User talk:Opabinia regalis

From Wikipedia, the free encyclopedia

This is a Wikipedia user talk page. For other uses of Opabinia regalis, see Opabinia regalis.
I only have five eyes, so I can't keep track of threaded discussions that are scattered all over the place. If you leave me a message here, I'll reply here. If I leave a message elsewhere, I'll watch it - please reply there. Thanks!

Old stuff: Archive 1 (May - 15 Aug 2006) • Archive 2 (16 Aug - 19 Oct) • Archive 3 (20 Oct - 30 Nov) RfA stuff here • Archive 4 (30 Nov - 31 Dec) • Archive 5 (1 Jan - 31 Jan) • Archive 6 (31 Jan - 11 Mar)

Contents

[edit] Beta barrel

Hi there, Opabinia. If you have time, I'd like to ask you for two favors: I've just added this image to the beta barrel article, which was conspicuously lacking illustrations. I'm now wondering as to whether it's appropriate—TIM barrels are a tertiary structure "in their own right", aren't they? I thought I'd ask our resident protein maven for some feedback :) If you think there could be a better image to illustrate this article, would you mind making a suggestion? There are plenty of beta barrel-containing proteins, and I'd like the article to have a nicely "textbook" example. I couldn't find a single side view diagram of a porin, which was the first to come to my mind. Perhaps we should have one? ;) Thanks in advance and sorry for the bother, Fvasconcellos 22:37, 11 March 2007 (UTC)

No problem - I remember intending to make a porin image last time I looked at that article and apparently forgot ;) Beta barrel is now decorated with a porin and an RBP. Yeah, TIM barrels are usually separate from beta-barrels, partly because they're necessarily alpha/beta and partly because a lot of people define beta-barrels as being necessarily antiparallel.
Now a question for you - I put the image you used into the triose phosphate isomerase article, because the structure it had was a side view, which is obviously suboptimal. I rarely use the protbox template (obviously I should, if I'm a maven and all ;) and I don't know how to force the sizing of the image in the protbox. Right now it looks really large compared to most protboxes. Am I template-impaired? Opabinia regalis 02:50, 12 March 2007 (UTC)
Thank you, that's exactly what I had in mind! I have got to get that PyMol :( As for the protboxes, I have the same problem, both with {{Protbox}} and {{Protein}}—see amylase, to which I recently added images which apparently default to 220 or 250px and cannot get any smaller. I'd ping Boris or Arcadian, who, if memory serves, were the main "coders" of Protbox and Infobox Protein respectively. Thanks again for your help, Fvasconcellos 14:15, 12 March 2007 (UTC)
Hi again! Sorry, but I think I may have misled you—I've just checked the {{Protbox}} history, and apparently User:GAThrawn22 was its creator and main editor. I don't know where I got Boris from—I'm sure I've seen his name in related discussions. Either way, I thought you might like to know, and sorry for the brain-freeze. Fvasconcellos 01:26, 13 March 2007 (UTC)
Well sure, after I already left Boris a message... Thanks, I guess I must trust you since I didn't think to look ;) Question posted to the correct user this time. Opabinia regalis 01:40, 13 March 2007 (UTC)
Argh. Bad timing, sorry... I hope I'm right this time ;), at least you can be sure you're not template-impaired...Fvasconcellos 01:48, 13 March 2007 (UTC)
That's good. It's embarrassing to have five eyes and still miss things like template parameters ;) Opabinia regalis 02:46, 13 March 2007 (UTC)
LOL. OK, I'm leaving now, while I still have an... what's the SI unit for self-confidence again? :) Fvasconcellos 03:04, 13 March 2007 (UTC)
I think that would be the egowatt ;) Anyway, now I see amylase at normal size, TIM still at slightly-larger-than-average size, and neprilysin at ginormous size. Has the appearance of these templates changed for you, or should I just give up and blame my browser? Opabinia regalis 00:53, 14 March 2007 (UTC)

(dedenting) Ah yes, the egowatt—I wonder what its lowest submultiple would be :) The amylase page history tells me Arcadian fixed the width parameter—apparently, all it took was removing the "px" appended to the desired width. I've set it to 240 px in neprilysin; does that look good to you? By the way, this issue is also present in {{Drugbox}}: if you leave the | width = parameter blank, it defaults to the image's actual width! I have no idea as to what's going on in {{protbox}}—I never use it, and I don't even know if there is a size parameter. Have you gotten a response from GAThrawn22? You could always ask on the template Talk page. I'd have a look at the code myself, but template syntax is usually over my head. Fvasconcellos 02:00, 14 March 2007 (UTC)

Smallest unit? I like the sound of the picoegowatt. Any smaller and you vanish in a puff of self-deprecation ;) Neprilysin now appears at a sane size to me - I was afraid that huge protease was going to eat my head. And I think I've fixed the protbox - by dumbly copying and pasting the width code from {{protein}} - anyway, that looks right now too. I can't figure out what's up with the drugbox, though; it looks like it already should do the default-width thing? It's embarrassing, since I'm supposed to be a computational biologist and all, but I am template-impaired. Javascript-impaired too, as I found out recently. Uh-oh, ego shrinking... Opabinia regalis 05:25, 14 March 2007 (UTC)
:) I'm glad it worked out then. Yes, drugbox already does the default-width thing, as long as the width parameter is implicit (?), i.e., not in the wiki text. What ungodly resolution are you using? Neprilysin was completely obscuring my screen—even the WP sidebar was gone! And don't get me started on Javascript. I'm completely code-illiterate. On a side note, dop you think this could be used to illustrate ankyrin repeat? Fvasconcellos 12:23, 14 March 2007 (UTC)
Yep, everything seems to be sorted out now. My monitor is a glorious 1920x1200, the highest I could find last time I bought a new computer. It's sad, really; I have an old monitor from the early(ish) days of LCDs at 1024x768 and it's awful to look at now ;) That image looks very nice for ankyrin repeat (amazing all these articles that never got their pictures!), but what's that extra disconnected red line? Opabinia regalis 02:03, 15 March 2007 (UTC)
It is a fragment of the spectrin-binding domain, apparently included in the model to improve solubility (that's what a quick reading of the paper tells me). Should I GIMP it out? I thought of uploading a surface rendering as well, but I'm not sure whether it would be useful to the article. Fvasconcellos 22:26, 15 March 2007 (UTC)
Ah, ok. I'd usually just render it without the extra fragment - definitely take it out to calculate the surface - but it's fine as is if you explain what it is. Actually, showing it with its sidechains might show something about the binding mode. Or maybe that's too specific; whatever you like ;) I think surfaces are nice. Hm, maybe that article needs more content to balance out all these pictures and infoboxes... Opabinia regalis 02:53, 16 March 2007 (UTC)
I think I'll leave it as is then, and amend the caption? I did create a fragment-free version, but haven't uploaded it yet; maybe it won't be necessary. As for the surface, I rendered this yesterday (before reading your comment :) Surfaces aren't my specialty, so I could use some guidance on whether this looks good or not—orientation, style, color (or lack thereof)... What do you think? I don't remember seeing many surface images on WP—one on FKBP if memory serves. And yes, these articles could certainly use some more balance (hint, hint). Fvasconcellos 15:02, 16 March 2007 (UTC)

Oh, all right ;) In retrospect, the colors on the FKBP image are really garishly ugly, aren't they? I think just clarifying in the caption for the cartoon image is a good idea - for the surface, actually, maybe render both as surfaces, in two different colors? Or, different shades, I suppose; I really like the look of the current one. That would be nice to see how the two surfaces interact. Make a pretty picture in the next five days or so (I think that's the rule these days) and you can probably get it on the front page on DYK. Opabinia regalis 02:43, 17 March 2007 (UTC)

Thanks! So FKBP is yours, eh? I don't think it looks garish FWIW. I'll clarify the caption on ankyrin. Do you mean rendering both the repeats and the spectrin-binding domain as surfaces, each in a different shade? My powers of reasoning are slowing down :) Say, DYK would be nice. You seem to be a frequent contributor... Fvasconcellos 03:12, 17 March 2007 (UTC)
Yes, that's what I meant about the surfaces, sorry. The FKBP images were the pre-Pymol days - I remember creating that just after reading The Billion Dollar Molecule (hm, redlink... it's a book about the early days of Vertex Pharmaceuticals, when they were trying to develop a 'better' FKBP binder than FK506. Kind of overwritten, but interesting.). Anyway, I don't really do the DYK thing unless I have a pretty picture, but it's nice to try to get more science people to use it; it's one of the few domains of wikipedia that seems to have more historical stuff than anything else. Opabinia regalis 03:37, 17 March 2007 (UTC)
Will do. I'll submit them for your consideration when I'm done :) Fvasconcellos 15:20, 17 March 2007 (UTC)

Just in case you still remember me, I haven't forgotten, ya know :) I've just been very busy, and creating a nice, appropriate image is somewhat more time consuming than just tagging Talk pages and formatting refs. I guess DYK will have to wait until the next one... Fvasconcellos 14:59, 25 March 2007 (UTC)

Oh, I understand... btw, I stole your 'busy in meatspace' notice yesterday. Just keep it in mind for your next cool article ;) Opabinia regalis 04:38, 26 March 2007 (UTC)

[edit] FA FAQ

Hi Opabinia. (Is there an appropriate diminutive for Opabinia regalis?) I was wondering if you had any further feedback on the suggested FAQ? There's a talk discussion started here. I've seen that we probably agree about "likely to be challenged" but I've wondered if I may have gone to far in the other direction on the FAQ—I absolutely don't want to suggest to general readers that they can't challenge an assertion. I think this could be a useful page, but we need to be very careful how we phrase things. Marskell 19:39, 12 March 2007 (UTC)

[edit] Test of semi-automated generation of taxonomy pages

Hi Opabinia,

How are you? My time with my sister and old friends was wonderful; it's really ego-flattering to be the focus of such affection from their various children. :D I hope I was helpful, too, in taking care of the baby, who was remarkably good-natured and susceptible to waltzes. ;)

As I wrote to Tim, I'm auditioning that nightingale Daisy, who claims to be able to make Wikipedia stubs for arbitrary sets of taxonomy pages. Could you also make suggestions on her output? Here are the first three pages that Daisy made all by herself:

She started with the missing classes of the Archaea, but Daisy is very versatile. :) Once these drafts are perfected, she can craft the missing orders, families, etc. of any branch of the tree of life. Of course, I uploaded the pages for her; I don't think passerines are allowed to have user accounts on Wikipedia, are they? I'm rather daunted by the pywikipedia thing, although I suppose I could try. Thanks muchly for your help, Willow 23:08, 12 March 2007 (UTC)

P.S. Now that I look at the pages myself, I see that Daisy forgot to add the stub template. :( Even nightingales skip a note now and then.

Hey, glad you had a good trip and good to see you back! Now, if leftovers from the Cambrian era can have accounts, I don't see why birds shouldn't.. :) The stubs look nice; I just hope people will find and expand them over time. I noticed that these are all in a redlinked category; is that because the tree of life category system doesn't contain any taxa that we don't currently have articles for, or because the category exists under a different name?
I like Tim's suggestion of importing the references - good way to point people in the right direction for adding more content. Other than that I think the current content looks good. I don't think I have any intelligent suggestions about setting up the pywikipedia framework, since I've only used it once, but presumably you don't want to upload thousands upon thousands of articles ;) If I get a chance I'll download the current version and have a look. Opabinia regalis 01:17, 13 March 2007 (UTC)

Thanks very much! :) I asked a couple of questions on my Talk page and would love to hear your ideas. I'll do the categories tomorrow, and thanks for looking into the scary py-thing. ;) Sweet dreams to me and you, Willow 04:45, 13 March 2007 (UTC)

Hi O,
I know you're busy in "meatspace" ("seafood-space"?) but, if you can spare a moment, I could use some help proofreading the taxonomic journal references, as described on my Talk page — thanks muchly, and good luck to you, Willow 22:08, 20 March 2007 (UTC)
Trying to catch up on natural selection tonight - maybe in the next couple of days if you guys don't run out ;) BTW, since one of the suggestions at the peer review is to reduce the history section, maybe some of your older stuff should be exported to history of evolutionary thought instead?
To answer the below question, there's always http://www.python.org/doc/, which is actually quite good, if a little disorganized. O'Reilly's Learning Python is pretty good, or so I hear, though I guess it's very basic; Programming Python might be a better choice for someone who already knows the simplest stuff. But I do this stuff the disorganized way ;) Opabinia regalis 04:22, 21 March 2007 (UTC)

[edit] Hi; and thanks

Hi O, I just wanted to say "thank you" for writing that Python script; I don't think that I could've done it. I have the feeling that this is going to be good, don't you? The pieces are coming together nicely, thanks to all of our efforts. :) I love feeling part of a well-meaning and wonderfully smart community of editors.

Hunting for another cool card to wiki-send you, Willow 23:12, 16 March 2007 (UTC)

P.S. Oh, could you look over that wickedness again and make any suggestions that occur to you? I'd appreciate your insights. It's getting close to April 1st!

Eh, if you can do C, you can do python. Especially if you do string stuff in C ;) Though I have to say the pywikipedia documentation, such as it is, is not good. I'll take a look at the other stuff 0 it's a bad sign when you run out of time to read the satire, isn't it? Opabinia regalis 05:37, 17 March 2007 (UTC)

Do you know a good book or website where I could learn some more Python? It does seem C-like, so I might be able to learn it, although I'd have to get used to dropping the extra-smiley semicolons. ;)

BTW, I spruced up the historical section of Natural selection a little, but please revert whatever you don't like. The Empedocles quote was actually from Lucretius, who gives an OK summary of the natural selection idea, albeit rather poetically; Lucretius was inspired by Empedocles, but far more sensible. E's theory was wild, even dreamlike; he describes an era when the various organs were only partially assembled (arms without shoulders, eyeballs with no forehead) and went wandering, mating up in random ways, of which only the most successful combinations survived and reproduced. (The literary precedent for "wandering eyes", as it were. ;) Aristotle lampoons Empedocles for the idea of "man-faced oxen" and rejects the notion that Nature can be acausal. Talk to you soon, Willow 15:11, 19 March 2007 (UTC)

[edit] userbox issue

Regarding your statement about the relevance of the userbox issue on Wikipedia:Requests for adminship/RevRagnarok, you may want to take a look at Wikipedia:Requests_for_adminship/Froth. —KNcyu38 (talk • contribs) 02:40, 17 March 2007 (UTC)

Why? Unless you're obliquely making a point about relevance... Opabinia regalis 02:49, 17 March 2007 (UTC)
I just meant to say that almost all oppose votes in Froth's RfA are based on his answer to Q1, which is "just about the weakest and least convincing opposition meme I've ever seen gain traction in an RfA". Much weaker and less convincing, I feel, than the "userbox issue" on RevRagnarok's RfA. Although I have to admit that I feel somewhat personally insulted by that anti-EU userbox, as I also told RevRagnarok on his user page. He doesn't trust the union of states I'm living and believing in (however flawed it may be, compared to the flawless USA), so I feel I cannot trust him with the admin tools. At any rate, I'm not going to support him. —KNcyu38 (talk • contribs) 14:52, 17 March 2007 (UTC)
Hmm, poorly thought-out reasoning for Wikipedia activities vs not trusting a political entity. (Is trusting a political entity ever a good idea?) Glad we've got our priorities straight. Opabinia regalis 05:13, 18 March 2007 (UTC)

[edit] page deleted?

Hi, I'm trying to find out why you (and another admin.) deleted the Nigel Bradbury page. I started it, and it looks asif someone continued after that. We had a lot to say about Nigel, but are new to Wiki and wanted to verify/ check permission before adding much more. Did I do something wrong? As far as I remember, pretty much all I put was that he was the inventor of the Mutator (made by Mutronics : http://www.mutronics.co.uk/). This is FACT, and I am a little worried in case you thought this was not so. I didn't put a link to Mutronic's website in the wiki because I wasn't sure about the rules and stuff. He used to be M.D. but no longer has any contact with them (for about 10yrs). He's done a fair bit of stuff in his lifetime, it was a legitimate link from another page (OOOD), and I would have thought that inventing something like that was wiki-worthy. It is a popular bit of kit in professional recording studios, and has been used by the likes of Madonna. If you complain about verifiability I shall scream and tear my hair out. There has been publicity saying someone else is responsible for the Mutator, but it's not true, and apparently someone (not I) recently added to Mutronics' web site putting the record straight. If I had seen it, I would give you the link. I may look for it later. I see content all the time on wikipedia which is marked as 'source needed' or something. I saw him make the thing, and witnessed all of the early days of setting up the company. How much more reliable does it get? I'm sorry if this was the wrong way to go about asking, but it took me ages to even get this far. -edit: I can't find the stuff I was told was on the website, but I did find a load of BS from Mark Lusadi claiming to be the 'co-creator'. Actually, the thing was already built and he just put money in afterwards. It makes those of us who know the truth very angry when we see these claims- many in printed media- and I did hope to get the gods-honest truth up on wikipedia. HELP!!! Any advice would be welcome. Monalisaa 17:50, 17 March 2007 (UTC)

The entire content of that article was a single unsourced sentence. Please see the speedy deletion criteria, specifically criterion A7, for the minimum content a new article should contain to avoid speedy deletion. It doesn't help that the speedy tag was placed by a user who is a strong defender of new content.
From your post here, it sounds like you should also read our attribution policy if you haven't already, because Wikipedia is not a place for promoting what you believe to be a correction to a misunderstanding. You absolutely will need reliable sources stating that Nigel was the inventor (where reliable requires independence from Nigel himself). Your personal experiences, unless they have been published in a reliable source, are not adequate basis on which to make a claim in an encyclopedia article (otherwise we'd have all sorts of nonsense about UFO abductions and images of Jesus in people's croissants and whatever else). I recommend writing a draft article in your userspace, for example at User:Monalisaa/Nigel Bradbury, and only moving it to the mainspace when you're sure it meets notability and verifiability requirements. Opabinia regalis 18:27, 17 March 2007 (UTC)

ok thanks for the advice and the speedy reply- I was worried that it was a) too short and b) had no references. I may be able to locate sources but not in the near future (stuff published 10yrs ago). As a general point, and not specifically about wiki, I am now quite alarmed about the phenomenon of 'history being written by the winners'. There's not much to be done about this- but if lies are propogated enough, it seems they eventually become 'fact'. Shades of Orwell. I didn't want to get into any 'corrections of misunderstandings', just state simple fact- sorry. But it does make me wonder just how much of what we take as history is pure fabrication...hmmm Monalisaa 19:23, 17 March 2007 (UTC)

[edit] Peer review on cholangiocarcinoma

Thanks much for your considered comments at Wikipedia:Peer review/Cholangiocarcinoma/archive1. Your feedback was very useful. I've gone ahead and tried to address the points you raised. If you have a chance, take another look at the article and see what you think of the changes. I'm likely going to nominate it for featured article status. Thanks again. MastCell Talk 19:02, 20 March 2007 (UTC)

[edit] Government/Norte Chico

Thanks again for the comments on the Norte Chico civilization FAC (still unfortunately under-reviewed). I've added a small note to the Ruth Shady article and replaced "Maritime dietary component" with "seafood." I post here because I thought another set of *'s would be a mess, and because of the government issue, which needs some explanation.

I don't quite know what to do. I am mimicing the source (1491), which specifically notes Mesoamerica separately but does not explain the caveat. There's no intimation in the sources that gov't migrated from Peru to Mexico (and it's not commonsensical); I'd like to point that out but it would actually be OR. At the same time, it would be wrong to note 3 emergences of gov't rather than 2 + maybe 1, because the source doesn't do so... So I'm sort of just stuck repeating an unsatisfactory point.

As a last point, I really love Proud product of the Cambrian explosion :). Marskell 19:05, 21 March 2007 (UTC)

Well, in a sense, we're all products of the Cambrian explosion, right? ;)
That is so strange that the sources don't describe what's going on with Mesoamerica - in the 'traditional' formulation, before Norte Chico was discovered, did people typically say that government arose twice, in Sumer and Mesoamerica? (Also, I could've sworn that China was a separate instance, but that's foggy half-remembered guessing.) I don't know, I just find the if Mesoamerica is included separately very unsatisfying; it sounds like there's more of a story there than I guess there is. But the article's excellent anyway, and I had no idea that this had even been discovered until I read it. Incidentally, what's up with the low number of reviews lately? It's weird to have some nominations with ten obvious objections, and then others that are actually good get no useful response. Opabinia regalis 00:41, 22 March 2007 (UTC)
Another proud product of the Cambrian explosion
Another proud product of the Cambrian explosion
Sure, we're all products of the Cambrian explosion. That's why I liked your note—humble and grand at once (Gould-like, let's say :). My Wiki wanderings often take me to ET pages; some theorists argue that the critical event on this planet was not the emergence of life, which has almost certainly occurred elsewhere, but the Cambrian explosion, which may be unique. (The third candidate for top event in this case is the appearance of Homo sapiens.) The ROM has a little slice of the Burgess Shale I looked at when last home. Fantastic creatures.
On the gov question, I can find sources describing Mesoamerica, but if I try to answer the question of one, two, or three it'll be OR. What did people typically say before? This amateur would have to go into sources of sources for a decent answer. The six cradles (Sumer, Indus, Egypt, China, Peru, Mesoamerica) are canonical, but I'm not sure about "emergences of government." I think the problem in this case is one of "me too." Everybody knows Eurasia/Africa must have at least one emergence of government. Necessarily, so must the Americas (unless you have some kooky idea about Egyptians sailing to Mexico), but because the Americas are often tacked on as an afterthought to Civ discussions the point isn't made properly.
Commonsensically, a migration of government across the isthmus seems unlikely, as government (unlike maize) can't be picked and carried thousands of kilometers. (Note also Jared Diamond's argument about the difficulty in diffusing ideas and tech across degrees of latitude, as opposed to longitude). Thus an argument for two emergences in the Americas is completely sensible. I'm thinking that if anything should be looked at its our page on government—the word "history" doesn't occur once. Marskell 09:04, 22 March 2007 (UTC)
Yikes! Good thing I'm a bit too small to make that dino a good lunch. I hope. I'll just sit down here in the mud for a bit...
Thanks for linking that article - I've vaguely heard of the book but am not really familiar with the theory. Seems a little farfetched, though, to think that axial tilt is a requirement for complex life. But a lot of these discussions seem to implicitly equate 'complex life' with 'Earthlike life', where I want people to think seriously about how to make self-replicating entities in gas giants, or out of what we call 'inorganic' materials. (IIRC someone proposed that the first self-replicating entities on earth were forms of crystalline structure in clay - living clay would be cool.) And it's damn depressing to turn on the TV, watch for five minutes, and think 'these people may just be representative examples of the most intelligent form of life in the galaxy, possibly the universe'.
About governments - I guess we just have to wait for the standard textbooks to catch up then. I'm afraid I don't remember enough of that one world history class I took to know just how under-billed civilization in the Americas really is.
Oh, by the way - while I have never been to the Royal Ontario Museum or seen a Burgess Shale fragment, I did feel compelled to get some of these not too long ago ;) Opabinia regalis 02:09, 24 March 2007 (UTC)
Rare Earth is a polemic; they select only the evidence that emphasizes Earth's rarity and downplay or ignore that which doesn't. But polemics have their uses—it really stirred up the ET debate. Here is a website you might like to track. I do agree with one basic idea: the Cambrian Explosion is more important than the emergence of life because it took 3 billion years for it to occur. It's a sample of one, of course, but it suggests that complexity is in no way a given once the microbes have appeared. Thus, we may have a universe full of bacteria but no other lions and tigers and bears. As for "self-replicating entities in gas giants," Evolving the Alien has just such a thought experiment. I can dig it up and describe how they go about it, if you like. Finally, I should have also linked to my baby (I know, I know, we don't own them). It actually needs an overhaul—my ref formatting decisions were insane.
On the under-billing of the Americas, see this. It was my best book purchase of the last year.
Are the toys for your own idle moments ;)? Marskell 08:55, 24 March 2007 (UTC)
The toys were intended for me, but my cat thinks the whole world exists for her entertainment, especially those portions of the world that are small and made of plastic. So I have to keep them on a tall shelf to keep her away. Strangely, she's recently developed a fascination with the destruction of a large biochemical pathways poster on the wall. (Why, yes, I do have a biochemical pathways poster on my wall.)
It seems like my reading list is in an inflationary phase lately, and you're not helping! ;) 1491 just may be next on the list. Maybe I'm overgeneralizing and maybe I'm just being properly skeptical, but drawing any conclusions other than 'complex life is possible' from our one measly little sample strikes me as fundamentally suspicious, even general conclusions about rates. (I feel compelled to compare to molecular dynamics simulations of protein structure formation - start multiple simulations from slightly different initial conditions and watch some finish in tens of nanoseconds, and some well into the hundreds.) Since much of what I'm familiar with in the thinking about extraterrestrial life is focused on 'intelligent' life, I've also wondered how we would recognize thought processes that occur on very different time scales than our own. If it were possible for something to topologically and functionally duplicate the human brain, except that signals were transmitted on a timescale of minutes to hours, we'd never see the forest for the trees; I doubt any meaningful communication would occur. I'd like to know what they came up with in Evolving the Alien; I suppose I'll have to put that one on the list too.
Broadly, I'd be willing to bet on lots of bacteria-like extraterrestrial organisms, though there may be some latitude in what we're willing to call 'life'. I've always been sympathetic to the notion that intelligent life is not readily seen in the universe because it tends to blow itself up after acquiring a certain technological sophistication, and also to the somewhat related notion that any given planet can support many forms of complex life, but only one intelligent species. Your habitability article is interesting (and very nice, by the way ;) - I can't say I've given much thought to the potential problems of sustaining life in a binary star system, for example. (But it happens all the time in science fiction!) Still not really buying the axial tilt thing, though; given the range of what Earth life can do, I can imagine these problems being relatively surmountable - even the matter of temperatures that hit the boiling and freezing point of the solvent could be escaped. I'm thinking of a prolonged unicellular state that's much more hardy than the complex multicellular form - or even a slime mold-like life cycle. Opabinia regalis 07:00, 25 March 2007 (UTC)
Others agree on axial tilt.
Fermi Paradox has some info on your other comments (another FAC of mine, but actually a sloppy page and given to cruft). It has (or at least had at one point) the suggestion about thought processes of differing timescales. Now, I don't know molecular dynamics simulations from a barndoor, but my commonsensical objection: in a universe where threats can appear in nanoseconds, how is a species going to come anywhere close to our sophistication if they process threats over minutes or hours? Surely "think fast" is a universal rule for intelligent life? Or maybe that's a dummy take on things...
thumb|right|150px|The two suns of Tatooine (tell me if I'm boring you.)
Sci-fi and binary stars. When Luke was mourning his uncle and aunt on Tatooine I recall two stars hanging limpidly in the background... Wait one second...ah yes, our wiki page on the subject notes "the two suns are named Tatoo I & Tatoo II." As a boy, I enjoyed two-thirds of Helliconia ("hard science fiction") but never found the third book in the trilogy...
I'll dig through Evolving the Alien and briefly describe their thought experiment...it had something to do with balloons... Also, Chemical synapse is sitting on FAR. Is it something you could help with? Cheers, Marskell 13:06, 25 March 2007 (UTC)
Ah good, I'm not completely missing the point on the axial tilt - good to know! ;) The slow-thinker thing actually originated from a long... umm, armchair philosophizing session with people who, like me, probably have no particular insight into this problem, and had to fill some idle time... but the idea is surely just as applicable to a hypothetical species that transmits internal messages hundreds of times faster than a human would. Also, what threatens a human may not be a threat to these slow-thinking creatures (I imagined them very large, for whatever reason.)
Anyway, yep, Tatooine was the first one to come to mind - though I was unaware of the names of the stars. I'm very far behind in the Star Wars universe, though I enjoyed some of the books a bit more than they probably deserved... also, I love the word 'limpidly' ;) I noticed chemical synapse on FAR and wondered if I should do something about it, but a) if I don't deal with natural selection soon, it'll never happen; I've been talking about working on it since October, and b) I'm kind of tied up in the real world right now, and not being especially productive lately. So probably not, at least not in the near future, unfortunately. Opabinia regalis 04:53, 26 March 2007 (UTC)
I was going to link you to "speed of thought," but it only goes to a film thriller... I very very vaguely recall a quote from Sagan about how everyone thinks thought moves nearly as fast as light but if you literally represented it, it's about as fast as a donkey walks...
After an hour looking through Evolving the Alien, I was reminded of how much of the book is over my head... Basically they imagine blimps in a Jovian type atmosphere. Molecular machinations at the phase boundary within the gas giant (that's about as competently as I can describe it) form chains which eventually form rings that they call "cyclozygotes"; a double-membrane is formed and "molecular machinery sucks hydrogen from the surrounding ocean [and eventually the ensuing creature] rises like a hot air balloon." Mature blimps drop trillions of tiny packages of genetic material back through the atmosphere to keep the cycle going... I dunno; if, as I'm guessing, you have chemistry or biology degrees, I'm sure you'll be much better able to appreciate it. But buy Rare Earth before Evolving the Alien; it's a call-and-response. If Rare Earth and life-must-be-like-us is too unimaginative, I do wonder about the converse—that because someone can imagine startling means of self-replication, we should assume startling means of self-replication occur elsewhere...
As a last point, I've only been posting these long responses as a healthy diversion from policy debates which are driving me mad. Also because I like talking about aliens. (An interest in ancient civilizations seems to naturally converge with an interest in aliens, as far as I'm concerned...) Marskell 21:42, 26 March 2007 (UTC)
Hmmm, these hot-air-balloon creatures sound interesting... dammit, now I'll have to actually read these books, instead of just saying I will ;) It's fun to think about things that are bigger and more speculative than 'what rotamer state is this amino acid in'. (Yes, my background is in biochemistry, but I really do computational biology. So none of the mess and fuss of an actual lab.)
Long posts about aliens are always welcome here (or, for that matter, ancient civilizations), and are much preferable to 'why did you delete my perfectly good article about my left buttock?!' You have more patience than I for getting involved in the whole ATT mess (yes, I rather like it over here with my head in the sand). In the end, it doesn't really matter all that much; you could write Wikipedia:How to fall off a log (god, I hope that's red) and someone would still find a way to do it wrong. Opabinia regalis 06:34, 27 March 2007 (UTC)

[edit] Barnstar

The Reviewer's Award for Opabinia regalis, for help on Norte Chico civilization and for all of your review work at FAC. Your five eyes are greatly improving the quality of reviews.
The Reviewer's Award for Opabinia regalis, for help on Norte Chico civilization and for all of your review work at FAC. Your five eyes are greatly improving the quality of reviews.

[edit] Orphaned EB site?

Hi O,

Could you look at Encyclopædia Britannica Online and tell me if it should be deleted? I don't know that much about Wikipedia's policies on commercial links and such. I'd appreciate your opinion in any case; thanks! :) Willow 23:10, 23 March 2007 (UTC)

Meh, the current state of that article is crap and I don't see a good reason to have it separate, so I just redirected it to EB. If it does merit its own article, it would've needed to be completely rewritten anyway. Opabinia regalis 02:30, 24 March 2007 (UTC)
Thanks very much for your decisive action on that, which makes a lot of sense. I've now nominated Encyclopædia Britannica for FAC; if you had any time to look it over, it'd be much appreciated! :)
I love the way Spring is returning. I spent a beautiful weekend preparing my garden, cleaning it, removing dead stalks, pruning, turning the soil and working in the compost, etc. Several berry bushes have already broken bud! :) Hoping that seafood-space is treating you well, Willow 01:59, 26 March 2007 (UTC)
Thanks; glad that worked out. I'll take a look at the main article when I get a chance. I saw some crocuses and whatnot (er, that'd be the technical term, right? ;) flowering today. I'm so glad winter's ending; I hate snow - I'd say 'with the fire of a thousand suns', but evidently not, since that would solve the problem altogether. Opabinia regalis 04:56, 26 March 2007 (UTC)

[edit] My RfA

Thank you for support in my unsuccessful RfA. I appreciate the support, and am disappointed on being judged by what in most opinions seem to be the wrong things. Until next time, edit on! And thanks for the wonderful quote! :) — RevRagnarok Talk Contrib 03:31, 24 March 2007 (UTC)

[edit] Cholangiocarcinoma

Thanks for your comments and suggestions regarding the featured-article nomination of cholangiocarcinoma. I've tried to address them as best I can; when you have a chance, take another look and see what you think. MastCell Talk 17:05, 27 March 2007 (UTC)

[edit] Page deleted

Hi there,

Sorry if it isn't the proper way to reach you, but I haven't found any other. I just wanted to know why you deleted the Degree_(project) page? Is "long ad" the reason? If yes, what does it mean (sorry, I'm no native english speaker) ? As I saw the EGEE and Nordugrid project (which are closely related to the Degree project) were there, I thought it would be nice if Degree was there as well, so I'm not sure what I did wrong...

Cheers, Mathieu.

The article was deleted because it read like an advertisement or publicity promotion for the project, without specifying why they were notable or encyclopedic. The speedy deletion criteria - specifically A7 and G11 - apply here. Related articles probably weren't deleted because no one noticed and tagged them, or because their writing is less promotional; I haven't looked at them and don't know if they merit deletion. If you want to work on the degree article to make it appropriate for inclusion in the article space, I can put the text back in your userspace for further work, though removing the promotional tone won't guarantee that it's notable enough. Opabinia regalis 04:55, 28 March 2007 (UTC)
yes please, I'd like to work on it in my userspace and try to improve it. I think projects about computing grids are notable enough to deserve to be on wikipedia, but maybe I should rather make it a part of another general arcticle about computing grids instead of having it on its own page? What do you think? My username: Lejatorn

[edit] Re:Chromosome mutation images and genetic linkage illustration

Re your message on my talk page.

Sure, ill give it a go! Genetic linkage wont be the easiest thing to demonstrate, being a probabilistic event, but should be possible...
lol, forgot to sign - Zephyris Talk 14:49, 28 March 2007 (UTC)

[edit] Metabolism FAC

Hi, O. regalis. Thanks for your help with this. TimVickers 15:30, 30 March 2007 (UTC)

[edit] Equipartition theorem

On another really random whim (well, I was getting bored with proofreading the taxonomic files), I started working on the Equipartition theorem. I wasn't going to bother you when you're so busy, but then I remembered your flying ice cube, and thought maybe that you would enjoy reading this. If you have time, any suggestions would be very welcome. Thanks muchly as always, yours friendly, Willow 16:41, 30 March 2007 (UTC)

P.S. Could you maybe summarize here what I still need to work on for improving Encyclopædia Britannica? It's getting a little confusing for me — thanks! Willow 22:29, 30 March 2007 (UTC)
Equipartition - a quick skim looks good, but the lead could use some cleaning up; it currently reads like there's been an attempt to make it 'accessible' but the result is just hard to follow. There's a lot of repetition of the phrase 'forms of energy' without explanation, which is in that unfortunate middle ground of being both imprecise and unclear to those unfamiliar with the concept. The wikilinking is also a bit much - mass, spring, speed, etc. - for an article whose readers are surely familiar with these basic concepts. The last sentence is a little awkwardly worded, but that's minor.
Thanks for your suggestions, I'm still working on it; we'll see how it turns out. Did you enjoy reading it? It was more for your delight that I sent it, rather than to burden you with yet another wiki-review.
EB - the criticism section still seems too long and too detailed compared to the other sections. It seems a bit odd that the 'awards' section mostly concentrates on one award and doesn't go back before 2001, but I suppose nobody gives out 'good encyclopedia' awards. I would still put the date of Burr's writing and at least which edition he was criticizing in the blockquote; you shouldn't have to click the footnote to find out this is about the 1911 edition, especially since preceding sentences have discussed current problems in keeping up to date. I'm not sure why the abridgment of 'adhesives' falls under the criticism section, since it isn't one of the topics that critics have objected to. The sentence 'The Britannica-appointed contributors are occasionally mistaken or unscientific.' is undoubtedly true, but poorly supported by the example of Gleig (reaching so far back in history to find a misinformed/out of date contributor is awkward, as is the fact that he is introduced here in the present tense as 'chief editor' and not as someone writing centuries ago). The examples of racism and sexism read, to me, like someone's school paper - this would be much better supported with a respected commentator who has made specific claims about racist or sexist content, rather than pulling up 1911 text and expecting the reader to judge just how beyond the pale it was for the time.
In general, I think the perceived slant of this section may partly come from its structure; it's sort of a bunch of miscellaneous criticisms strung together. It would read better if organized chronologically (early editions were criticized for A and B, the 1911 edition was criticized for C, the current edition for D and E...) or more coherently by topic (group criticisms about the structure, the editorial policies, bias/slant/topic choice, etc.) Opabinia regalis 02:54, 3 April 2007 (UTC)
I tried to give the section a topic sentence that laid out the organization of the section, but it got reverted. :( I did succeed in re-arranging the section a bit, and added the more precise time-stamps for Burr and Gleig that you asked for; I agree, they do improve the section! The "Adhesives" clause was removed; it was just there to verify that the EB do es sometimes remove material, a fact that had been contested by another Wikipedian.
The sexism and racism charges are taken directly from Thomas' book; she's the authority who cited the KKK articles and the absence of a biography for Marie Curie, for example. The women typesetters' controversy is from another authority, however.
Wishing you were here, but also that things are going well for you, Willow 21:39, 3 April 2007 (UTC)
Maybe the article's OK now? The Criticism section got shortened considerably this morning, because the Britannica deleted that incorrect material from its open.britannica.com website. Hoping that your seafood-space projects are going — swimmingly, con affetto, Willow 17:15, 5 April 2007 (UTC)

[edit] Thanks for your support.

Dear Opabinia regalis,

Thank you very much for your kind words and supportive comments on my recent RfA. I've been shot down again, so it won't be happening this time. I hope, though, that I can hear from you again next time around - and there definitely will be a next time.

Best wishes,

-- Earle Martin [t/c] 20:51, 31 March 2007 (UTC)

[edit] Just checking?

Hi Opabinia,

I just wanted to make sure you're OK? You're probably just busy — maybe your boss is coming down on you? — but I was feeling a little uneasy and thought I should reach out to you, and let you know that we're sending friendly, supportive vibes your way. :) If you get this message, please reflect the following signal back to me: gnip.

An affectionate worry-wart, Willow 03:20, 8 April 2007 (UTC)

Thank you, and kind wishes. :)
Thank you, and kind wishes. :)
Uh, thanks, didn't mean to give the impression that I'd gone off and died or something ;) Working, traveling, and doing other real-life business. Also, I appreciate your concern, but this is the internet - people come and go all the time. I certainly wouldn't want people actually worrying about me every time I scaled back activity here. Opabinia regalis 07:33, 8 April 2007 (UTC)

Of course, of course; I was just imagining that you might be under stress at work, for which a friendly shout-out is an excellent cure, no? Good luck with all that, and thank you for your message, Willow 11:25, 8 April 2007 (UTC)

[edit] F←EB→A

Hi Opabinia,

Just a little note to let you know that Encyclopædia Britannica reached FA, with your help. Do you remember when you set it all in motion? Your wonderfully detailed comments at FAC helped me both to improve the article and showed me a higher way to feel about the Britannica. I wanted to be good, but was not; your gentle remonstrances made me a better person. Wishing you happiness and success wherever you're wandering, Willow 11:03, 12 April 2007 (UTC)

Belated congratulations! (And don't go blaming me for all of that ;) Opabinia regalis 05:04, 17 April 2007 (UTC)

It's natural that a five-eyed Opabinia would be alert to pitfalls and want to worm her way out of them. ;) But it's also sweet to recollect our shared dreams in the quiet moment after they come true, no? Your "marvellous" has been my companion these past few months, and even now she continues to make me smile — a really, really silly grin. ;) Missing you, but wishing you sharp eyes and quick, umm, paws? to keep everything you're juggling up in the air, Willow 05:35, 17 April 2007 (UTC)

P.S. The garden is coming wonderfully back to life; all my berry bushes have broken bud and made full-fledged leaves. :)

[edit] Mary Wollstonecraft's Original Stories

I would appreciate one of your thoughtful peer reviews on my article about Wollstonecraft's children's book Original Stories from Real Life. It hasn't garnered much attention at peer review yet, I'm afraid. It is not a very long article! Awadewit 02:42, 13 April 2007 (UTC)

I don't have too much time lately, and I can't vouch for the thoughtfulness ;) But I posted a few comments on the peer review page. Opabinia regalis 05:03, 17 April 2007 (UTC)

[edit] Long-term potentiation

Hi there, Opabinia! You made my life a whole lot easier a few months back when you reviewed Long-term potentiation for WP:FAC. I think I've responded to most of your concerns at Wikipedia:Featured article candidates/Long-term potentiation, and was wondering if you'd be interested in reviewing the article again. Your comments would be much appreciated. Thanks! --David Iberri (talk) 22:24, 18 April 2007 (UTC)

[edit] It never rains, but pours...

Hi Opabinia,

If you find yourself with a moment's peace after reviewing long-term potentiation, I would love your impressions and suggestions of equipartition theorem. After your flying ice cube article, I think it's something that you might enjoy! :) Willow 22:41, 18 April 2007 (UTC)

[edit] Some Thoughts Concerning Education

Way back when you peer-reviewed Some Thoughts Concerning Education you suggested that I add more about the reception of the book. Well, I have finally found some more information (on the "eve" (not literally) of the page appearing on the main page). I was wondering if you could take a quick look at the "Reception and legacy" section and tell me what you think. Thanks. Awadewit 03:07, 26 April 2007 (UTC)

[edit] "Oh, that I had power to execute my apprehended wishes..."

...you would be here every day — although I would rather you did what was best for you. :) If you can spare a moment, I would appreciate the awesome concentration of your five eyes on equipartition theorem, which is now a Featured Article candidate, perhaps prematurely. Several wonderful Wikipedians have kindly helped out already, as you might see from the scientific and normal peer reviews, but your insights and expertise are dearly wanted. Hoping that all your projects are coming up roses for you, just as everything is beginning to bloom in my garden, Willow 22:22, 27 April 2007 (UTC)

[edit] Peer review

If you have time in the next few weeks or so, I would appreciate your insightful comments on Sarah Trimmer. It is up for peer review right now. I plan on submitting it for FA (after I finish my current dissertation chapter), so no rush on the peer review. I, on the other hand, must rush on the chapter. Locke is calling me. Awadewit 06:00, 1 May 2007 (UTC)

[edit] Science Collaboration of the month

You voted for Carbon and this article is now the current Science Collaboration of the Month!
Please help to improve it to match the quality of an ideal Wikipedia science article.

NCurse work 21:06, 2 May 2007 (UTC)

[edit] Tree squabble

In the evolution article, on the talk page. Oh, dear God, all over the talk page! TimVickers 04:07, 18 May 2007 (UTC)

USB key? What do you mean? The tree is purely illustrational, I changed the terminal branch lengths to allow the long common names that were damanded on the talk page. The internal branches are still accurate, but this is just an illuatration now, rather than a real tree. TimVickers 04:28, 1 June 2007 (UTC)

I've responded to your comments in the FAC, I hope I have addressed your concerns. TimVickers 18:33, 1 June 2007 (UTC)

Sorry, I'm going to be out of town for a few days; I'll get back to this later in the week. In the meantime you may assume that I trust your modifications ;) Opabinia regalis 04:25, 4 June 2007 (UTC)

[edit] Science Collaboration of the Month

You voted for Carbon and this article is now the current Science Collaboration of the Month!
Please help to improve it to match the quality of an ideal Wikipedia science article.

NCurse work 19:52, 2 June 2007 (UTC)

[edit] My RfA :)

Thank you, Opabinia regalis, for commenting on my RfA, which closed successfully with a tally of 76/0/1! I hope I will meet your expectations, and be sure I will continue trying to be a good editor as well as a good administrator :) If I may be of any assistance to you in the future (or if you see me commit some grievous error :), please drop me a line on my Talk page.

Again, thank you, and happy editing! Fvasconcellos (t·c) 18:38, 10 June 2007 (UTC)

Thank you, Opabinia :) It's a shame you haven't been around that much. I look forward to seeing more of your edits popping up on my watchlist! Fvasconcellos (t·c) 18:38, 10 June 2007 (UTC)

[edit] Thank you

Hi O. regalis, Thank you for your comments at my RfA. I have been long aware of the great work you have been doing and guilty of not getting much into SCOTW, but many of the topics are beyond me. Let me know if I can help. Cheers. Shyamal 03:27, 17 June 2007 (UTC)

[edit] great name!

Can only approve of your name! But I would like to point out that the main article on the Cambrian fossil is in a truly shocking state - I'll revise it if you don't!  :-)

--Grahbudd 15:35, 22 June 2007 (UTC)

Thanks! By all means, go ahead on the article - it's sort of embarrassing that I don't think I've ever edited it. But despite the name, I'm more of a biochemistry person, so I'll leave it in your capable hands. Opabinia regalis 03:00, 23 June 2007 (UTC)

[edit] Alzheimer's disease

I was at a medical conference and heard the head of Alzheimer's education for Mayo Clinic say that the section on biochemistry in the AD wikipedia article on was incredibly well written. He uses it with physicians, med students, and with the public. I know you did a whole bunch of this writing and thought you might want to know that people in high places (along with the rest of us) really value your work. --Chrispounds 13:20, 1 July 2007 (UTC)

Thanks, that's nice to hear! I've been planning recently to start updating the articles on Abeta, APP, etc., when I get the time. It really is a fascinating system biochemically; Abeta is one of my favorite proteins. (Well, I like it on my mind, not in my brain :) Opabinia regalis 05:08, 2 July 2007 (UTC)
The Alzheimer's page has seen more than 500 edits in the last 6 weeks and looks to be on a trajectory to FA status. Just wanted to thank you again for your vast contribution in the earlier stage. The editors are looking at things like cleaning up the lead and standardizing reference formats rather than getting the basics of the biochemistry into the article. We have another neuroscientist who may be adding to your neurochemistry article. --Chrispounds (talk) 20:25, 21 February 2008 (UTC)

[edit] FAC

If you have time, you might want to take a look at the FAC on general relativity. In my opinion, the article is excellent, but the FAC has been hijacked be people against "introductions". Awadewit | talk 08:20, 14 July 2007 (UTC)

[edit] double yikes, Distance matrices in phylogeny

...and so I was innocently trying to bring Maximum parsimony into shape when I noticed a very large Alternatives section that was not directly related to the article & so should be moved out to other articles ... part pf it was about "distance methods"; a huge section... so I created Distance matrices in phylogeny just for a place to ship the excess to.. then, lo and behold, I find that the Computational phylogenetics article has a nice little Distance-matrix methods section... woe is me! Too much stuff in too many different places!

The original situation was untenable, but so is the current one. What should be done, then, o sage of the ages? Thanks, Ling.Nut 10:57, 26 August 2007 (UTC)

Never mind, I'll take care of it! It'll take me a while, and the new article will be a mess in the meantime, but it'll get done. Thanks, and good job on Computational phylogenetics -- Ling.Nut 06:51, 27 August 2007 (UTC)

[edit] Amyloid precursor protein

What are your thoughts about the recent bot additions? --Arcadian 01:46, 11 September 2007 (UTC)

Not a big fan; those expression-pattern graphs aren't even legible at the size at which they're displayed in the article, and the information they contain is unlikely to be directly relevant to anyone looking for an encyclopedia-level treatment of the subject. They should probably be hide-able, or preferably on a separate data page. But last time I checked, this page was being used as a test for the bot, so I assumed the current state was temporary. There's a good chance I'm out of date on that though. Opabinia regalis 01:45, 16 September 2007 (UTC)

[edit] Little update

Sisterly artists :)
Sisterly artists :)

Hi O,

It was nice to see you editing again, if but briefly, and it brought back very nice memories. I hope everything is going well for you in seafood-space, and that Kitty is healthy and happy. Tim has been adopted by a kitten of his own, did you know? There's not much to report on my end. My garden has done wonderfully this year, and I still have my job out there, although I also took on an apprenticeship in sewing. In here I've been flitting from article to article, working up the courage to tackle something complex and difficult like Knitting. I got as far as the Yarn and Tools sections (sort of), but I'm still brooding over its large-scale architecture. I've also made some wonderful new friends, whom I think you would like. Con affetto, Willow 03:01, 2 October 2007 (UTC)

[edit] gene vs protein

Hello, I started a thread over here on the gene vs protein topic, motivated by your recent change to APP. Your comments would be most appreciated... (And also noticed your comment above on the bot edits of APP. That general design has been approved for the full scale bot run, so if you've still got concerns on how that looks/works, please chime in quickly on the ProteinBoxBot's user page.) Cheers, AndrewGNF 16:23, 2 October 2007 (UTC)

[edit] Valerie Daggett

Hi Opabinia,

I kind of stumbled over the article on Valerie Daggett that you started almost a year ago, and it raised some flags regarding WP:NOT and WP:COATRACK. Could you have another look at it and give me your thoughts? Cheers and thanks, pedro gonnet - talk - 31.10.2007 08:34

Sorry, I'm not sure what you're referring to, unless you don't think the DOE grant is notable. Maybe bio articles are being construed more narrowly these days; I haven't really kept up. Opabinia regalis 03:53, 1 November 2007 (UTC)
The problem regarding WP:COATRACK is that the article has only one sentence on Prof. Daggett herself and the rest is all about the "dynameomics" project. The project may be a great thing and DOE-Grants are pretty good too, but this is an article on Prof. Daggett... Can you add or remove some information to make it more about her and less about the project? If not, maybe you could move it to an article on Dnaemeomics? Cheers, pedro gonnet - talk - 01.11.2007 09:24

[edit] Your 16 Oct. 2006: Conformational/mixing/Shannon entropy. Thermodynamic entropy.

Discouraged by non-scientists in WP writing about entropy after mid 10-06, I did not look at WP again as a contributor until now. Thanks so much for your 16 Oct. 2006 note. It raises questions that are specifically dealt with in my September 2007 JChemEduc article "Configurational Entropy Revisited" [1]. For clarity, in dealing with several issues, I have inserted numbers in your note:

"... I'm not sure that energy dispersal is a useful analogy (1) in conformational entropy (2) due to the additional effect of particle dispersal (3) (somewhat like the entropy of mixing case (4), although it is probably useful in explaining "where the entropy goes" when a protein folds. Still, I think it would be a very strained analogy to describe Shannon entropy (5) as energy dispersal :) Opabinia regalis 03:25, 16 October 2006 (UTC)"

[First, an insert: Oxonian Peter Atkins, author of the worldwide best selling physical chemistry text for at least 20 years, in his latest (8th) edition, has deleted 24 of the instances of describing entropy as "disorder" in previous editions and instead says "...entropy ...is a measure of the energy dispersed in a process...". Of course, I can not claim to have influenced Atkins' thinking, but his confirmation of the wisdom of so many US texts changing to this interpretation is significant.]

(1) Energy dispersal, as a measure of entropy change, is conceptual AND quantitative. (I am sure you did not mean 'analogy' as a 'put down' but it can be so interpreted.) (2) and (3) Particles never disperse without energy being involved; in contrast, energy disperses spontaneously if not hindered. This "particles disperse" without energy -- a denial of kinetic molecular theory -- is the fallacy in a minority of US chemistry texts that "Configurational [conformational] Entropy Revisited" was written to resolve. Conform/config/positional entropy values are all based on statistical counting of possible locations in phase space. HOWEVER, each such location is also characterized by specific momentum coordinates! Thus,(and the details of proof are complex but forthcoming in an important article) the traditional chemical and biochemical "counts" of positions on which you and I, for years, have depended are actually also counts of energy arrangements - but those arrangements are microstates, not static locations.

(This is what lies behind -- perhaps/probably without the authors' realization -- a dozen or more authors' texts when they show "the greater probability of particles becoming more spread out in more 'boxes'". (How do the particles get there? How are they behaving in those boxes. Devoid of energy at kT?? It is obvious, is it not, when you ask those simple questions that the energy accompanying and causing any motion/change of location has become dispersed?)

(4) The entropy of mixing? This is no 'separate case'. Whether two moles of gases mixing or a few mg of a water-soluble protein in a liter of water, what has happened is that both constituents have additional positions in space to occupy -- and that means additional energy distributions/dispersal in those 'positions'. No new phenomenon, as shown by the simple formula for calculating entropy of "mixing" in any phys chem text (Actually, it can be thought of by students as the entropy of "separation" of particles."

(5) Thermodynamic entropy theory and practice did very well from 1865 to 1948 (even without chemists thinking about what 'entropy' MEANT separate from their calculations!) Von Neumann's bad joke to Shannon to call his H function 'entropy" has caused tens of thousands (probably millions, in my opinion) of hours of wasted time and argument. My statements in "Config. Entropy Revisited" were called "both intellectually enlighening and compelling" by a hard-nosed Reviewer of the ms. (the best accolade I have ever received for a ms. suggestion). I urge you to consider them. I think you have the power to see where energy dispersal is clearly involved in your many many biochem phenomena -- and where that involvement is vague but perhaps can be experimentally tested. This is no small suggestion.

I apologize for having gone on so long, but your note indeed corresponded to much that is in my publication. I hope the article and this response will clear up some of the common misconceptions about thermodynamic entropy. I would be glad to continue communication via email and do not fear listing my email address because I have a very effective spam filter if some aberrant WK reader should pick it up: flambert@att.net . FrankLambert 23:19, 11 November 2007 (UTC)

[edit] Bacteriophage

I see you have made some previous comments on pages on this subject. I have left a relevant note at User talk:Sabedon. DGG (talk) 17:41, 23 November 2007 (UTC)

[edit] Wikipedia:Featured article review/RNA interference

Just a note that I've put this up for Featured article review - not because it's by any means awful, but because I really do think we could explain it to laymen better than we currently do, and this seemed a good way to get discussion on how to do this and draw people in. Adam Cuerden talk 17:13, 1 December 2007 (UTC)

Thanks. Can you point out what in the article is poorly explained to someone who has the necessary background (minimally, knowing what proteins are made of, what transcription and translation are, etc.)? The original comment on the talk page has some specifics, but if explaining what eukaryotes are is what he had in mind, then I disagree that there's much to be done here. Opabinia regalis (talk) 05:17, 11 December 2007 (UTC)

[edit] IBA

Hi Opabinia regalis,

I noticed this edit here - can you tell me where this is stated? Also what do you think of the article title for the proffesional IBA article? regards --Vintagekits (talk) 14:04, 14 December 2007 (UTC)

I know nothing at all about the subject and was just fulfilling a move request that wasn't objected to at the time (almost a year ago, no less). If that request was wrong, the title has changed, etc, feel free to move it to a more appropriate place. Opabinia regalis (talk) 07:00, 15 December 2007 (UTC)
Cheers for the feedback, I'll look into it. Also about your statement - "don't disambig the most common usage" - where does it say that - its just I had that argument with someone before.--Vintagekits (talk) 00:59, 16 December 2007 (UTC)
See Wikipedia:Disambiguation#Primary_topic. Opabinia regalis (talk) 06:03, 23 December 2007 (UTC)

[edit] NAD FAC comments

Hi there, thanks for your comments. Opinions on his article seem very divergent, could you look over some of the other reviewer's comments and see if you agree with their criticisms? Tim Vickers (talk) 23:41, 15 December 2007 (UTC)

Hi again, still struggling through this FAC. Would it be poossible for you to change your commnet into a support or oppose? Tim Vickers (talk) 10:50, 21 December 2007 (UTC)

[edit] Introduction evolution

Hey O,

I was wondering if you'd be willing to review Introduction to evolution scientifically. I remember the fun we had at natural selection, and I really think your insights are needed here. Could you please take the time to help out? If you didn't want anyone to see your comments directly, you could send them to me or to Tim by e-mail; you wouldn't have to do any editing yourself. Happy New Year and salicine salutations to the Eye in Wikipedia, Willow (talk) 17:06, 8 January 2008 (UTC)

PS. Hi to Kitty as well! :) WillowW (talk • contribs) 17:07, 8 January 2008 (UTC)

[edit] Happy (Old) New Year!

Two weeks too late, you say? Not in the Julian calendar!
Here's hoping the new year brings you nothing but the best ;) Fvasconcellos (t·c) 18:06, 4 January 2008 (UTC)
The design of this almost completely impersonal (yet hopefully uplifting) message was ripped from Riana (talk · contribs)


[edit] Puddingstone

I hope you don't mind that I made a minor edit to your Puddingstone draft essay. If you don't like my edit, I will not be offended if you revert me. Billscottbob (talk) 04:44, 19 January 2008 (UTC)

[edit] Informing past contributors of new TFD for Template:Maintained

As you were a contributor in the last TFD, I am letting you know that {{Maintained}} is again up for deletion. Please review the current version of the template and discuss it at the TFD. Thanks! — BRIAN0918 • 2008-01-30 17:48Z

[edit] Protein images

I mentioned your featured picture as an example of using public domain data to generate a free image of a protein. Would you be able to comment at Wikipedia:Media copyright questions#Protein Data Bank? Thanks. May have been archived by the time you see this. Carcharoth (talk) 00:40, 20 February 2008 (UTC)