Talk:Obsolete models of DNA structure

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Molecular Biology: Genetics / MCB

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Text and/or other creative content from this version of Non-helical models of DNA structure was copied or moved into DNA supercoil with this edit. The former page's history now serves to provide attribution for that content in the latter page, and it must not be deleted as long as the latter page exists.

Balancing information needed

So, the reason that mainstream scientists lost interest in the non-helical structure was the discovery of topoisomerases, and the implications for unwinding in bacterial chromosome replication. We need to have a section about that. These topics definitely have to be areas of intense ongoing research right now; any sources or background from anyone familiar with these topics would be greatly appreciated. Antony–22 (^talk⁄_contribs) 04:43, 2 June 2012 (UTC)[reply]

I am going to start collecting some sources below; please feel free to add more. Antony–22 (^talk⁄_contribs) 07:38, 9 June 2012 (UTC)[reply]

Kresge, Nicole; Simoni, Robert D.; Hill, Robert L. (1 June 2007). "Unwinding the DNA Topoisomerase Story: the Work of James C. Wang". Journal of Biological Chemistry. 282 (22): e17.
Champoux JJ (2001). "DNA topoisomerases: structure, function, and mechanism". Annu. Rev. Biochem. 70: 369–413. doi:10.1146/annurev.biochem.70.1.369. PMID 11395412.
Coelho, P. A.; Queiroz-Machado, J.; Carmo, A. M.; Moutinho-Pereira, S.; Maiato, H.; Sunkel, C. E. (2008). Pellman, David (ed.). "Dual Role of Topoisomerase II in Centromere Resolution and Aurora B Activity". PLoS Biology. 6 (8): e207. doi:10.1371/journal.pbio.0060207. PMC 2525683. PMID 18752348.{{cite journal}}: CS1 maint: unflagged free DOI (link)
Gellert, M. (1981). "DNA Topoisomerases". Annual Review of Biochemistry. 50: 879–910. doi:10.1146/annurev.bi.50.070181.004311. PMID 6267993.
Kim, R. A.; Wang, J. C. (1989). "Function of DNA topoisomerases as replication swivels in Saccharomyces cerevisiae". Journal of Molecular Biology. 208 (2): 257–267. doi:10.1016/0022-2836(89)90387-2. PMID 2549254.
Nitiss, J. L. (1998). "Investigating the biological functions of DNA topoisomerases in eukaryotic cells". Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression. 1400: 63–20. doi:10.1016/S0167-4781(98)00128-6.
Wang, J. C. (2002). "Cellular roles of dna topoisomerases: A molecular perspective". Nature Reviews Molecular Cell Biology. 3 (6): 430–440. doi:10.1038/nrm831. PMID 12042765.
Wang, James C. (2009). Untangling the Double Helix. DNA Entanglement and the Action of the DNA Topoisomerases. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. ISBN 978-0-87969-879-9.

A Commons file used on this page has been nominated for deletion

The following Wikimedia Commons file used on this page has been nominated for deletion:

Watson-Crick double helix.gif

Participate in the deletion discussion at the nomination page. —Community Tech bot (talk) 02:51, 5 July 2019 (UTC)[reply]

Evolution from obsolete to fringe theory

So I've been looking up the history of this area and doing some updates to the organisation of the article to focus a bit more on the historical context of why the theories were initially proposed in the '70s. I think it's probably worthwhile separating which elements are obsolete models before the evidence in favour of in vivo B-DNA became overwhelming, and which are modern day fringe theories (though there's probably no hard boundary between the two). As well as how to structure the History section, it will also affect whether the article is just in Category:Obsolete scientific theories, or also in Category:Fringe science. T.Shafee(Evo&Evo)^talk 12:52, 5 July 2019 (UTC)[reply]

I've found this to be a fascinating topic since I came across it. I think it's telling that the non-helical models were taken seriously enough in the 1970s that Crick felt the need to write a paper specifically to refute it [1]. This paper [2] IIRC gives a good historical perspective on this. There's a lot of room to improve this article to give the details of this debate.

For the more recent fringe-science incarnation, I wonder how many third-party sources there are about it? The only one I'm aware of is the Gautham comment [3], but I haven't really looked. The treatment of the Wu and Xu papers is undue; they probably each deserve a sentence or two in the context of it being a fringe theory. Antony–22 (^talk⁄_contribs) 22:02, 5 July 2019 (UTC)[reply]

Yes, ironically, the current incarnation as a fringe theory is sufficiently fringe that it'd probably be non-notable in the absence of the historical relevance. The most recent publication on the topic in 2018 was in a journal that also offers to ghost-write student assignments! For contemporary general public discussion, I've done some google and google-news searches, but only found posts by a single person (user:notahelix/user:User:Voice_of_5-23) across multiple internet forums and a kickstarter campaign, so not sure that aspect is notable despite being an interesting phenomenon. T.Shafee(Evo&Evo)^talk 06:10, 6 July 2019 (UTC)[reply]

Work from Xu, Y. C.

I have just made this edit to copy edit and tidy references added by Ycxu2019 and Catslash. Ycxu2019 had asked for help at the Help Desk and the Science Reference Desk. Catslash obliged but noted the apparent SELFCITE issue. In correcting the refs, I noticed that reference 36, on which Xu has commented (reference 37), is from F1000Research, which is new to me as a publisher doing peer review after publication. Two reviewers raised issues needing change with that paper and the third rejected it outright. The book chapter by Xu is published by IntechOpen (which redirects to predatory publishing) and the paper in Symmetry is published by MDPI, who were on Beall's List, and is dated 25 November 2019. My concerns include:

Is this material suitable for inclusion under WP:RS?
Is it WP:FRINGE or worse? It's not my area but I thought the discovery of topoisomerases ended the concerns about helixes and replication.
Is it meeting WP:DUE and being weighted appropriately?
If user Ycxu2019 is in fact the author Xu You Cheng of references 21, 34, 35, 37, and 38, then we appear to have WP:COI and WP:SELFCITE issues.
I note that reference 21 refers to a red-linked journal (the International Journal of Applied and Natural Sciences, print ISSN 2319-4014, online ISSN 2319-4022) and publisher (the International Academy of Science, Engineering and Technology) and that while this page lists the article, when I click on it I get a "File Not Exists" notice... and the same for other articles I've tried.

I will cross-post requesting help from the Science RD thread, and the Chemistry, Genetics, and Molecular and Cell Biology WikiProjects. EdChem (talk) 04:08, 13 December 2019 (UTC)[reply]

Note to all: I have welcomed Ycxu2019 at his user talk page, inviting his participation in this discussion and advising of issues of WP:SELFCITE and WP:COI. EdChem (talk) 02:35, 14 December 2019 (UTC)[reply]

Regarding the F1000 article, the standard practice is to consider an article 'published' (and included in pubmed) only if it has two ticks or one tick and two question marks and the author has not responded to those. In this case, doi:10.12688/f1000research.18134.1 should be treated as a preprint with significant concerns raised by reviewers.

Regarding the Symmetry article, MDPI is a very mixed bag publisher. Although I've certainly found high-quality articles in their journals, but plenty of very dodgy ones.

I would say that self-citation is justified to support non-controversial statements, however they shouldn't be the sole support for any contentious claim. Such citations could be appropriate as part of a section discussing the modern incarnations of anti-helicism as a fringe theory, but not to support statements of scientific fact.

My opinion is that due weight would be to summarise the post-1970s information to a paragraph or two about the persistence of the fringe theory. T.Shafee(Evo&Evo)^talk 06:52, 13 December 2019 (UTC)[reply]

Thomas, thanks for your input and addition to the article. IIRC, there was a three-strand DNA structure proposed by Linus Pauling before Watson and Crick's model was published, which had protonated phosphates at the centre, linked by hydrogen bonds. I don't recall if it was a helix, though. Do you think this and other early DNA structures belong here, rather than just a focus on the 1970s work and since? EdChem (talk) 01:59, 14 December 2019 (UTC)[reply]

It's an odd mix I agree. The page was originally just the contemporary 'anti-helicist' material, and the historical work (like Pauling's triplex) was added later. However, the Pauling triplex was a helix (structure), so the page title might be better as 'obsolete/previous/ models of DNA structures' or similar (per Category:Obsolete_scientific_theories). T.Shafee(Evo&Evo)^talk 06:47, 15 December 2019 (UTC)[reply]

Headbomb, I note that you have recently edited to remove a predatory source and citing WP:UNDUE. Both of these edits relate directly to the topic in this thread, so I wonder if you would like to make any comments on the various issues raised here? Thanks. EdChem (talk) 02:35, 14 December 2019 (UTC)[reply]

If there are other issues, my opinion is to WP:TNT the edits and selectively restore what's salvageable. Headbomb {t · c · p · b} 02:38, 14 December 2019 (UTC)[reply]

I'll first have a go at stripping it back to re-balance first. If possible, I prefer to preserve the history, but TNT can be a backup option if it still ends up accumulating fringe or POV material. T.Shafee(Evo&Evo)^talk 10:50, 19 December 2019 (UTC)[reply]

@Evolution and evolvability: I'm not sure that expanding the scope of this article to include the Pauling structure is a good idea, since the two are completely unrelated except for both being obsolete. In fact, I think there's a good opportunity to create a new article on Pauling DNA structure proposal (or a similar title), since there's more than enough history to be covered about each obsolete structure individually. Antony–22 (^talk⁄_contribs) 00:22, 20 December 2019 (UTC)[reply]