularly difficulties associated with morphological data. My entire knowledge of cladistics stems from methods in multiple sequence alignment. So, I won't stand in the way if you or other knowledgeable people want to take a crack at it. (If no one is working on it, I'll probably give it a little editing just to make it not suck.)


 * Also, regarding your comment here - this article was promoted a long, long time ago, so it's very much not representative of current FAs. Opabinia regalis 08:21, 28 December 2006 (UTC)


 * Okay, I'll see what I realistically have time to do. Yes, I had not thought of the obvious, just that standards have changed a lot with time.  This is good.   KP Botany 19:16, 30 December 2006 (UTC)


 * Opabinia, do you think the article needs tweaking of individual claims (with addition of the proper references), or has more basic intellectual problems? I know that the language of the field seems woolly, and certainly Joe Felsenstein has questioned the logic of the 'cladistics' school in some of his writings. I have not read many of the responses to Felsenstein, so I don't know how accurately his objections can be countered.  EdJohnston 05:14, 3 January 2007 (UTC)
 * I initially thought the former, but in light of Aranae's comments on the FAR page and my own subsequent research, it has more fundamental problems than I saw at first glance. The terminology is muddled - granted, some of it's muddled in the literature also, but that should be explained in the article or in the terms' subarticles. (I had thought of applying an in-development idea we're planning to use for genetics-related articles, a expandable template glossary for the basic definitions, but wanted to work out the kinks with the genetics stuff first.) The article is also not comprehensive, spending much of its text on PhyloCode and giving short shrift to dissent within the field (or objections to the idea at all); personally I'd certainly expect at least an example or two where the cladistics model produces a different taxonomy than phenetics. There is also the matter of 'total evidence' and the size and quality of datasets used to make classifications - currently the article has essentially nothing on the computational techniques involved (though computational phylogenetics does cover some of that ground) or the associated problems with coding and classifying data.
 * It is the disputes within and about the field that I feel inadequate to cover, as I am not familiar with the literature on the subject and don't know much about the internal 'politics'. I was actually totally unaware that Joe Felsenstein had an account here until today, but I thought it would be a total shame to let the article languish without having at least dropped him a note. Opabinia regalis 06:02, 3 January 2007 (UTC)

Proteasome question
Hi there, me again. I was having a look at proteasome and thought I should ask you something since you're apparently its most eager contributor. I came across today and wondered if you were aware of it; it's the structure of an S. cerevisiae proteasome with bortezomib bound, and I thought a close-up of an active site with bortezomib might make a nice addition to the "Proteasome inhibitors" section and/or the bortezomib article. I'm going for something like this (Tim's work) or this (mine). I've had mixed success so far (my PC keeps crashing), but if you think it could complement the article I'll keep trying (or drop a line on Protein request?). Thanks and sorry for the rant, Fvasconcellos 23:43, 29 December 2006 (UTC)

P.S.: Feel free to move this to Talk:Proteasome if you feel it's more appropriate there.


 * Excellent idea, thanks - that would definitely add to both articles. I'll try to do this tomorrow night when I'm back from vacation and have a decent internet connection again (unless you beat me to it :) Opabinia regalis 07:22, 30 December 2006 (UTC)


 * I seriously doubt I'll beat you to it, but I might try in my spare time :) Thanks a lot, I appreciate it. I'm a big fan of your protein images. Fvasconcellos 16:05, 30 December 2006 (UTC)
 * That took a very long time for not-so-impressive results - my brain must still be in vacation mode. But I did add this image to both articles. I think it looks 'messy' and might take another shot sometime tomorrow. Opabinia regalis 08:01, 31 December 2006 (UTC)
 * I think it's pretty great, actually. I don't think it's messy at all — maybe a bit "busy". If you'd really like to try again, maybe it would look better if there was greater contrast between the bortezomib molecule/catalytic residue and the rest of the image; maybe if it could be made a bit lighter (I have zero experience with PyMol, so I don't even know if this is possible). If not, don't worry; it could just be me being picky. Before I forget, thank you, and Happy New Year! Fvasconcellos 20:35, 31 December 2006 (UTC)
 * Tried changing the color of the carbons and cropping it a little closer - Image:2f16 bortezomib pink.png. I can't make the surface any lighter without making it look like a big blob, because the shadows don't really show up well. Is that better? Opabinia regalis 04:18, 2 January 2007 (UTC)
 * Yes, it does. The pink carbons make the pinkish boron atom a little bit harder to see, but it definitely looks better. I actually think the cropping made the most noticeable difference! Thank you again for coming to the rescue. I'm waiting for FAC now... :) Fvasconcellos 13:21, 2 January 2007 (UTC)

Oh damn, I forgot to even put the boron in the legend. The new version (slightly different crop because I moved the window by mistake :) has it yellow - odd color for boron, I suppose, but it stands out from the carbons now. It'll be on FAC soon. No, it's on FAC now :) Thanks for pointing out this structure! Because Splette's diagrams were already there when the collaboration started, I never really went through the PDB for proteasomes. Opabinia regalis 02:36, 3 January 2007 (UTC)
 * Thank you! I guess I should read the whole thing through before adding my support :), but this is an excellent article, I've no doubt it'll be on the Main Page in no time. Best, Fvasconcellos 13:19, 3 January 2007 (UTC)

Influenza images
Previously I've copied stuff onto this site, is there anything that still needs dealing with? TimVickers 16:50, 31 December 2006 (UTC)

Your recent edit to Image:EM of influenza virus.jpg
I reverted this edit of yours because this image is the one that also appears on the main page, and thus should be marked with  instead of. Thanks. Zzyzx11 (Talk) 00:24, 1 January 2007 (UTC)
 * Thanks - I missed that that one was the main image. Opabinia regalis 00:51, 1 January 2007 (UTC)

Thanks
My mistake on the revert in Evolution. :: Colin Keigher (Talk) 03:23, 4 January 2007 (UTC)
 * No problem, apparently the same person has been making these little changes all day, with no edit summaries. Opabinia regalis 03:47, 4 January 2007 (UTC)

Thank you for your consideration
Thank you for the consideration you gave to my RfA. To be chosen as an administrator requires a high level of confidence by a broad section of the community. Although I received a great deal of support, at this time I do not hold the level of confidence required, and the RfA did not pass. Yours was one of the neutral votes, and raised concerns. I am more than willing to discuss those concerns with you if you are interested. Please let me know. Sincerely, --BostonMA talk 13:07, 4 January 2007 (UTC)

Umm, still more thanks?
Hi O!

Thanks so much for your excellent review of Laplace-Runge-Lenz vector! :D As always, you hit the nail on the head with the Kepler problem, which had been nagging me for some time, but which I'd been too lazy to fix. :( I'll tackle it in a few days, along with a well-intended counter-review of Proteasome &mdash; it looks great! I realized that I'd forgotten about improving the cutaway diagram; should I still try to do that?  I think I can lash PyMol into behaving; being a hemi-demi-semi-Coordinatrix has its advantages! ;)

Speaking of which, if ClockworkSoul stays away for a longer time, do you want to volunteer to shoulder some of the responsibilities, along with me? Tim has a lot on his platter already, and might appreciate the help and your organizational powers. Split several ways, the work might not be too onerous? Besides, I can think of no one more clued in, competent and altogether suited to be a Coordinatrix than you. ;) ClockworkSoul seems to be recovering well, though, so maybe we don't need to worry about it.

My little niece is still very young &mdash; too young to really learn how to knit, at least from this teacher :( &mdash; but my intuition is that she won't be a biochemist, but rather an artist, judging from her furious drawing. ;) Princesses are a common theme running through her oeuvre hitherto, but perhaps I can coax her to make a ribbon diagram? ;)

I've been laid low by a ferocious and remarkably tenacious cold (I think), one of my worst ever. An unwelcome guest, it doesn't seem to want to go away, and keeps getting ruder. :( In books and opera, being consumptive is so fashionable and cool, but the reality is a lot more &mdash; phlegmatic. ;)  It's ironic that I should contribute to immune system when my own is being so lame.

Trying to stay cheery and thinking of you all, Willow 13:37, 4 January 2007 (UTC)


 * If you can beat PyMol into submission, that would be awesome. (BTW - there's my skeleton of a Pymol tutorial that I haven't really gotten back to yet, if you have any additions or suggestions.) I'm happy to do any project-related stuff that needs doing, though I don't know how Clockwork was updating the worklist. But it's good to see he's semi-back at least.


 * Hmm... did someone say protein art? This guy even provides instructions, if your niece ever gets tired of knitting... :)


 * I'm also suffering from a nasty cold at the moment - my sister gave me a generous gift of rhinoviruses last week - so, err, hopefully I'm still coherent. (I don't know why, but my mental model for 'literary consumptive' is Katerina from Crime and Punishment, which is not so fashionable :) Oh, I should probably go read immune system again, shouldn't I? (Also planning on finally populating the genetics glossary with more terms and putting it in the main article soon. I keep getting distracted.) Opabinia regalis 03:20, 5 January 2007 (UTC)

I'm just about to crash, but I noticed your reply and couldn't leave without saying Hi in real time :)

I'll try my best scorpion on PyMol tomorrow and see what I can do. Thanks for the tutorial! :) If you have any special wishes on how it should looks, please leave instructions as detailed as possible; I'm not very intuitive about that! :(

A lot has indeed changed on immune system and, I think, for the better. Tim's really good at making a silk purse out of my sow's ear prose, and there's a wonderfully collaborative feeling there; a lot of people are contributing, mutually helping each other &mdash; Wikipedia at its best. :) I just added a skeletal draft of one section, though, that may tax even Tim's powers. ;) BTW, do you know anything about the age dependence of the immune system?

Oh, that reminds me! Check out the ; maybe it'd be an alternative way to do the glossary? I tried it out for fun at immune system for "eukaryote" but it got reverted today (not to worry, T!). It's not ideal, though, since the normal wikilink mouseover function dominates; one needs good coordination to position the mouse just so to see the Template mouseover text. Sweet dreams and get well yourself, Willow 04:02, 5 January 2007 (UTC)


 * Ah, looks like I missed the real-time thing. I didn't get far enough on the PyMol tutorial to have any specific ideas, other than wanting to give a 'this is the minimum you need to get started' type of introduction, because the manual can be daunting. Also a few tips and tricks that aren't easy to find in the manual or aren't necessarily obvious from the interface, and basic features of selection syntax, which I find obtuse compared to VMD or even Rasmol).


 * If Tim ever gets bored with research proper, he certainly has a career in science writing. Immune system is excellent now, and I was really impressed with some of his changes to proteasome that didn't affect the meaning but made it much more readable. I don't know anything specific about age dependence of immune responses, but I'll do some poking around tomorrow if you guys don't beat me to it :)


 * I used that mouseover-definition idea once in an old web project, and apparently at the time (quite awhile ago in internet terms) it was considered bad style for handicapped accessibility reasons. (I think it had something to do with screen-reader software.) I don't know if that's still true or not. On that same line of thought, though, print readers would have difficulty both with explain and with the popup glossary. I haven't tried to play with it, but I wonder if there's a way to populate the entries in the popup box on-the-fly from the genetics glossary page (or equivalent, with simplified formatting), and put a link to the page in the title of the glossary box. That way readers with old browsers and so on will just see a link to a static page, and print readers will have another printed page to refer to. (On the other hand, maybe I'm thinking too much about .1% of the readers?) Opabinia regalis 06:19, 5 January 2007 (UTC)

Oh, had I power to execute my apprehended wishes, I would whip some programs with scorpions and lash proteins into ribbons...

Sigh. PyMol whipped me more than the reverse. So much for my dom career. ;)

I got the selections to work well, but I was stymied by the apparently simple operation of adjusting the atom sphere size independently for the alpha subunits and the active site residues. Then the program seemed to freeze up and not allow me to change any atom sizes; so I was stuck with 5 Angstroms.

FWIW (see, I'm learning!), the file is Image:Proteasome_cutaway_PyMol.png. I gave it more of a "looking from above" feel to accentuate the depth.

I'll e-mail you the PyMol session file and the cutaway PDB file, so you can play with them yourself; you'll probably have more luck. :)

Sick again, I may have overdone it today. :( Willow 01:04, 6 January 2007 (UTC)

P.S. Drat. I can't e-mail you the files since they're too big. Umm, so to make the PDB file, you'll want to delete chains H, M, N, 1 and 2 from 1G0U. Once uploaded into PyMol, you can generate selections for rings 1-4 by

select alpha_ring1, chain a+b+c+d+e+f+g

select alpha_ring2, chain o+p+q+r+s+t+u

select beta_ring1, chain i+j+k+l

select beta_ring2, chain v+w+x+y+z

The alpha subunit centroids can be selected by

select alpha_subunits1, alpha_ring1 and resi 137 and name cb

select alpha_subunits2, alpha_ring2 and resi 137 and name cb

while the active-site residue can be selected by

select active_site1, beta_ring1 and resi 1 and name ca

select active_site2, beta_ring2 and resi 1 and name ca

Then you can "show" the atoms of the latter four selections as spheres, and hide the lines of the first four selections. Color at will. Then use

set sphere_scale=3.0

to get a more decorous 3 Angstrom sphere. I'm not sure how to work it together with selections, though. :( <- Bummed Willow 01:21, 6 January 2007 (UTC)


 * Ah, PyMol is a harsh mistress... thanks, I'll see if I can make this work. Opabinia regalis 03:45, 6 January 2007 (UTC)


 * Is this more like what you were thinking of? Turns out that changing the sphere sizes independently requires creating objects rather than selections, by using  instead of "select...". You can then change the sphere size for each object separately with  . The session file is about 19MB if you want it - is that too big?


 * BTW, is there a particular reason why you edited the pdb file first instead of just hiding the extra chains? I used the latter method, and I can't think of a reason they'd produce different results, but maybe I'm just dense today :) Opabinia regalis 03:15, 7 January 2007 (UTC)


 * That looks great, I knew you would conquer it! I didn't even know that you could create objects; PyMol still seems rather mysterious to me.  The coloring of the beta chains is especially nice; that eluded me, too.


 * No reason for deleting the chains in PyMol, which makes it so easy to make things invisible. I had just deleted them earlier for convenience with other visualization programs.


 * You're the best judge of what would be helpful in the Proteasome article, but I would align the Figure vertically to agree with the other Figures, make the green spheres bigger as in the other schematics, and maybe highlight the residues in both beta rings? Honestly, though, the more I work on it, the more I worry that the cutaway picture might not help people understand the proteasome. :( Willow 21:01, 7 January 2007 (UTC)


 * Oops, I didn't even notice the missing spheres on the top ring. I'm thinking of repeating this with 2F16, which has bortezomib bound, to show binding as well as the location of the active site. Opabinia regalis 00:54, 8 January 2007 (UTC)
 * Just did this, it's in the article now in the proteolysis section. You can't actually see the inhibitor that well in the thumbnail, but the spheres help. Opabinia regalis 05:32, 10 January 2007 (UTC)

Help on Sweater design
I just discovered that Sweater design is up for deletion! :( Could you help me understand what they're objecting to, and how I might fix it? I think sweater design is a valid encyclopedic topic, having been studied and described by many important fashion designers.  How would it be any different from architecture or boat design?  Confused and unhappy Willow 21:01, 7 January 2007 (UTC)

PS. Is there an AfD page where people are going to vote on its fate? I couldn't make that out from the template. I'd like to postpone a vote until there's a chance to salvage the article.
 * Looks like this has been sorted out - it was a proposed deletion tag, which requires no discussion and which anyone can contest. Also - at least in theory - admins who delete old prodded articles read them first to see if they're legitimate articles that nobody got around to contesting. It looks like a perfectly good article to me, and if anyone tries to take it to AfD I'm sure it'd survive. Opabinia regalis 00:51, 8 January 2007 (UTC)

Please help, Sweater design is now officially Afd. Today is a bad day for me, too. :( Willow 12:39, 8 January 2007 (UTC)

PS. I added some stuff to Immune system about the computational prediction of antigenicity, but I didn't have any references. It seems right up your alley &mdash; could you help there, too? Thanks!

A long rant about speedies and other deleting
I am still pretty confused about this deletion business. I have had one article speedied and then userfied for me by Killerchihuahua. It is at User:Filll/Peter Cusack. I am still do not understand what was so wrong about it. Although it is a stub, This guy is a
 * professor at a college in London
 * an artist who collaborates with many musicians and other artists
 * host of a regular radio show in the UK for the last 8 years
 * working on some high visibility sound scape projects in london
 * working on official government art works in china
 * working in Siberia and other places on art projects
 * had links to his page before I even wrote the article; 6 links (one from an article I wrote: Frere Jacques)
 * has a large number of recordings etc out there.
 * I had two people on the talk page saying they would back me up and argue for it not to be deleted. And I thought that was all I needed. Next thing you know, it was gone. A speedy nuked it. And I have been disgusted enough not to work on it since and just leave it userfied. I have seen lots of short stubs. I have written some. They never got in trouble before. Now all I see and hear about is deletion, deletion, deletion.

I disagree with the statement of Wales that we have all the articles we need and all we have to do is improve what we have. Just the last couple of days:
 * I wrote a bio for the author of about 30 books, member of National Academy of Sciences, AAAS fellow, 3 honorary doctorates, former chairman of Princeton Bio department John Tyler Bonner and it got hit with a speedy. I begged and the editor just sort of ignored me, and gave me a snide reply, and then slammed me again with another speedy a day later when the article was now twice as long (maybe I should not have removed the speedy? I dont know the rules). DGG pointed out that this was the most famous living biologist (that I wouldnt know or know how to evaluate). Hopefully this article will survive. But he had no article. Seems like we have holes if the most famous living biologist has no bio, dont you think?
 * I came across Harry Rimmer, one of the founders of the US creationist movement who has probably 50 or 100 books. And was in a famous famous lawsuit that everyone followed (20s? 30s? not sure when). And no article. I run into these holes in Wikipedia all the time.

I do not claim Peter Cusack is so important. Not like Rimmer or Bonner. At least not yet anyway. But wow the aggressive deleting. I fought like crazy to keep Hinduism and creationism the last few days and I barely managed to keep it (but had to make a lot of compromises). And I fought quite a pitched battle over Support for evolution which will probably survive with a name change. For a while it looked like that would go down in flames too. I just get tired of this. And I am still not so sure what the rules even are.--Filll 01:53, 8 January 2007 (UTC)


 * Comments--I apologize to O.r. for putting it on her talk page, but perhaps this is the reasonable place to keep the discussion oft he details.


 * Crusak--the original article seems to have read only: "Peter Cusak is an artist and musician who is a member of CRiSAP (Creative Research in Sound Art & Performance), and is a research staff member of the London College of Communication." For even the version on your user page it will need listings of his research articles, listings of his musical projects, and, particularly, listing of reviews of his music and comments on his research. Bonner has so many publications it isn't necessary, and if it were there would be no difficulty finding a few dozen published tributes. For Crusak, it is necessary, and enoguh can surely be found.


 * Hinduism. Any creationist stuff is tricky.  I made some initial attempts to edit--on both sides, but found it too frustrating to keep arguments intact & have more or less avoided the topic.  I think the edits on this particular article ended in a satisfactory way. There is no need to refute the final section. There is nothing one could say that would show the nature of the position in a truer light. It is much stronger left as it is. Those who believe will continue to believe, but nobody else.


 * Support for evolution. I have added my comments on the discussion. A very brave article to attempt. it should hold, and this one is certainly worth any amount of effort.


 * FJ.  I do not consider the article well organized, and I assume this is because of the need to add facts to meet objections. But any attempt to delete or soften it would have been altogether wrong. There are people automatically over-suspicious of anything that can be thought trivial (or sexual,  or racial, or evangelical. Left to myself, I would delete all articles about rock musicians from the 1980s on--i'd use the speedy for lack of content. (smile).


 * Rimmer. I think the article much too negatively POV, & have made some edits.


 * Noah;s ark, needs a separate posting. Frankly, I find the discussion a little unsophisticated. God was stated as assisting the builder, and probably 90% of genera are insects. I'll post on orangemartin's page. There is a wonderful tough-in-cheek illustration in Diderot's Encyclopédie, emphasizing the sanitary arrangements--it should be PD.

DGG 04:22, 8 January 2007 (UTC)
 * What I really hope to catch is new ones as they come up, so we can see the judgement on the article as it existed at the time.
 * O.r., I'll certainly ask your help if needed, but I hope to catch them in time.


 * Not to be offensive, but look at this one:Franko biggererio--Filll 02:21, 8 January 2007 (UTC)


 * Filll, the original version of the Cusack article really was marginal - bear in mind that standards tend to be a little higher for newly created music articles due to the torrent of vanity articles on totally non-notable garage bands, student music projects, performance art groups, and miscellaneous nonsense. (Take a look in CAT:CSD sometime; yes, there's a few false positives that get tagged or even deleted when they shouldn't, but 99% of what's in there is complete garbage.) The one that's in your userspace does still need a bit of fleshing out. The Bonner article was obviously silly to tag for deletion - there are a lot of people running around tagging new pages like it's a race - but I think enough people have communicated that to the user.


 * As a general note, I don't think anybody believes that 'we have all the articles we need' - IIRC Jimbo's statement was in the context of improving referencing, to make the point that there are no longer so many or so large gaps in coverage that any article is better than nothing at all. (I can't find it now, but there's an essay in someone's userspace on why having nothing in the little gaps is better than having a crap article, because redlinks invite editing by readers and crap articles just turn people off.)


 * Creating articles in userspace and then moving them to mainspace when they have references and clearly asserted notability is a good way to avoid getting caught by overzealous newpage patrollers. Most don't spend more than a couple of seconds looking at a new article, so if it's already been edited enough that it's well-written, polished, and referenced, they won't usually bother you. The general rules for what might be nominated for deletion are in the deletion policy and guide to deletion.


 * I'm not sure what you mean about Franko - that appears to have been entirely made up, and needed deletion. Opabinia regalis 05:25, 8 January 2007 (UTC)

Blocking search engines from user space
I've been looking for prior discussions on this topic. Dragons flight thought you might have started a thread on this at one of the village pumps (policy or proposals, probably) in the last couple months. If that's so, or if you know of a discussion, could you give me a pointer/link to it? Thanks. John Broughton |  Talk 13:34, 8 January 2007 (UTC)
 * I did start a thread about it, after googling my namesake fossil and finding my userpage in the top ten hits. I guess the pumps aren't archived that far back, but IIRC this was the last post in the thread. It was in technical; I thought at the time that userspace wasn't supposed to be indexed, but apparently people use google to dig up spammers using their userpages as free adspace. Opabinia regalis 01:08, 9 January 2007 (UTC)
 * Thank you for the link; very informative. I wonder if editors realized the irony in touting the value of being able to use google searchs of userpages to detect spam, since robots.txt would essentially eliminate both such spam and the need to search for it.  (Well, technically, much spam might still be on user pages, but it would be impotent because unfindable.)  John Broughton  |  Talk 02:33, 9 January 2007 (UTC)
 * True for search engines that respect robots.txt, at least - though I guess if spammers know their userpages won't work, they might post more dreck in mainspace? I still think not indexing userspace, and quite possibly talk spaces, is a good idea; I can think of at least one case where a user got very upset after finding his name in a google index of a talk-page archive and thinking it was a new post. Opabinia regalis 03:20, 9 January 2007 (UTC)

Journal name abbreviations
Opabinia, where do you stand on that Object? If you need help converting them in order to address the Object, I can help. Am I missing something, or would we actually have to do every one by hand? I can't find a database that can be used to automate it - if you feel it has to be done, we can divide up the work. I still resist the idea, since it would take a lot of manual work, and the PMID should suffice, but if you need help, I'll dig in. Sandy Georgia (Talk) 16:14, 8 January 2007 (UTC)
 * In the short term, my plan is to do nothing, since Circeus hasn't responded to the subsequent comments on his suggestion. I left him a note about opening this for wider discussion; a substantial change in style recommendations affecting as many articles as this one would deserves a wider discussion than a thread in an obscure FAC nomination. IMO it would be a bad precedent for future science-related FACs to make that change in response to one user's opinion without collecting some wider input.


 * I don't know of an intelligent automated way to get this information, other than clicking through PubMed's journals link and screen-scraping the equivalents of pages like http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Journals&term=%22Dev+Cell%22[Title+Abbreviation] sorry, can't get the link with brackets to parse right . If there's a larger discussion I'll certainly oppose this on practicality and text-clutter grounds, unless someone finds a common way of searching for references that requires the full names. FAC doesn't need more shrubberies. Opabinia regalis 01:30, 9 January 2007 (UTC)
 * Without raising the long-term policy question, I don't think it would be that hard to convert the journal names in Proteasome. Assuming the reference uses a journal in the NLM list, you should be able to look up its journal name at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Journals. This screen has a search box, where you can type in the standard journal abbreviation, and hit 'Search'. You then get back the full name of the journal. I also managed to download (by ftp) a plain text file called J_Entrez.txt (4 megabytes in size) that has both the abbreviation and the full name for every journal I checked. You could do a 'Find' on the abbreviation, and get the answer. So if you need help converting those references, I'd be available. EdJohnston 02:26, 9 January 2007 (UTC)
 * Don't you think our readers would put up with the 'clutter' that would be caused by spelling out these not totally self-explanatory abbreviations? EMBO J, Cell Death Differ (my favorite), Mol Cell, FEBS Lett, PLoS Biol. I know that 'J Biol Chem' looks easy but not all of them are. EdJohnston 02:50, 9 January 2007 (UTC)
 * Thanks for the offer. I doubt it would take long to convert this article - anybody who's done biology work probably knows 80% of them anyway - but I'm strongly inclined not to set that as a standard for future articles, not least because there are screen-scraper scripts for importing PubMed references that would need to be extensively modified. I realize they're not all intuitive (my personal favorite official "abbreviation" is J Phys Chem B Condens Matter Mater Surf Interfaces Biophys) but as far as I've ever known, it's actually better for searching to have the abbreviation than the full name, because almost every database uses the abbreviations. Do you know of any common databases or search methods where that's not the case? I asked Circeus on the FAC page to elaborate why/where he had had trouble, but he hasn't responded yet. Opabinia regalis 03:49, 9 January 2007 (UTC)
 * Right - the problem is not *this* article (which I'll help do, if that what it takes to get rid of the object) rather the sheer volume of manual work that would be required across all Wiki articles, with little benefit. I would also strenuously object to the change in policy, since it requires manual intervention for every journal, to replace the info PubMed provides.  Just wanted you to know I could help if needed, but agree it should not be needed.  Sandy Georgia  (Talk) 04:16, 9 January 2007 (UTC)
 * Thanks Sandy. I left a note in the FAC nom that this proposal does not currently have consensus. Raul's a smart guy, and I'd honestly rather kill this dead did I say that? figure this out than get a gold star faster :) Opabinia regalis 05:50, 9 January 2007 (UTC)

I have replied to this at some length just now, on User talk:Circeus. My own favorite is J electroanal chem inter electrochem, but the real gems are the changes in Crasp and JchemSoc. DGG 06:18, 9 January 2007 (UTC)
 * I hope the FA nomination of this article doesn't become a test case for changing the rules. Getting unanimity on reference style would be a Herculean task. I personally think that both the fully-spelled-out and the abbreviated styles should continue to be accepted, so long as a reasonable system of abbreviation is used. These days, many articles have at least their abstracts on line. Adding an abstract link to a reference would (in my view) be of more value than spelling out the journal name, though that also would be labor-intensive for a long reference list. EdJohnston 17:55, 9 January 2007 (UTC)
 * Well, deep study of the article shows you already have PMIDs on everything, so please ignore last comment! Since this is true, expanding the journal names seems less important.  EdJohnston 18:03, 9 January 2007 (UTC)
 * Right - I insist on PMIDs on FA reviews, partly for that reason - spelling out journal names is redundant when the link is given, and it would be a Herculean task to bring all FAs up to that standard. On the other hand, requiring PMIDs makes sense, and covers many bases.  Sandy Georgia  (Talk) 18:11, 9 January 2007 (UTC)
 * Thanks for all of the comments. I suppose this is somewhat moot now anyway, as the article was promoted earlier today. Ed, I'm not intending a test case for general standardization (incidentally, I posted in this unrelated thread my opinion that ref styles ought to follow the format of the article's field, and that complete standardization is hopeless), but I was concerned about this suggestion proliferating.
 * The presence of PMIDs (arXiv links, etc., as appropriate) is more than sufficient, I think, and obviates any need for full journal names. (Even if I do consistently forget to include them :) Even given DGG's summary on Circeus' talk, the link to PubMed/arXiv/etc. should provide more than enough information for anyone to track down the paper, if not a direct link to the online version. Opabinia regalis 01:16, 10 January 2007 (UTC)

Please Review
Could you please review my response to you on FAC for Folding@home. Thank You.--Foundby 16:25, 8 January 2007 (UTC)

Barnstar

 * Note for the curious: sockpuppet of a banned user. Also, logrolling in action: his sock gave him a barnstar. Heh. Opabinia regalis 01:27, 11 January 2007 (UTC)

Proteasome FA



 * Let me be the first to second those congratulations! (get it? :) It's truly an excellent article. Well done. Fvasconcellos 22:18, 9 January 2007 (UTC)

The more the merrier, no? You deserve so much credit for proteasome; such an important subject, so well-written and so wonderfully digestible... It's a gift to us all. Happy third helping of "you're awesome" pie :) Willow 13:28, 10 January 2007 (UTC)


 * Thanks, and excellent choice of painting and caption. Hmm, from now on I should use cool works of art instead of barnstars and congrats notices. Opabinia regalis 01:22, 11 January 2007 (UTC)

My RFA
Have replied to your oppose on my rfa. I hope that is OK. → Aza Toth 03:02, 10 January 2007 (UTC)

Foundby
Yeah, I thought so too as soon as I realized that Foundby started his account in less than a week after Records was blocked. User:Foundby was blocked as a result of the checkuser request. Guess we should speedy the FAC nomination for Folding@Home too. AZ t 23:33, 10 January 2007 (UTC)
 * Also see Raul654's talk page and activity at Today's featured article requests, which are disruptive. Sandy Georgia  (Talk) 23:53, 10 January 2007 (UTC)
 * Thanks Andy. I didn't even notice the account creation dates - it was pretty late when I filed the checkuser request. Should've just trusted my original instincts, I suppose; he was busy being obnoxious in a lot of places. Opabinia regalis 01:20, 11 January 2007 (UTC)

EB and ineluctable snarkiness
Hi O,

I'm so happy that you liked the painting; it's cute, no? It made me think of us and smile; you're the one with the crown.

You're probably busy now, too, but I'm having trouble with the Encyclopædia Britannica &mdash; or rather, trouble with myself, which you might be able to help with. You'll probably laugh, but I'm having trouble controlling some seriously snarky impulses. I guess I feel a little too strongly about some things, because I can't seem to find alternate wordings for certain noteworthy facts. Usually, my brain is swimming with alternate wordings, a cage of little birds where I can reach in and grab the one I want; so it's pretty significant to me that I'm frozen. Anyway, I really want to bring this article to FA sometime, but I want it to be NPOV, broadly acceptable and, more importantly to me, a worthy article, noble in word and thought. Can you help when you have a chance? Sections that are nagging at me include the "2nd version of the 15th edition" section of the History, and perhaps the Contributors section and a few others that will likely leap out at you. There's no rush, but i would be very grateful, Willow 22:38, 11 January 2007 (UTC)

PS. I may go to bed early tonight, so that I can clear my head about it, and start afresh tomorrow.

Internal intussusception
Amazing. There actually is such a thing. Good idea to totally remove the history and create from scratch. Fan-1967 01:49, 14 January 2007 (UTC)
 * Yes, that was a mental image I really could have done without. Opabinia regalis 04:33, 14 January 2007 (UTC)

This month's MCB Collaboration of the Month article is Peripheral membrane protein!
– ClockworkSoul 18:54, 14 January 2007 (UTC)

Double redirects
I was under the impression that most of the "double redirects" were taken care of. A quick glance through the what links here at Levels of support for evolution seems to confirm this. --ScienceApologist 18:14, 15 January 2007 (UTC)

your work on Gene
Dear Opabinia,

I like your rework of the article Gene. Maybe we can make this article feature standard again. I realise you are not a fan of statement headings as common in some textbooks, e.g. you changed "The genome contains most genes of an organism" to "The genome". I would like to argue that the longer statement headings are more thought-stimulating than the word headings you used. But I realise that this is a matter of taste. Maybe you can explain your preference for short headings.

Also, I would like to ask why you deleted the section on the evolving concepts of the gene without integration, replacement or comment? Or did I overlook it? I think it's very interesting information and the most up-to-date part of the article. Please explain.

Best, Jasu 11:13, 18 January 2007 (UTC)


 * Hm, the headers are easy - stylistic consistency. The vast majority of wikipedia articles use descriptive noun phrases as headers. (One of the cases where my biases agree with convention.) Shorter headers have a more 'encyclopedic' tone and make the TOC easier to read.


 * More generally, I got distracted and never really finished what I was doing with that article, so it's not currently in what I'd consider good form. I think the stuff on DNA replication and inheritance needs compression; it has to be in the article to link Mendelian and molecular inheritance, but there's just too much off-topic material in there taking up space. I never did anything with 'evolutionary concept of a gene' either, and major topics - pseudogenes, lateral gene transfer, various issues surrounding the definitions of RNA genes, etc. - are missing. The content in the 'evolving concepts' section (reproduced on the talk page) had been flagged in a comment by another editor as being entirely too specific, and I agree. That sort of material should certainly be in the article - especially RNA-based inheritance - but that way of presenting it is awkward, especially in an article that's realistically going to be read mostly by high school students. Some of the other stuff might better be placed in gene regulation. I just never got around to that part of the rewrite.


 * If you're interested in editing/expanding/improving this article, don't worry about me 'owning' it or anything - I was asked to review it in August and have been trying to punt it ever since :) Opabinia regalis 01:57, 19 January 2007 (UTC)

After your work on gene, will you be working on Gene Gene the Dancing Machine ?--Filll 02:39, 19 January 2007 (UTC)
 * Just a little bit :) Opabinia regalis 06:21, 19 January 2007 (UTC)

Trans fat
Hi there, thanks for the comments on the Trans fat FAC. I am a bit concerned with the article organization proposed, and I have a suggestion over there that I'd appreciate some feedback on. Thanks! -- cmhTC 13:52, 19 January 2007 (UTC)

Akhmim Wooden Tablet

 * Akhmim Wooden Tablet. Thank you for the link. I had forgotten about this area. Most of my recent work has used blogs. Today I posted the AWT info, so it is ready to review. Thanks for the heads up. Milogardner 14:21, 19 January 2007 (UTC) moved from User page Fvasconcellos 22:20, 19 January 2007 (UTC)

Thank you for the comments on my talk page. My recent work has only cited scholarly work, and linked the ancient texts (from which Ahmes and the RMP were constructed). It may appear that my personal analysis is attached to this linking up of documents, a step that others have oddly not attempted. However, I have no idea where current and future reviews of the Middle Kingdom texts will take the discussion of ancient Eguyptian mathematics. That is, each document makes little sense - read as an independent event.

What I do know, and anyone can read, several Wikipedia posters have oddly placed their personal stamps on their writing, strongly suggesting in myopic ways, considering only one text, or one set of facts, that scribes like Ahmes did not know every much. Why are you not complaining about this Wikipedia inconsistency, and obvious scholarly error?

One day I'd like to publish additional papers on Egyptian arithmetic, one that actually redefines subtraction and division as scribes thought and wrote. Today these and other math topics have been seriously garbled, as you may have seen. For now, I'll continue to link the texts, and allow Wikipedia members determine for themselves the meaning of a particular text and its relationship to its parents, brothers, sisters and children texts. Milogardner 14:22, 20 January 2007 (UTC)

A response to your comment on my talk page has been completed. Thanks for the suggestions. Milogardner 01:46, 22 January 2007 (UTC)

Alpha sheet
Sure, no problem. A few questions though: I'll be working on them while you decide :) so drop me a line when you get this, and I'll upload the relevant one for your appreciation. Damn, I hope I can make this accurate ;) Fvasconcellos 14:31, 20 January 2007 (UTC)
 * Would you like explicit carbons, as in the Pauling/Corey paper, or implicit, skeletal-style?
 * Would you like colored atoms for contrast (O = red, N = blue) or all black?
 * Expanded radicals (HC-R) or compact, as in the original diagram (-CHR)?
 * OK, what do you think of this? I'm glad you share my aesthetic preferences as I didn't get around to the expanded diagram! As you can see I was heavily inspired by Pauling and Corey's landmark paper :) I'm not too happy with the residue positions—do you think they give an accurate idea? As for the beta sheet diagrams, they actually look very nice to me; emphasis on nice, not informative though. Any particular requests or preferences? Fvasconcellos 01:13, 21 January 2007 (UTC)
 * Done: antiparallel and parallel. Again, I hope they're accurate, and I'm glad the alpha sheet one was to your liking. I might redo Image:BetaPleatedSheetProtein.png as well, though I don't really think it's necessary—maybe just for consistency? Anyway, thank you for asking me, and if you need anything else or if I've committed some vicious inaccuracy, my Talk page is always open... :) Fvasconcellos 18:03, 21 January 2007 (UTC)
 * Ouch, I can't believe I just let that slip—I was cloning and pasting all over the place and didn't even check against my sketch or some basic knowledge of chemistry :/ *pauses, bangs head on desk* The new version's up, purge your cache if it's not displaying. I'm glad I don't openly advertise my graphic services... Fvasconcellos 13:25, 22 January 2007 (UTC)
 * Phew, thanks for understanding... :) The layout's great, they were both antiparallel though; I presumed this was unintentional, and added the parallel one as well. I thought you would keep the old ones beside these—I'm a little taken aback by your trust in my capacity :D Anyway, sorry again for the "mishap". If you need anything, I'm here. Fvasconcellos 13:13, 23 January 2007 (UTC)

Articles for deletion/Ill Mitch (2nd nomination)‎
Hello. Re your vote at the article's original AFD, you might like to comment at the AFD for its recreation. Cheers. The JPS talk to me  00:54, 21 January 2007 (UTC)

Your expert trained eye
I have just completed Bees and toxic chemicals and if you would cast your expert eye on it and see if I have made any gross mistakes I would be grateful. I gather it will probably get featured in "Did You Know" in the next day or two, so it is best if I do not say anything too outrageous in it.--Filll 01:22, 21 January 2007 (UTC)

No wonder
No wonder you gave Baby Gender Mentor such as detailed review. I didn't realize until just now that you are part of the Molecular Biology WikiProject. Thank you very much for your time and contributions to Featured article candidates/Baby Gender Mentor. You raised many excellent points. I have made numerous changes to the article. I also made a detailed reply to you at Featured article candidates/Baby Gender Mentor. If you read my reply, you will see that a couple of your questions cannot be defnitively answered at this point. For instance, I explain my understanding about Acu-Gen's relationship to BioTronics. Unfortunately, no one source comes right out and says that Wang is running Acu-Gen from inside BioTronics building, so but I am being careful to stick with the sources and not to venture into drawing my own conclusion, which would be original research. Even on this point, I think I was able to make the known connection more clear. So, with this and the other changes I made, I feel I have addressed all your points.

I would be much in your debt if you could take another look. I hope you can now support the article for FA. If not, I hope you will comment furhter so that I may continue to improve the article up to FA standard. Best regards, Johntex\talk 10:04, 21 January 2007 (UTC)
 * Thanks again for your help in getting this article to FA. I have made several changes to try to address your points and I have explained the changes here. Johntex\talk 18:38, 22 January 2007 (UTC)
 * Good question! I don't really know the answer, but my thoughts on this are here. Johntex\talk 03:54, 23 January 2007 (UTC)
 * OK, you are probably right. I added that information into the section on vanishing twin. Please let me know if it reads OK.  Thank you, Johntex\talk 18:05, 23 January 2007 (UTC)

Defining intoxication
I personally would have preferred not to define intoxication, and at some point in the future I might remove it. The reason it is there (and several other sort of silly things as well) is to try to "immunize" the article against AfD to a certain extent. For about a week I asked "bee experts" and a few "writing experts" repeatedly for their opinions, and that was one of the demands from one of the people who was pretty negative about the article. I had 3 or 4 people who gave me a list of demands, sometimes with an only semi-veiled threat of AfD. So, I tried to accommodate everyone. Even if I personally disagreed. Because you cannot really write what you think is a reasonable article here with the threat of AfD. And then of course one has editing by others. I will say that most of the edits since it was moved out of the sandbox I have agreed with, but some I do not. I think it is best to let people have their say and see how it evolves. At least now I hope it avoids AfD. I really find those AfD things tiresome. So that is why the definition is there, and a few other peculiarities as well.--Filll 13:15, 21 January 2007 (UTC)
 * Most AfDs are well-deserved :) And I think most people would think twice before AfD'ing an article with 42 references. Opabinia regalis 02:31, 22 January 2007 (UTC)

Maybe. But I have had enough of AfDs, so I want to do whatever I can to avoid them.--Filll 02:36, 22 January 2007 (UTC)

Newyorkbrad's RfA
This is to thank you for your early support on my RfA, which closed favorably this morning. I appreciate the confidence the community has placed in me and am looking forward to my new responsibilities. Please let me know if ever you have any comments or suggestions, especially as I am learning how to use the tools. And as for your comment that "it's about time," I guess I figured it was better to wait awhile too long than run a few weeks too early, but in any event it's done now. I look forward to working with you as a colleague. Best regards, Newyorkbrad 17:47, 21 January 2007 (UTC)

My RfA
Thank you for supporting me in my RfA! It succeeded, and I now have The Tools – which I'm planning to use as wisely as I possibly can. I hope I will be worth your confidence. Thanks again! :-) –m y s i d ☎ 20:44, 22 January 2007 (UTC)

Hi! :)
Hey, so you should check out this, which can be spruced up or paired if it would help you. Thanks for the help on Macropædia, too; I don't always see the right course sometimes. :( You also might've noticed that some cquotes escaped the recent conflagration and are beginning to proliferate again in the EB articles. ;)  Hoping that you forgive my fondness for cartoons, affectionate Willow 00:34, 23 January 2007 (UTC)
 * Looks nice! Hope you don't mind if I flipped it so it'd fit in the article and play nice with the text.


 * Oh no, the cquotes are taking over! But given the amount of work you've put into these articles, I suppose we can tolerate this particular invasive species... (bquote does have its advantages though). Opabinia regalis 02:22, 23 January 2007 (UTC)

Hey O!

Thanks for using the picture at alpha sheet, which I'd never heard of before but which seems really cool. Did you want a pair of them H-bonded? I also wasn't sure about the proper choice of dihedrals; the strand has a slight bend even at -45°, -45° (the smallest I tried); should it be straight? I was a little surprised that repetition of one pair of dihedral angles and then its opposite didn't give something straight (from symmetry), but maybe it's a by-product of the Cα chirality and the slight asymmetries in the Engh&Huber bond geometry? BTW, the peptide dihedral angle ω was exactly 180° (trans).

I tried out bquote at History of the Encyclopædia Britannica; I like the attribution aspect, but I kind of miss the dramatic swashes on either side that signal the quotation. Drama queen, what can I say? ;D I'm waiting for others to say what they like there.

If you have some time, I could really use an impartial insight at Talk:Micropædia; thanks! Hoping all's well with you, Willow 02:18, 24 January 2007 (UTC)


 * I actually discovered the alpha sheet fairly recently too, after reading the Daggett papers on Abeta fibrillization, but I guess they haven't released any structures from their simulations. I do have more to add to that article though. I think a hydrogen-bonded pair would be excellent. I would've thought they'd come out straight alternating exactly the same dihedral - and Pauling and Corey's 'flat' sheet is directly alternating - but I guess the bond isn't quite symmetrical, is it? Now I'm trying to rotate peptide bonds in my head and it's way too late for that :)


 * Ahh, the drama of cquotes... I suppose they do have a degree of visual flair. Most of the alternatives a bit duller. (Isn't there one with an offset box? Still not too exciting, but a bit more contrast with the text.)


 * Will look in on the Micropedia. /too lazy to make a fancy ligature :) Opabinia regalis 07:57, 24 January 2007 (UTC)

New name
Any comments at the talk page of level of support for evolution? --Filll 20:12, 25 January 2007 (UTC)

RNA interference
Sorry about the revert, I thought it was a cleverly disguised vandalism, as I didn't know the term existed. --Wirbelwind ヴィルヴェルヴィント (talk) 05:43, 27 January 2007 (UTC)
 * The word "cleavage" being the problem, I assume. The verb "to cleave" does have a whole set of associated ambiguities. Opabinia regalis 23:18, 27 January 2007 (UTC)