User talk:Opabinia regalis/Archive 2

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Protein and Gene entries[edit]

Hey Opabinia -- (love your user name) Anyway, it seems to me the protein and gene entries are ripe for revision ... They are in extreme need of references. Given your expertise, perhaps you could easily slap some in? Just a suggestion Satyrium 01:13, 16 August 2006 (UTC)

You're right, both of those could use some attention. Thanks for giving me a poke, I'll see what I can do. (Ditto on the username. At least yours has a classification :) Opabinia regalis 02:21, 16 August 2006 (UTC)
Also, I just learned my new fact of the day. Of all the weird things to name your band - Protein? Opabinia regalis 02:23, 16 August 2006 (UTC)

Phi value analysis[edit]

Hi.. sure would love to contribute to the area of protein folding and related material. These are my first few days in the wiki-world, so still learning things along the way. I realized that my para on 'errors associated with phi-values' was a little 'confrontative'. Thanks for editing it. I have made a couple of minor corrections to your edit. SirHaddock 15:01, 26 August 2006 (UTC)

Protein tissue[edit]

Proposed for deletion and I think you'll agree. Please weigh in at Talk:protein tissue. The Crow 18:02, 26 August 2006 (UTC)

x% homology[edit]

I ran into the statement "as little as 16% homology" on the Globin_fold page. I don't have the references right now but I believe this usage is not correct. Homology is a qualitative state. If two sequences are judged homologous we mean that the genes are related by descent. What you mean to say is that there is X% similarity or identity between sequences. If you want me to document this lemme know. Telliott 14:01, 28 August 2006 (UTC)

Wikipedia:Requests for adminship/Netsnipe[edit]

I've only realised very recently that IE doesn't like superscripts inside <span> tags. I use Firefox on Linux hence the blissful ignorance of a standards compliant web browser. Does my new superscript-less signature render OK in your browser? --  Netsnipe  ►  03:54, 29 August 2006 (UTC)

I'm actually also using Firefox and, while I like the new version better, I didn't have problems rendering the old one. I just think altering the text background is distracting and can be hard to read. Thanks for being so responsive, though; I'll clarify my comments. Opabinia regalis 04:57, 29 August 2006 (UTC)

Molecular and Cellular Biology Wikiproject Newsletter![edit]

We have a new newsletter!
As you've no doubt noticed, there's a new Molecular and Cellular Biology Wikiproject newsletter, which will be sent out about once a month to all WP:MCB members. This newsletter is designed to perform two equally important functions. Firstly (and obviously, perhaps) it will serve to inform the members of the MCB project of such things as important discussions, votes, and article improvement drives. Secondly, and perhaps more importantly, the periodic correspondance will hopefully encourage a greater level of participation from the MCB community by acting as a gentle reminder of many of the the interesting tasks that are awaiting completion. If you prefer to receive this newsletter in the form of a link, or not receive it at all, you can add your name at Wikipedia:WikiProject Molecular and Cellular Biology/Newsletter/Opt Out List.
New project feature: MCB Article Improvement Drive
Have any pet MCB subjects that you think need attention? Have you been longing to be part of a team of like-minded editors working toward a common goal? If so, the MCB Article Improvement Drive is for you! On the first of every month a new article is selected by the MCB with the goal of promoting it to good article status. Make your nominations and cast your votes now, because the first article will be chosen on September 1!
In an effort to organize and motivate the MCB activities, it has recently been proposed that a member of the MCB project take the role of "director", who would be responsible for the administrative side of the MCB project, including but not limited to coordinating recruiting efforts, spamming the newsletter, and maintaining the Article Improvement Drive and MCB Portal. A special discussion/vote page has been created for this proposal, and the vote will run until 23:59, 10 September 2006 (UTC), unless the community decides otherwise.
Odds and ends: what else you got?
Signed...
ClockworkSoul
06:39, Sunday August 27, 2006 (UTC)
If you wish to opt out of having the newsletter posted on your talk page in the future, you may add yourself to the opt out list
Newsletter concept and layout blatantly "borrowed" from the Esperanza newsletter
.

My RfA[edit]

Thanks!
AMule.png

Thank you very much for voting on my recent Request for Adminship. The request was ultimately unsuccessful - which wasn't entirely surprising - and so I'll be taking special care to address the concerns raised by the opposing !voters before running again. If you have any feedback for me, please don't hesitate to leave it at my talk page. Thanks!

-- RandyWang (chat/patch) 13:41, 29 August 2006 (UTC)

Denatured protein[edit]

I am having some problems with the referencing .. can u help me out with it?? check Denaturation midpoint,Denatured protein and Chevron plot.SirHaddock 18:11, 29 August 2006 (UTC)

Hi, SirHaddock, welcome to Wikipedia! It's great to find other protein enthusiasts :D I was working on Equilibrium unfolding today, and dug up a few references that might be helpful to you on Denaturation midpoint, particularly the first one by Nick Pace (1975).
Thanks Willow. I am new to the wiki-world. I just added the above mentioned articles and I had problems in editing the references section as it was giving some strange results. Maybe you can help me out in it. Well check out my additions and maybe we can merge it together. I almost started writing the section you just wrote. Anyways looks like we need to split things up so that we do not end up writing the same thing.SirHaddock 21:21, 29 August 2006 (UTC)
Looks like you fixed it, SirHaddock; I don't see any problems with those articles. I did make some minor clarifications to chevron plot including adding names to the ref tags, but they seemed to be working fine.
Hi, SirHaddock, thanks very much for the corrections to equilibrium unfolding; I adjusted the definition of K_{eq} to make the signs, etc. work out. It's great that we're developing a community of protein folders here; it's a cool topic! :) But I'm a relative newbie here, too, so I don't know how everything works, especially the referencing — I just list the references and hope that some nice Wiki-gnome will format them. Looking forward to seeing your future edits, Willow 15:36, 30 August 2006 (UTC)

MCB assessment[edit]

Hi O! You've probably already noticed, but there's now a mechanism for making a molecular biology worklist using the MathBot. I took a shot at assessing a few articles on their respective Talk pages, particularly the structural ones, but I'd appreciate your opinion — too harsh? too nice? Hi to k, Willow 19:50, 29 August 2006 (UTC)

Looks good. I didn't know until looking through this just how bad some of the cell bio articles are. It does seem like there's some ambiguity between start-class and stub-class, probably due to inconsistent stub tagging. 3 10 helix is tagged as a stub but is more complete than the start-class EF hand (which I seem not to have ever made an image for), and beta helix is in the start category but tagged as a stub. Also, it's probably selection bias in what gets assessed first, but we seem to have a high proportion of top- or high-importance articles. Opabinia regalis 02:02, 30 August 2006 (UTC)

Thanks very much for taking the time to look over the assessments! I'm very glad that the list seems top-heavy by importance; I was worried that editors might think that the assessments of importance were too low, e.g., PCR was rated as "Mid-importance". Everyone has their own best-beloved article, and receiving a "Low-importance" rating might sting, although (as I understand it) that means only that the article is too technical for most readers, and not essential for high-school students and freshlings to learn.

It's not only the cell-bio articles that need major work; biochemistry and structural biology are hurting badly as well. Check out Lipid (which got reviewed by Nature last December) and Fibrous protein — oh, the horror! ;) Seriously, it's daunting; hopefully, some experts will emerge from the woodwork and bail us out! Willow 14:38, 30 August 2006 (UTC)

Hmm, hopefully people would be more bothered by a low quality rating than a low importance one? Personally, I like working on the more technical and hence lower-importance articles better (hence the badness of some of these fundamental topics is kind of depressing :)
Does it seem to you that there aren't enough "bins" to sort articles into? With FA and GA as independent processes, we have no way of saying "minor but nontrivial work needed" - ie, neither "complete" and thus A-class nor in need of "considerable editing" and thus B-class. This seems to be the standard scale, but I'm surprised at that division. Seems like B will be a very diverse category. Opabinia regalis 03:03, 31 August 2006 (UTC)

I totally agree about the number of bins. I don't feel qualified to rate an article above a "B"; I merely copied over the existing FA, A and GA assessments. I wish there were two extra ratings: one between Stub and Start, and another between Start and B. There were several articles that had a few paragraphs about their topic, but didn't really merit a Start assessment and, similarly, several articles that didn't really deserve a B rating, but were significantly better than a Start.

On a diferent topic, my experience at Photon has set me brooding. Do you think that we as a community could come up with a standard set of questions that should be considered to make a biochemistry article "complete", e.g.,

  • biological/cellular function
  • activity (what does it do?) and passivity (what is done to it?)
  • synthesis/expression, modification and degradation
  • what does it bind to?
  • cellular location/transport process
  • biochemical pathways/biological processes involved
  • Close relatives, homologs

along with subquestions for each of these, such as

    • regulation
    • energy source/spontaneous
    • what inhibits/activates?
    • duration/timing
    • history of discovery

It might be useful to have some kind of checklist for editors to help gauge how complete an article is. What do you think? It's more of a thought for a thought. Willow 15:15, 31 August 2006 (UTC)

The outline looks good for protein/complex articles. Hope you don't mind, I copied these to the MCB proposals talk page to continue discussing the article assessments in a more accessible place. Opabinia regalis 04:01, 1 September 2006 (UTC)

Thanks for reviewing Enzyme[edit]

Hi there. Thanks for having a look at this article. I'm trying to reach consensus on the FA nomination talk page, did you have any other thoughts or suggestions? TimVickers 15:24, 30 August 2006 (UTC)

Thanks for reminding me. Replied over there. Opabinia regalis 03:04, 31 August 2006 (UTC)

This month's WP:MCB Article Improvement Drive article[edit]

ClockworkSoul 22:54, 4 September 2006 (UTC)

FYI[edit]

Re: your comment at Wikipedia talk:Expert Retention

These problems have been discussed at length for years off an on in such public venues as Wikipedia:Village pump there is nothing new about them. --DV8 2XL 00:57, 10 September 2006 (UTC)

Of course they're not new; you're describing a perennial problem, and substantively similar complaints been discussed at length on Usenet and in pretty much every forum that's ever been disrupted by cranks. That doesn't mean there isn't value is aggregating these observations in one place (not a transient one like the village pump) and giving the exopedians a chance to stumble across it. The subject-matter experts who are mildly irked but not yet fully disgruntled would probably support some of your proposed changes but are unlikely to participate in the proposal process. It would be a shame if the organized effort you and others have initiated were to fall apart out of plain lack of time to gain momentum. Opabinia regalis 01:24, 10 September 2006 (UTC)

Nuclear transport[edit]

In the cell nucleus article you added some info re. transport without a source stated. Some of the info I wasn't sure about, (although it should be noted I'm reffering to a '96 review):

  • "Importins bind their cargo in the cytoplasm and pass through the nuclear pore, after which an interaction with the protein-GTP complex Ran GTPase induces a conformational change in the importin that causes it to dissociate from the cargo."
    • I thought the Ran hydrolyzes the GTP in order allow the cargo-importin to cross the NPC
    • However if the above is correct, I'm not sure what causes the cargo release
  • The resulting complex of importin and Ran-GTP complex then returns to the cytoplasm [...]
    • Do you mean one complex consisting of "importin + Ran-GTPase"? I'm under the impression that they don't associate until, (in the cytosol), the importin binds the cargo.

Do you have any source you could recommend for the above issue?

Cheers. ShaiM 14:07, 11 September 2006 (UTC)

Sorry, the whole section roughly follows the Lodish text, but I didn't include as many footnotes as I should've because it felt kind of redundant after a while. I went back and added a couple of citations. On your first point, I think you might be thinking of the Ran-GTP-GEF interaction? Ran-GTP is moved from the nucleus to the cytoplasm, where it hydrolyzes GTP due to the interaction with GEF. Then the Ran-GDP complex moves back to the cytoplasm where the GAP interaction causes it to re-bind GTP, which is the state in which it induces the conformational change that releases the cargo. (This is why we really need a diagram.)
I think your second point is about the same question - the importin-Ran-GTP complex goes from the nucleus to the cytoplasm as a unit and then falls apart due to the interaction with GAP, which restores Ran to its GTP-bound state. It's not clear to me whether the Ran-GDP actually associates with, or just is just transported with, the the importin-cargo complex. The Lodish book implies that it's not a direct association but it's obviously not the most current possible source. Opabinia regalis 01:29, 12 September 2006 (UTC)

Yeah, that cleared things up for me. I was wondering about Ran GTPase, is there such a protein? It is more correct to say that the protein Ran is a member of the Ras-related GTPase superfamily and forms a complex RanGTP. Unless you've seen it refered to as Ran-GTPase, I don't think the article should. ShaiM 09:45, 12 September 2006 (UTC)

Well, GO references Ran GTPase, so I don't think it's that bad of a name. You're right that it's more of an abbreviation than anything, though - whatever you think would be clearer is fine with me. Opabinia regalis 13:05, 12 September 2006 (UTC)

In-depth review of Photon[edit]

Hi, O, you're a gem! Thanks so much for your in-depth review of Photon; it's amazing what you don't see if you look too carefully. ;) You and Peta hit the nail on the head, although I'm afraid that it will take serious time and effort to write a good lead and to fix the more cringe-worthy gaps in logic/flow. :( There's no rest for the wicked, indeed. ;) Willow 15:02, 13 September 2006 (UTC)

No problem; glad to see so much effort put into explaining a challenging subject well. (Looks like it's coming along nicely, btw.) Opabinia regalis 04:23, 15 September 2006 (UTC)

Arbcom appeal[edit]

I have launched a second appeal against the article ban, and have quoted your opinions in the statement of case based on a contribution of yours on the Administrators' Noticeboard. Just wanted to alert you in case I was quoting you out of context. David | Talk 19:57, 16 September 2006 (UTC)

FA nomination Enzyme inhibitor[edit]

Hi there. I was impressed with the thoroughness of your review of Enzyme during that page's FA process and was wondering if you might consider having a look at this nomination. Thank you. TimVickers 20:28, 17 September 2006 (UTC)

Thank you for your feedback, your suggestions have greatly improved this article. TimVickers 21:59, 18 September 2006 (UTC)

Molecular and Cellular Biology WikiProject Votes[edit]

Nuvola apps kcmpartitions.png The Molecular and Cellular Biology WikiProject has recently opened two surveys that will help to decide the direction of the project. First, nominations are currently being accepted for the position of coordinator of the project. Second, votes and additional suggestions for the official title of that position are also being taken. As a member of the project, we hope that you'll drop by and voice your opinion. – ClockworkSoul 03:53, 18 September 2006 (UTC)

Hydrogen FA[edit]

Thanks for responding to the queries. - Samsara (talkcontribs) 19:02, 18 September 2006 (UTC)

No problem. I'd been meaning to get back and fix those citations, but got distracted and forgot. Opabinia regalis 03:19, 19 September 2006 (UTC)

My RFA[edit]

I have so many article namespace edits, 2000 under ForestH2 and more under Sugarpine. Sugarpine t/c 01:14, 21 September 2006 (UTC)

But both accounts have many more user talk than mainspace edits - your current one, over twice as many. Your mainspace contributions are substantially vandalism reversions and other minor changes, and to be honest I'd like to see more than maintenance of a list of TV episodes as your most notable contributions. Sorry, you may have the raw edit count but you don't seem to have the necessary encyclopedia experience yet. Opabinia regalis 01:44, 21 September 2006 (UTC)

Wikipedia:Articles for deletion/Allen High School (Allen, Texas) (second nomination)[edit]

Are you sure you didn't forget to post a vote with that comment? - Mgm|(talk) 08:57, 22 September 2006 (UTC)

Nishkid64's RfA thanks[edit]

Mad scientist.svg Thank you very much for participating in my RfA, which closed successfully earlier today with a result of (60/9/4). Although, I encountered a few problems in my RfA, I have peacefully resolved my conflicts and made amends with the people involved. If you have any further questions or suggestions, feel free talk to me. I hope I will live up to your expectations. --Nishkid64 22:14, 26 September 2006 (UTC)

Enzyme kinetics[edit]

Thank you for your input on this article, if you have any more comments or suggestions, it is up for FA candidacy and the discussion page is here. Thank you. TimVickers 20:31, 28 September 2006 (UTC)

Enzyme kinetics has now been made a FA. Thank you for all your efforts. TimVickers 23:25, 9 October 2006 (UTC)

Structural images[edit]

I use SwissPDB viewer which has model-building and alignment functions built in. TimVickers 02:27, 30 September 2006 (UTC)

DNA Clamp[edit]

Can you re-render your DND clamp picture much larger than it is now? I'd like to nominate it to be a Wikipedia:Featured picture -Ravedave (help name my baby) 16:09, 30 September 2006 (UTC)

Sure, thanks. How big do you need it? Opabinia regalis 21:35, 30 September 2006 (UTC)
AS big as you can make it? I noticed there is a bit of anti-aliasing, so making the image mega large then scaling it back might get rid of it. So I am hoping for a final resolution around 1200x1200 maybe? -Ravedave (help name my baby) 21:44, 30 September 2006 (UTC)
I uploaded a new version Image:1axc.png at 1100x1199, rendered with slight antialiasing this time to clean it up against the white background. Is that better? (It isn't intensive to render, so it can be pretty much arbitrarily large, but eventually the file size will be too big.) Opabinia regalis 00:06, 1 October 2006 (UTC)
Thanks, I have nominated it here: Wikipedia:Featured_picture_candidates/DNAClamp. One user is askign for "labels" but I am not sure what could be labled in the picture. Are there labels that could be added? -Ravedave (help name my baby) 04:47, 3 October 2006 (UTC)
I'll respond there. Thanks; I never really wander into the images area here and wouldn't have thought to nominate it. All credit goes to the particularly photogenic protein :) Opabinia regalis 04:51, 3 October 2006 (UTC)
There is another question there that is beyond what I understand about it. Thanks -Ravedave (help name my baby) 14:26, 3 October 2006 (UTC)

College-Ready Math-Science School[edit]

The article about College-Ready Math-Science School may have been unclear about when the school opened, but I edited the article to make it clear that the school is already open, albeit at a temporary location. It will move to the groups of the university in 2007. Could you please take another look at Wikipedia:Articles for deletion/College-Ready Math-Science School ? --TruthbringerToronto (Talk | contribs) 06:49, 2 October 2006 (UTC)

Done. I still don't see what could possibly be notable about this, though. Opabinia regalis 00:04, 3 October 2006 (UTC)

Review[edit]

Hi, if you've got some time to spare from hard sciene, I was hpoing you'd give me some feedback on the biography I've written on Frank Macfarlane Burnet. Thanks. --Peta 10:13, 2 October 2006 (UTC)

Looks very nice! I'll give it a more thorough reading later tonight, but it looks good at first glance. Opabinia regalis 00:08, 3 October 2006 (UTC)
Thanks for the once over; I've made most of the suggested changes.--Peta 00:42, 4 October 2006 (UTC)

Irony[edit]

Mello and Fire win Nobel prize. LOL ;) David D. (Talk) 20:11, 2 October 2006 (UTC)

I'm actually surprised that one of the plant people or Victor Ambros were not included. i suspect they decided to honour the more therapeutic side of the phenomena rather than the basic research on the phenomena. David D. (Talk) 20:15, 2 October 2006 (UTC)
I spoke to soon. Just saw this quote in the NY Times
Was it unfair for plant biologists who laid the basis for the new field to be excluded from the Nobel prize? “You have to say they had their chance, and yes it was interesting biology, but they didn’t trace it to double-stranded RNA,” Dr. Cech said. “The field exploded after the Fire and Mello paper.”
Wow, I'm amazed Tom Cech had the nerve to say this. It is completely wrong. I believe this will be viewed as a very large controversy and an example of the ignorance that most animil biologists have of plant research. Not to mention that this Nobel prize was pushed through with unprecedented speed. It will be interesting to see how it plays out. David D. (Talk) 20:26, 2 October 2006 (UTC)
Sorry to harp on this but i found an interesting paragraph from a review that is an external link in the RNAi page. The link is to Planting the Seeds of a New Paradigm, a PLoS primer on plant biologists and the understanding of RNAi. To quote from the article:
To recap: by 1998—the year in which RNAi was reported—plant scientists had documented sequence-specific RNA degradation (PTGS), sequence-specific DNA methylation that triggered TGS, and RNA-directed DNA methylation. They had also proposed models for PTGS involving dsRNA (Lindbo et al. 1993; Metzlaff et al. 1997), small RNAs, and RDR (Lindbo et al. 1993).
RNAi was discovered in experiments designed to compare the silencing activity of single-stranded RNAs (ssRNAs) (antisense or sense) with their dsRNA hybrid. While only marginal silencing of a target gene was achieved after injecting worms with the individual strands, injection of a sense–antisense mixture resulted in potent and specific silencing (Fire et al. 1998).
I wonder who will be the first person to be sending these papers to Tom Cech? David D. (Talk) 20:37, 2 October 2006 (UTC)


Heh, perfect timing :) I was also very surprised by this announcement just because it's so quick. This would make more sense if there had been major therapeutic advances with dsRNA already, but as it stands it seems a bit premature. When Brenner, Horvitz, and Sulston won it was something like forty years after the original work (though that was pretty overdue IMO).

Cech seems to have planted his foot in his mouth pretty thoroughly, especially since dsRNA wasn't really even expected to do anything in C. elegans when the work began. I guess I'd never read that link in detail though (or I'm contributing to the anti-plant bias :) - I didn't realize dsRNA had been proposed in plant silencing. To be fair though, it isn't really a well-developed hypothesis in the Lindbo paper. Opabinia regalis 01:47, 3 October 2006 (UTC)

There is no doubt that the Lindbo plant paper was not very sophisticated. However, if i remember correctly, the Balcaumbe papers had already identified the small RNA's that are the product of the dicer complex. The RNA dependent reverse transcription had already been proposed too, if not identified. I am sure (hope) the Nobel committee have a rational reason for giving it to Fire and Mello alone but it is certainly not due to the reasons Cech opined. I bet the UMASS poster is having a bad day today. David D. (Talk) 01:55, 3 October 2006 (UTC)
I remembered incorrectly, the Baulcombe papers were 1999 and 2000, however, the hypothesis for dsRNA was well estabished if not nailed. I guess that is the emphasis that the Nobel committee is going with, absolute proof of dsRNA rather than a working model. See these paper for historical context.
Dalmay, T., Hamilton, A.J., Rudd, S., Angell, S., and Baulcombe, D.C. (2000). An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell 101, 543-553.
Hamilton, A.J., and Baulcombe, D.C. (1999). A species of small antisense RNA in post-transcriptional gene silencing in plants. Science 286, 950-952.
David D. (Talk) 02:02, 3 October 2006 (UTC)
Thanks for the refs; I'm running out of time tonight but I'd like to read them when I get a chance. I imagine you're right that the therapeutic potential was a major motivating factor for focusing on the animal work. I do remember hearing that the attribution of the discovery to Mello and Fire was largely a "gentleman's agreement" because there were so many other groups that had contributed small pieces of the puzzle, but they don't award Nobels based on rumors :) Opabinia regalis 05:19, 3 October 2006 (UTC)

This month's WP:MCB Article Improvement Drive article[edit]

ClockworkSoul 21:07, 2 October 2006 (UTC)

Thanks, and hi again[edit]

I came back after another family trip and found your really great letter, which cheered me up a lot and made me think of that Goethe quote about the "peopled garden". BTW, knitting is the only thing I'm really good at; everything else is being lucky in remembered trivia and quadrivia. ;)

I also saw that you were getting much worse personal attacks than I've ever seen; I hope that person has gone away for good! :(

Another happy event is that Photon got promoted to FA status while I was away. It's strange, but I didn't get all jubilant; I felt instead like I was carrying a glowing coal within, warm and satisfied. Anyway, I just wanted to thank you for all your help on that, and on everything else over the past few months. Willow 22:29, 3 October 2006 (UTC)

Congratulations on photon; you did a great job with it - good luck keeping the coal glowing, especially if/when it hits the main page :) Our friend from UMASS has been blocked for spamming (not to mention nicely ironic timing). Despite some people's arguments for entropy death of Wikipedia articles, I think there's been a lot of improvement in the science areas since I actually registered, and you're responsible for more than your share. (I've got to cherry-pick my trivia and quadrivia; music and grammar go straight out the window.) Opabinia regalis 05:16, 5 October 2006 (UTC)

My RfA[edit]

Nuvola filesystems folder home.png Thank you for participating in my RfA, which passed with a tally of 91/1/4. I can't express how much it means to me to become an administrator. I'll work even more and harder to become useful for the community. If you need a helping hand, don't hesitate to contact me. NCurse work 15:29, 8 October 2006 (UTC)

PLEASE CHECK![edit]

You have wondered about my credentials? Would you please check http://en.wikipedia.org/wiki/Talk:Entropy#Non-notable.3F

I don't know if this will reach you, so (new to exploring Wikipedia) will try another route also.

Thank you. FrankLambert 05:02, 9 October 2006 (UTC)

Thanks![edit]

The whole reason for that ungodly long waste of space was the demand by "Sadi Carnot", Pjacobi. et akl that what I was presenting was solely my POV, with no peer-reviewed articles, and no corroboration/support from others -- i.e. what hard data do you have... Fine. 36 authors of 15/16 multi-edition US textbooks are a rather unusually powerful OTHERS' POV! This approach is thus PROVED fine for chem beginners. (Authors don't risk their reputations -- or present/futurs fortunes -- on crap.) Why can't the physicists and other specialists consider the problem of students in other majors? (And chem sureashell serves bio!

Seeing entropy as energy-related is extremely important in bio, I would think. Gimme an instance in teaching or research in which you see/think of entropy as a factor -- betcha dime phrasing the problem in terms of energy and energy dispersal will be clarifying! FrankLambert 18:41, 9 October 2006 (UTC)
(Thx greatly for patient explanation. I understand the need for proving 'notable by others' and shouldn't have used the word 'credentials'.) What edition of Oxtoby do you have? The 4th edition is less than perfect because of its attempting to define disorder in terms of macro arrangements of playing cards. That illustration is not present in the 5th, according to my notes from 2005, but I have ordered a copy to make sure that is the case: that the disorder discussion has been removed.FrankLambert 05:03, 11 October 2006 (UTC)
I'm looking at the 5th edition (2002). It introduces entropy in terms of spontaneity and then relates spontaneous processes with accessible microstates. What mathematics it gets into, are introduced via the Carnot/Clausius statements of the second law and its applications to heat engines. What I don't see is any mention of "energy dispersal". No mention of scattering cards either - the example for microstates involves four molecules arranged in various ways in a two-compartment container. I don't think their presentation is so bad and prefer discussion of microstates to generic "disorder", but I don't see the energy dispersal idea as a beneficial one; it seems that it will only lead to subsequent confusion about, for example, information entropy or conformational entropy. But, I don't and wouldn't teach total chemistry novices, so I suppose I'm not that relevant :) Opabinia regalis 01:07, 13 October 2006 (UTC)
Hey -- you're too kind! (I couldn't imagine you'd take the time to report on your Oxtoby or I wouldn't have ordered. Oh well, it's a used copy :-) and I should have one -- he's now the pres of Pomona College, 8 mins. away from me. ) and the good news is that my notes were accurate (i.e., he did get rid of that disorder section and shuffled cards (two of my big articles) and he does have one of the best intros to microstates in gen chem texts. He didn't pick up "energy dispersal" but getting 16 new editions of established texts 'on my side' within 4 years ain't bad :-) Such authors certainly wouldn't adopt anything but a solid idea that unifies the topic. Click on:

http://en.wikipedia.org/wiki/Talk:Entropy/Archive4#Spontaneous_entropy_increase_always_involves_the_dispersal_of_energy Neat you mentioned info entropy and conformational entropy! My ms. clearing up these old problems was accepted in Aug, in print in Feb-March. Click on http://www.entropysite.com/calpoly_talk.html :-)FrankLambert 04:26, 13 October 2006 (UTC)

Got my 5th edition today and as you noted, it was published in 2002 -- same time as my 'dispersal of energy' so no way could he have included it. To underscore value: ALL conformational entropy is better understood as a result of or equal to dispersal of internal energy ... from folded protein to surrounding water! Dya know Schneider's NIH stuff? http://www.ccrnp.ncifcrf.gov/~toms/ -- info 'entropy' that is actually thermo entropy because binding sites are involved :-) FrankLambert 02:23, 15 October 2006 (UTC)
Ah, I didn't realize the timing. Interesting; thanks for the links. I'm not sure that energy dispersal is a useful analogy in conformational entropy due to the additional effect of particle dispersal (somewhat like the entropy of mixing case), 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 as energy dispersal :) Opabinia regalis 03:25, 16 October 2006 (UTC)

Congrats![edit]

1axc tricolor.png
An image created by you has been promoted to featured picture status
Your image, Image:1axc tricolor.png, was nominated on Wikipedia:Featured picture candidates, gained a consensus of support, and has been promoted. If you would like to nominate an image, please do so at Wikipedia:Featured picture candidates. Thank you for your contribution! NauticaShades 09:50, 12 October 2006 (UTC)


On a side note, I award you this barnstar, and a second (you deserve two!):

Posting a thanks here too :) Moved to my user page in Willow's spiffy awards section. Opabinia regalis 02:07, 19 October 2006 (UTC)

My RfA[edit]

Thank you for suppoorting my RfA, and for appreciating what I'm trying to say regarding WP:IAR!

Atlant 12:55, 12 October 2006 (UTC)

Well, it's been a week now that I've been an administrator and I'd like to take this moment to once again thank everyone who supported my RfA, and to let you all know that I don't think I've screwed anything up yet so I hope I'm living up to everyone's expectations for me. But if I ever fall short of those expectations, I'd certainly welcome folks telling me about it!
Atlant 14:27, 25 October 2006 (UTC)

Phylogenetic tree[edit]

I appreciate your clarifying that previously cumbersome article. DGG 08:30, 13 October 2006 (UTC)

Computational phylogenetics[edit]

I have sadly failed the GA nomination, please see it's talkpage for my reason for the decission. AzaToth 23:21, 14 October 2006 (UTC)

One more vote for the coordinator of the Molecular and Cellular Biology Wikiproject[edit]

Since two of the three editors nominated for Coordinator of the MCB Wikiproject declined their nominations, one more vote has been posted: should the remaining nominee, ClockworkSoul, be named as the coordinator, or should nominations be reopened? Every opinion counts, so please vote! – ClockworkSoul 17:50, 17 October 2006 (UTC)

Request for help![edit]

Hi Opabinia,

I’m sending this message out to about 4-5 people I’ve worked with here on Wikipedia. Its not a blind carbon copy to 1000 people. Sorry its only partially wiki-related...

Basically as you probably know I make a lot of diagrams for use on Wikipedia in my spare time while studying a Biochemistry BSc (hons) degree at the University of Sussex in the UK. Next year (in my final year) I’m planning on starting up a medical graphics company. Its been suggested to me more than once that some of my diagrams are as good as, if not better than those presently in research papers and text books, so it seems like a good logical progression (and more so something I enjoy!) to start up a company producing them.

But without a reputation, and as a nameless student work will be stagnant or non-existent. So I’m desperately trying to make a small name for myself and to build a credible reputation as both a scientist and artist. So to cut to the chase what I’m messaging people about is just to say please please please, if you or any of your colleagues are publishing research articles/text books etc. and need bespoke diagrams please get them in touch, I would be forever grateful! I’m very very happy to do the jobs for free as I enjoy them anyway and the exposure would help me no end! They have nothing to lose, if they don’t like what I produce its not like they paid for it, and are under no obligation to use it. I can’t stress how helpful a diagram in a published work would be for me. I do have a portfolio of generally better work than the pics here on Wikipedia, but examples to show colleagues are those such as:

”Caeliac Disease, Upper Jejunal Mucoasl Immunopathology”

Anyway, as always if you need any diagrams done here on Wikipedia, I’m an email away! If you do by any chance know of anyone seeking a scientist/artist then please be sure to get them onto me! (My email is nick-daines@hotmail.com). Thanks!

WikipedianProlific(Talk) 15:03, 19 October 2006 (UTC)


WP:RFA/Cynical[edit]

Crying emoticon.PNG Thank you for contributing to my RFA. Unfortunately it failed (final tally 26/17/3). As a result of the concerns raised in my RFA, I intend to undergo coaching, get involved in the welcoming committee and try to further improve the quality of my contributions to AFD and RFA. All the best. Cynical 14:58, 19 October 2006 (UTC)