Talk:Cyclol

message: 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.
=== Comments ===
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)
replies: text: 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! Willow 13:37, 25 November 2006 (UTC)

text: 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)
thread_title:  Proposal for new "scientific method section" 

message: 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)
replies: text: 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! Willow 13:37, 25 November 2006 (UTC)
thread_title:  Comments 

message: 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)
thread_title: Not relevant

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thread_title:  External links modified 

message: 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)
replies: text: There is considerable uncited text, and the article should be submitted to WP:FAR, as the note above is almost a year old. SandyGeorgia (Talk)  03:29, 22 February 2022 (UTC)
thread_title:  Issues with this article 

message: This needs a bit of a touch-up for the current FA criteria, mainly for dealing with uncited text. Hog Farm  Talk 16:32, 11 March 2021 (UTC)
replies: text: There is considerable uncited text, and the article should be submitted to WP:FAR, as the note above is almost a year old. SandyGeorgia (Talk)  03:29, 22 February 2022 (UTC)
thread_title:  [[WP:URFA/2020]]