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Willow, you've done a great job with this article. (Did we really not have an article on the subject before? Wow.) As a general thought, the headings are rather long and wordy; ie, the first one could be just "historical context" or similar. Subsections are also nice - I use very high resolution and the text still looks a bit blocky, so I imagine the text blocks look even longer and denser to most readers. Other thoughts:
I don't have a strong opinion on the list in the lead, but I bet it'll get complaints at a FAC.
Labeling figures as "figure 1", etc sounds sensible, but just makes it more difficult to reorganize later if you add or move an image and then have to go chasing down all the subsequent numbers. I wish we had LaTeX-style labels but I suppose those would just get borked up eventually too.
There are multiple times when Dorothy Wrinch is referred to as "Dr. Wrinch", but everybody else just gets a last name. Any reason?
There's a few words that stand out as 'this doesn't belong' - "Unfortunately, the Langmuir-Wrinch hypothesis...", "unscientific rejection of its elements..."
Piles of 3 or more citations for a single statement could be condensed into one footnote with multiple papers listed.
The end section says "The cyclol model was the first hypothesis for the structure of globular proteins" but the initial history section implies that other models for proteins were extant when the cyclol model was proposed.
More on those naturally occurring cyclol bonds would be useful - even an image of one of these peptides with the cyclol bond highlighted.
Did Wrinch ever retract the cyclol model or publish anything acknowledging its failure?
I'm not sure how much the rejection of the hydrophobic folding model along with the cyclol model really means ("unscientific rejection...") - at the time it wasn't clear that the hydrophobicity idea had legs to stand on outside the cyclol model.
In fig. 3, maybe put the hydrogens on the hydroxyls? Might be easier to look at and know they aren't peptide carbonyls. (fig4, though, is very cool-looking as it is.)
You're such a gem — thanks! You're totally right on every count although, for some, I'm not quite sure what to do. The easiest ones to fix are those a little embarassing to me, little outcroppings of feeling rather than cool-headed encyclopedic professionalism. The "Dr. Wrinch" penchant is, I think, me being subconsciously defensive of her, which is silly and unreasonable, given how long ago that all was. The same is true of the "unfortunately" and whatnot although, there, my loyalty is to the field of protein science. Thanks for making me aware of my POV; it's not always easy to see, although it should be easy to fix.
To my knowledge, the cyclol model was the first structural model of globular proteins, rather than a theory about its chemical composition. Astbury had some ideas about the alpha and beta structures in fibrous proteins but I don't believe that he really specified atomic positions or even that fibrous protein structures such as the alpha helix would appear in globular proteins. I guess that most protein scientists were shy of making models on so few data.
I don't think Wrinch ever retracted her theory in print; her attitude was more of "well, even if this exact model is incorrect, features of it may well be observed in globular proteins". Peptide cyclolization and the beautiful regularity/symmetry of her model seemed to exert a powerful hold on her imagination; she seemed to find it hard to believe that Nature could pack atoms tightly but irregularly, and that proteins could be so, well, sloppy and floppy. The affectionate obituary by Dorothy Crowfoot suggests that she couldn't relinquish hope for her theory altogether.
I thought about adding the hydroxyl hydrogens, but I'm honestly not sure where to put them. My first thought was to make a "round robin" set of hydrogen bonds within each set of three hydroxyls, but one could also point the hydrogens outwards to make hydrogen bonds with the equidistant lone-pair of the nitrogens. What do you think?
I don't know, the model is very nice and regular, but especially the space-filling model just seems to be saying "Ow, my hydrogens!" I know everything is obvious in hindsight, but I'm still surprised at how many people expected proteins to have a regular and symmetrical structure - and most of all, a regular and symmetric structure in common - considering the diversity of things proteins do.
On where to put the hydroxyl hydrogens... I think I take my suggestion back. I think the only reason I keep seeing them as carbonyls is that I spend too much time looking at real proteins, so this is probably less of a concern than I thought for the average reader. The three-way 'round robin' hydrogen-bonding pattern exists in water clusters, so it might be somewhat favored in water, but I kind of think that choosing one or the other representation might confuse readers, who could think that the hydrogen arrangement was part of the cyclol model. Opabinia regalis04:17, 7 November 2006 (UTC)[reply]
Hi, O, you're right; the steric clashes are the most damning part of the cyclol model a priori, and I don't think Wrinch ever really gave an adequate answer on that topic. But just imagine how cool it would be if the elementary charge were only ~25% larger, a nice even 2x10-19C — cyclol proteins galore! ;)
I'll try to make a diagram of the modern cyclols tomorrow and fill in that section more. Is there anything else you'd recommend before submitting it for peer review? Thanks again for your help! Willow20:15, 7 November 2006 (UTC)[reply]
Sorry I didn't get back to this too quickly - the only text thing I can think of that's likely to stand out is the presence in the "see also" section of items that have already been wikilinked in the text. (IMO this is a silly guideline, but there it is.) The reaction image is nice but might be better with the three molecules arranged linearly, so there's not a blank white space in the lower right? I'm not sure how wide that would look on some screens, though. Opabinia regalis04:08, 11 November 2006 (UTC)[reply]
The following suggestions were generated by a semi-automatic javascript program, and might not be applicable for the article in question.
Consider adding more links to the article; per WP:MOS-L and WP:BTW, create links to relevant articles.
Cyclol is linked from most relevant articles, such as protein and primary structure. Being an obsolete theory, it will be found mainly under the "History" section of protein-science articles.
Per WP:MOSNUM, please spell out source units of measurements in text; for example, the Moon is 380,000 kilometres (240,000 mi) from Earth.
Added links to all units in the article.
Per WP:MOS#Headings, headings generally should not repeat the title of the article. For example, if the article was Ferdinand Magellan, instead of using the heading ==Magellan's journey==, use ==Journey==.
Removed "cyclol" from all section headings.
Please reorder/rename the last few sections to follow guidelines at WP:GTL.
Moved "See also" ahead of the References; was there something else?
This article may need to undergo summary style, where a series of appropriate subpages are used. For example, if the article is United States, than an appropriate subpage would be History of the United States, such that a summary of the subpage exists on the mother article, while the subpage goes into more detail.
I feel that the unity of the subject matter is best served by a single article, especially since it is obsolete theory of protein structure. The modern cyclol molecules could perhaps have their own article, but that is only one section of the entire article.
There are a few occurrences of weasel words in this article- please observe WP:AWT. Certain phrases should specify exactly who supports, considers, believes, etc., such a view. For example,
correctly
might be weasel words, and should be provided with proper citations (if they already do, or are not weasel terms, please strike this comment).[1]
I don't see the weasel words — would you please be more specific?
As done in WP:FOOTNOTE, footnotes usually are located right after a punctuation mark (as recommended by the CMS, but not mandatory), such that there is no space inbetween. For example, the sun is larger than the moon [2]. is usually written as the sun is larger than the moon.[2]
A cyclol is a reaction and a family of compounds (like "alcohol" or "ketone") so it seems hard to make the usual chembox. The cyclol fabric and cyclol molecules predicted by Wrinch have not been observed at all, so it would be difficult to give any parameters for them. Similarly, the SMILES format might be hard-pressed to describe a cyclol fabric.
The cyclol model of globular protein structure is an interesting example of the role of hypotheses in
developing a scientific theory. As a hypothesis, the cyclol model was not
revolutionary: it lay completely within the generally accepted basis (paradigm) of
natural product chemistry at the time, notably the confidence that the structures of biological molecules, even the most
complex, obey the general priniciples of physics and chemistry. However the hypothesis showed an unusual simplicity and
generality of application, which made it attractive to other scientists.
It has been argued that the cyclol hypothesis should never have been advanced,[84][85] because of its a priori flaws, e.g.,
it does not accommodate proline in protein structure;
the cyclol reaction is (supposedly) thermodynamically disfavored ; and
the high lateral density of the cyclol fabric is inconsistent with known repulsion between non-bonded atoms.
These criticisms are somewhat anachronistic. The cyclol model cannot accomodate proline in its simplest form, but neither
could any other model of a regular arrangement of amino acid residues. It is now accepted that proline residues cause a change in
the structure of the peptide chain from regular packing (α-helix or β-pleated sheet) to a less regular structure:
similar minor modifications of the cyclol model would have been sufficient to account for the observation of proline in
proteins. The cyclol reaction is thermodynamically disfavored in the gas phase, but Wrinch and Langmuir correctly predicted
that it may be favored in solution, where solvation is both important and difficult to calculate.
The progress of the cyclol model also demonstrates, both by its proponants
and its opponants, a well-known problem with falsificationism. The cyclol hypothesis could be (and was) falsified, but the techniques necessary for its falsification
required a certain confidence in the theoretical background of other models which were still in their infancy, such as
X-ray crystallography, molecular spectroscopy and the various theories of chemical bonding, and in their
application to small quantities of complex biological molecules. These problems in the interpretation of experimental and
calculational results explain in part the long survival of the hypothesis. On the other hand, the rejection of
covalent bonding in favor of hydrogen bonding as an explanation of protein structure, championed by Pauling, led to
the neglect of the role of hydrophobic interactions for many years.
The legacy of the cyclol model was the general acceptance that the observed density of globular proteins implied that their
structure be, at least in part, regular: this came to be known as the secondary structure of proteins. Such regular
structures are much more amenable to analysis by X-ray crystallography, particularly given the meagre computing resources
which were available at the time. The development of crystallographic techniques, promoted by the study of the cyclol model,
led to the identifcation of α-helices and β-pleated sheets, and to the elucidation of the structure of DNA.
The description of the tertiary structure of proteins required greater developments in techniques and in calculational
methods: the first such structure to be described was that of insulin in 1967, more than thirty years after the
development of the cyclol model.
I tentatively propose the above as a replacement for the current scientific method section, which I feel doesn't do justice to the various differences of opinion as to what, exactly, the scientific method is. I haven't replaced the existing section, because I feel that the above will need some editing, and maybe expansion. All the same, I hope it can provide a framework for improvements in this area. Physchim62(talk)14:39, 17 November 2006 (UTC)[reply]
Hi, Physchim62, thanks for your hard work and thoughts on making Cyclol more accurate and expressive. Please forgive my delay; I've been trying to familiarize myself with the basic arguments in the field. Unfortunately, I also see from your draft that I failed to convey several salient points of the cyclol history; if you don't understand, then I'm sure few others will. :( I was trying to be delicate and respectful of the people involved, but I seemed to have sacrificed clarity. My family is still visiting for Thanksgiving, but I'll begin work again on Monday; please be patient — thanks! Willow13:37, 25 November 2006 (UTC)[reply]
This is not relevant to the article, it can perhaps be moved to the article about Wrinch, however I'm not sure if such speculations are really notable, probably most scientists speculated along these lines. Weren't it well known by then that proteins are found in all life?
Wrinch speculated that proteins are responsible for the synthesis of all biological molecules. Noting that cells digest their proteins only under extreme starvation conditions, Wrinch further speculated that life could not exist without proteins.
It sounds too much like someone wanted to defend her in that although cyclol didn't work she had some good ideas. I don't think she or the article needs such defense.Enemyunknown (talk) 10:20, 15 September 2008 (UTC)[reply]
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It seems to me that this article has hardly been edited since it was promoted to featured status over a decade ago. Also, it is in such an overly colorful and prosaic style that none of its sections can be read in isolation. I think the sections need to be made more self-contained and the tone of the article made more encyclopaedic. Lastly, I think much of the speculative, discussion points (such as how it is a case study of the scientific method) should be removed or be put into a more generalised, objective context (e.g. criticisms of the theory: X criticised the theory because...). Jamgoodman (talk) 02:30, 27 June 2019 (UTC)[reply]
The following is an archived discussion of a featured article review. Please do not modify it. Further comments should be made on the article's talk page or at Wikipedia talk:Featured article review. No further edits should be made to this page.
This 2006 FA was noticed as having considerable uncited text a year ago, and there has been no progress. If someone engages, other deficiences can be listed. SandyGeorgia (Talk) 20:53, 8 March 2022 (UTC)[reply]
I've gone though the paragraphs that previously completely lacked refs. They mostly were supportable with reuse of refs already cited in the page, so I've favoured that for the most part.
The actual content and images are up to standard in my opinion. I'm not a big fan of figure numbering in Wikipedia articles, since in makes addition and removal of images more fiddly. However this article is stable enough that it doesn't make a huge difference so I've not removed them.
There's a few relevant recent papers that might be worth integrating.
The lead refers to figures which are found much later, in the body of the article. (???)
Page numbers are missing on books.
The "Illustration of the Scientific Method" appears to contain original research (page numbers and quotes needed to determine if WP:SYNTH is present).
Statements that require independent sourcing are cited to Wrinch.
Editorializing, sample: "In her initial article, Wrinch stated clearly stated" (there is more).
"cyclol reaction itself" was verified, but cyclol reaction is a redlink (as is cyclol fabric); if this is the correct article for discussing those, there should at least be redirects. Naming in general: renaming to cyclol hypothesis, and creation of cyclol reaction, should be discussed. And the implausibility of the hypothesis should be mentioned in the first few lines of the lead. MOS:OVERLINK review as well ... beauty ?
Disappointing topic. From my admittedly superficial reading (I am not expert on this field), this article pitches a largely discredited/ignored/niche set of papers as something significant, which it does not seem to be. Take the example of J. Am. Chem. Soc. 1941, 63, 2, 330–333. The article has been cited a grand total of 4x. Or "The Cyclol Hypothesis" by Wrinch, Dorothy in Nature, Volume 145, Issue 3678, pp. 669-670 (1940), which has been cited 3x. And "Nature of the Linkages in Proteins" D. M. Wrinch, Nature 139, 718 (1937). Cited 1x. The article also is sort of case study about the scientific method, I guess in a sort of harmless way. One might say that the article is a case study in WP:UNDUE. Lots of famous people and papers cited (Bragg, Pauling, Einstein, ...), but those citations seem contrived and seem to be intended to add weight to a fluffy report. If one wants to discuss Xray crystallography, bonding, or quantum theory, modern sources should be cited IMHO. But no modern source would cite the cyclol hypothesis, because it didnt work out ("dustbin of history") just like most early work when scientists are muddling around, trying to figure things out. Apologies for my directness, which is intended to help. --Smokefoot (talk) 16:28, 10 March 2022 (UTC)[reply]
That confirms my impression; it also struck me that a lot of the content fits better at Dorothy Maud Wrinch, and that some sections are original research (like Scientific Method, relying on sources that don't even mention the hypothesis). And that one has to read too far in to realize it's in the dustbin. SandyGeorgia (Talk) 18:25, 10 March 2022 (UTC)[reply]
I'd disagree with this. I think that discredited theories warrant inclusion from a history-of-science perspective, especially since this page is clear that it's an obsolete model. I remember this topic being noted in my biochemistry undergrad as an example of the early wild west of biochem along with things like the pauling DNA triplex and the ox phos wars (both of which I would like to see have wp pages eventually). Indeed Category:Obsolete_scientific_theories is surprisingly slim. I agree with the 'Cyclol hypothesis' or 'Cyclol model of protein structure' or similar would be a better page name. T.Shafee(Evo&Evo)talk06:06, 23 March 2022 (UTC)[reply]
Could be Improved But of course I would say that, since I wrote it fifteen years ago, my second and admittedly imperfect Featured Article. But after reading these reviews, I expected the article to far worse that it actually is. Yes, the article has flaws, but they are IMO readily remedied, such as trimming the lead and captions and mentioning that the theory is discredited in the lead. Yes, it is an article about a discredited scientific theory, but that alone shouldn't disqualify it from Wikipedia; consider other "dustbin-of-history" examples on Wikipedia, such as the Steady-state model (physics), Lamarckism (biology) or Phlogiston theory (chemistry). Since the article is concerned with the history of the theory, it seems relevant to cite the contemporary literature, although modern articles (such as those cited above in this review) relevant to the theory should also be cited. The suggestion to add modern-day literature on crystallography and quantum mechanics seems anachronistic, since the article is concerned with the methods and ideas of protein structure almost a century ago. I would ask the reviewers to take the time to read the article carefully and to list other objective, well-defined shortcomings of the article besides those given above. I for my part will try to amend them. Willow (talk) 23:06, 21 March 2022 (UTC)[reply]
A re-read and a few patches is not going to convince me this is or can be close to featured material, and WP:OTHERSTUFFEXISTS is not a good argument for the case. Some of it seems like material for Wrinch's bio, and the scope and name of the article are also problematic. SandyGeorgia (Talk) 23:24, 21 March 2022 (UTC)[reply]
I'm open to changing the name of the article; what about Cyclol model of protein structure? The redirects to cyclol reaction, etc. also seem like good suggestions. And I have no objections to improving the writing, e.g., the overuse of "however" and "also". The figure captions can also be shortened. Some captions are long only to help the reader to understand what is being depicted.
The scope of the article is to describe this discredited scientific theory, which was the first three-dimensional model of protein structure, as well as its development and demise. Although others may disagree, I would argue that the histories of discredited theories (such as the three others mentioned above) deserve a place on Wikipedia and should not be barred a priori from becoming Featured Articles. Thought experiment: Would we strip Island of stability of its FA status, if it were definitively refuted?
Whether this article deserves to be a Featured Article is not within my power to decide. What is within my power is to improve the article in response to well-defined and actionable criticisms, which I politely request. Willow (talk) 00:31, 22 March 2022 (UTC)[reply]
My objection is not because it's a discredited theory; it's how the article is put together. I suggest a sustained amount of work would be needed to address all of the issues. There's the lists of issues on the page already (just an overview, on closer examination, more is typically found), and there seems to be WP:SYNTH in the "Illustration of the scientific method" section at least. Standards at FAC have changed considerably since this article was featured; page numbers and most recent scholarly sources are expected, and the two new sources listed above would need to be incorporated, as well as solving the naming and writing issues. I would not want to see this FAR stalled on the page unless there is truly a commitment from numerous editors to doing this work; it is quite a bit for one editor. Willow, you've been absent from Wikipedia for quite some time, and I'm unaware if you know how much standards have changed since 2006 to 2008?? SandyGeorgia (Talk) 00:43, 22 March 2022 (UTC)[reply]
I will do what I can and if Tim and others can contribute, then I will be only too delighted. Of course the cyclol model is not the most pressing issue on Wikipedia. If you want to end this FAR in the interests of time and because the task seems too great for one editor, then I accept your assessment with good grace.
Nonetheless I ask a boon. According to my understanding, an FAR may last 3 weeks, especially if the article is being worked on actively, as we see on the current WP:FAR. I request that editors be given until the 31st of March to improve the Cyclol article before sending it to FARC. Willow (talk) 07:27, 22 March 2022 (UTC)[reply]
FARs can last as articles are improving; that is not a problem. But because you have been long (mostly) absent, I just wanted to be sure you were aware of how much has changed in the standards of featured articles, but more significantly, that the kinds of collaborations that used to routinely happen in bringing and keeping articles at featured standard are now extremely rare on Wikipedia. There are fewer editors, and fewer FA-knowledgeable editors who have the time to help when a top-to-bottom rewrite is needed. That is, I wanted to be sure you understood the likelihood that you would have to a) do the bulk of the rewrite yourself, while b) perhaps not knowing that the standards today are much higher than they were when the article was first written. The expectation today is that everything will be cited to the highest quality and most recent scholarly sources; the days when FAs were an editor writing what they knew, and more or less attaching reliable sources to that text, are no more. And I'm not complaining that this article is somehow less important than the others, rather pointing out that very highly viewed and core articles are going without improvements for the very reasons I mention, so that you will go in knowing that getting help from others may not happen. I saw this, sadly, at History of Minnesota; Minnesota last decade had pretty much a featured topic, with almost everything about the state at FA level. That was when many editors collaborated and shared the work; today, the editors who attempt to save a rusty bronze star often find they are going it alone, and become discouraged and give up. Graham Beards and I, with a few others new since your time, have done our best in the biomedical realm, but much of Tim Vickers' work is now at risk. I am also worried that the one editor who can rewrite this article (you) has been fairly disengaged from Wikipedia; do you have the commitment to see this through? Those are things for you to ponder; as to how FAR functions, if you say you are willing to do the work, and productive work is ongoing, FARs are allowed to stay open. Best regards, SandyGeorgia (Talk) 08:49, 22 March 2022 (UTC)[reply]
I'm happy to help out Willow on this. She certainly knows the topic better than I do so I'll play the minor role, but a chunk of the issues are stylistic rather than substantive and I've sufficient background in the topic to not introduce errors when editing for style. T.Shafee(Evo&Evo)talk22:18, 23 March 2022 (UTC)[reply]
If we can get consensus for a name change and scope of article, and if the article is moved mid-FAR, please ping me to fix this page to the corrected names and moves, etc. No changes are needed in the articlehistory template on talk, as it was designed to withstand article moves (I sometimes see editors moving all the old pages in articlehistory, which is not necessary). My choice would be Cyclol hypothesis. SandyGeorgia (Talk) 15:17, 23 March 2022 (UTC)[reply]
Update, no edits, feedback or apparent progress after 22 March, since our last conversation, are not giving a reassuring feeling about extending the time on this FAR. SandyGeorgia (Talk) 10:40, 28 March 2022 (UTC)[reply]
Delist in its current state (have been lurking during during this FAR, and made a few edits). Too many issue; esp re that the theory has been discredited; the article seems to be in a half way state and doesn't seem to know what it is trying to say / cover. Ceoil (talk) 19:34, 9 April 2022 (UTC)[reply]
Delist - the section with SYNTH issues was removed on March 22, but much of the rest of the issues identified by Sandy remain, and improvements haven't been regularly happening since late March. Hog FarmTalk13:48, 13 April 2022 (UTC)[reply]