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Talk:Obsolete models of DNA structure/Archive 1

< Talk:Obsolete models of DNA structure
Latest comment: 12 years ago by Dcrjsr in topic Article trashed
Archive 1

Problems with article

Latest comment: 12 years ago11 comments4 people in discussion
  • Reads like an scientific paper, asking questions and giving uncited answers
  • May be a WP:CFORK of DNA

--NeilN talk to me 14:07, 22 May 2012 (UTC)

Dear NeilN: I just read about "Fork". Wikipedia editors, for their own reasons, may perchance choose to remove the "Non-helical DNA structure" article, but it cannot be made a fork of "DNA". Not that it would bother me -- I'd be delighted to do it. But if I do, get ready for a veritable hornet's nest of protest from the x-ray crystallography gestapo. These people are so incomprehensively narrow-minded, they actually believe that anything which cannot be crystallized is worthless (even though Crick himself openly conceded that their x-ray pictures of DNA, which pictures form the substance of the fork-proposed Wiki "DNA" article, were, and I quote, "rather poor" and "not...unambiguous"). The willingness of the crystallography gestapo to cheerfully ignore even well-documented scientific truths, and their power to groundlessly suppress them, is the reason why, 60 years after the original Watson-Crick publication, scientists still remain almost 100% ignorant about the structure of DNA inside the living cell nucleus. That is, all the DNA structures shown in the Wiki "DNA" article are laboratory structures, determined by x-ray crystallography studies of DNA yanked out of its normal environment, then deproteinized and dehydrated; i.e., these are laboratory artifacts by definition.

In sharp contrast, the non-helical DNA structures were all determined by an intelligent thought process, which sort of process is utterly despised by the crystallogrphy gestapo. Most of the time, our work is neither accepted, rejected, nor refuted, but just plain ignored. Their attitude is "why should we look at anything that can't be crystallized?" Yet, the fact of the matter is that, with only one exception (the unpublished work of Robert W. Chambers), every statement and figure in the "Non-helical DNA structure" article is from a respected and peer-reviewed scientific journal, each of which journals may be found in any major university library.

It would be very helpful to me if you would criticize specific parts of the article, so I can either attempt to defend them, or else either remove or revise them. Thanks.Notahelix (talk) 02:47, 24 May 2012 (UTC)

The entire tone of the article is incorrect. It reads as a research paper instead of an encyclopedic article. Please look at DNA to see how an article should read. A couple specific examples:
  • "Most of the details of the "traditional" Watson-Crick structure have been proven beyond all doubt, but, as we shall see, one aspect of the structure, namely the helical twist, has been problematical from the outset."
  • "Does DNA have a helical twist inside living cells? We do not know."

--NeilN talk to me 13:52, 24 May 2012 (UTC)

Dear NeilN (or other Wikipedia editor): I have completely re-written the first 5 of the 8 sections of this article (upto and including "Separation of the strands of duplex DNA..."). (The other 3 sections will be completed within a day or two). All questions, speculations, personal comments or reflections, and potentially promotional statements have been removed. Also, a number of un-referenced figures have had attributions added. I would greatly appreciate it if you would criticize these 5 rewritten sections with respect to the question "Are they now written in an appropriately encyclopedic style?". If not, are they at least moving in the right direction? Thanks. Notahelix (talk) 21:53, 25 May 2012 (UTC)

Dear Wikipedia: Figures 8 and 10 have disappeared. The source file had the words "<deleted file removed>". I removed those words, hoping the figures would re-appear, but they didn't. I created these figures from pre-exising art, which I fully attributed to its original source. Why were these figures removed? Thanks.Notahelix (talk) 00:43, 26 May 2012 (UTC)

If you look at the article history you'll see the names of deleted files in redlinks. Clicking a link will get you to a page that shows the reason - violation of Wikipedia:Non-free content criteria #1. --NeilN talk to me 01:33, 26 May 2012 (UTC)
I just wrote quite a large detailed response but my browser decided to delete it :(. In summary, the content of this article is interesting but it reads very much like an essay, and one which is trying to put across a point (as paralleled on www.notahelix.com). That is not to say that the thrust of the article is valid or invalid, and by the main author's own admission it is controversial, but that it does not suit for Wikipedia to try and put it across (see WP:SYN). My suggestion would be splitting the article into different pages as there seems to be the content for it, e.g. A DNA and Z DNA have their own articles, Form IV could have its own as well. The general history of non-helical DNA discovery may be better placed in another article or article(s). Also there are some stylistic issues, but that is secondary I guess. I have placed wikify and attention templates on the page, perhaps someone from WP:DNA or WP:MCB may be better equipped to review the page. -Zynwyx (talk) 02:06, 26 May 2012 (UTC)

A more thorough review

Hello Voice of 5-23 (aka Notahelix). First of all, thanks for contributing this extensive article to Wikipedia. A number of editors above have expressed concerns that this article needs to be re-edited to conform to Wikipedia's content and style guidelines, so I want to give you a more thorough outline of these issues so that they can be fixed.

In general:

  • Wikipedia has a much different writing style than scientific articles do. With the latter, the author is advancing a specific viewpoint based on evidence available to him/her. With Wikipedia, the goal is to write a neutral, balanced overview of different viewpoints by reflecting what has been said about then in reliable, published sources. All nontrivial statements must be cited to a reliable source. See the policies on Neutral point of view, Verifiability, and No original research, and Identifying reliable sources.
  • I notice you have used some copyrighted images from journal articles under a fair use justification. Fair use on Wikipedia is far more restrictive than it is elsewhere, as the goal is to make our materials available under a free content license. According to the Non-free content guideline, copyrighted charts and graphs may not be used because they can be recreated from the original data. For results of scientific experiments such as images of gels, the same concern applies as someone could create a free equivalent by running the experiment again and releasing the data under a free content license.

Notes on specific sections:

  • Terminology: mostly good. A rule of thumb we have on Wikipedia is that there should be at least one citation per paragraph; if the single citation at the end of the section applies to all the paragraphs in the section, it should be replicated in each paragraph.
  • Historical background: This overstates the important of crystallography in determining nucleic acid structure; there are plenty of solution-phase methods such as NMR, circularization assays, and the results of DNA nanotechnology. The editorializing about the pitfalls of crystallography are not supported by the source, and the Crick quote is taken out of context: the quote's final sentence "One must turn to evidence of quite a different type" is immediately followed in the original by "Fortunately, that evidence now exists and moreover goes to the root of the matter."
  • Circular DNA created conceptual difficulties in DNA replication: Mostly fine but it seems that Cairns himself did not doubt the double-helical nature of DNA in the two papers cited. The article should be made clearer on this.
  • First non-helical structures proposed: Mostly fine but I'm a bit concerned about undue synthesis in the criticisms of Stettler et al.'s work. Also, there I would like there to be more of a description of Crick's article responding to the model for balance. The chart from Stettler et al. does not meet the non-free content guideline.
  • Separation of the strands of duplex circular DNA without strand breakage: Mostly fine but needs to be copyedited for tone and concision. Figures 7A and 7B are unnecessary, as the results can just be described in the text, and their inclusion again dos not meet the non-free content guideline.
  • Topology of circular DNA explained by a non-helical model: This entire section is unreferenced. The discussion of the (currently removed) figure goes into far too much detail, and fails to note the effect of nucleosomes in biological DNA. The section lacks context; it should also discuss commentary by others on the work described.
  • Alkali denaturation data according to TN theory: Again, this is largely unreferenced, and too detailed, and lacks context.
  • Structure of the protamine-DNA complex: Once more, this is largely unreferenced, and too detailed, and lacks context. Figures 14, 17, and 18 fail the non-free content guideline.
  • Paranemic structure: This seems suitably referenced for the most part, but one of the references is a self-published source, which is not considered to be reliable. Again, I'd like to see some balancing viewpoints, as some of the arguments in this section seem a bit weak to me.
  • Summary: This is a good summary, but the first two points lack references.

Hopefully these will help you bring this article in line with Wikipedia's guidelines. I will be back in a couple of days and make cuts to material that has not been updated. Please respond here if you have any questions. Antony–22 (talk⁄contribs) 23:04, 26 May 2012 (UTC)


Hi Antony-22. Thanks for your critical commentary. This is a holiday weekend, and the earliest I can return to this article is Monday. So I hope your "couple of days" hasn't already started, because you have laid a rather extraordinarily heavy burden of work upon me, for a task to be completed in a couple of days.Notahelix (talk) 01:36, 27 May 2012 (UTC)

To Antony-22, or to whomsoever it concerns ---I took the article down. People have already posted incredibly ignorant and deceitful, self-serving lies on this page. You have done nothing about it, and presumably can't. I have replaced the article with an open letter, which no one will answer, because no one has the requisite knowledge, or love of the truth, to do so. BY ALL MEANS, GO AHEAD AND TAKE THE LETTER DOWN. HAVE YOURSELF A BALL.---If and when you wish to have an article on non-helical DNA structure, just ask. You -- Mr. Antony-22 -- I just read your Nanotechnology page. My God, of all the people to allow yourself to be muscled by these fools, you're the last one I would have expected. Your work depends more on the truth about DNA structure than most other people's. Do you really want to be a jerk for the rest of your life? Take a look at my protamine-DNA structure if you want to get your head out of the sand. As for Wikipedia, goodbye. As you have no use for me, so I have none for you. I may not ever look here again, so if you have anything to say worth saying, email me.Notahelix (talk) 04:53, 28 May 2012 (UTC)

I have restored the article and moved the text of Notahelix's open letter below. Antony–22 (talk⁄contribs) 04:58, 28 May 2012 (UTC)

Notahelix's open letter

Latest comment: 12 years ago20 comments6 people in discussion

I put this article up, and I’m taking it down.

This article is already being savaged by writers who are both incredibly ignorant and inexcusibly dishonest. You should all be ashamed of yourselves.

Here, gentlemen, are the facts in the matter. There are exactly TWO “establishment” articles on the planet earth which DIRECTLY ask the question “Is DNA really a helix?”, and which also provide experimental data which relate directly to the question.

If any of you brilliant editors out there can point to even a single additional article which addresses this question---DIRECTLY, not indirectly---DELIBERATELY, and not accidentally---PRIMARILY and not incidentally---let him produce that reference NOW, and not blubber and sputter about such irrelevancies as “60 years of research on the double helix can’t be wrong”. Isn’t that what the Catholic Church said in the year 1624 about geocentricity?

You editors all think yourselves smarter than me. PROVE IT. Show me the facts.

Ignorant journal referrees, in cavalierly rejecting articles on non-helical DNA structure, are fond of such assinine statements as “You are ignoring a mountain of evidence in favor of the Watson-Crick structure”. Yet if you ask them for even ONE single article from that mountain, most of them can’t even provide that. REMEMBER – we’re talking about an article that DIRECTLY asks the question, and persuasively provides the answer.

Well, I can provide it, because I know all such articles. And there’s not just one. Oh, no, perish the thought. There are FAR more than that. There are actually two.

Here, gentlemen, are the two articles that you skaters on thin ice are standing on. The first one is:

1. Stettler UH, Weber H, Koller T & Weissmann C (1979). Preparation and characterization of form V DNA, the duplex DNA resulting from association of complementary, circular single-stranded DNA. J Mol Biol, 131, 21-40. DOI:10.1016/0022-2836(79)90299-7.

I was nice to these authors when I first wrote this Wikipedia article, but now you’ve savaged my article for no reason, so I’m going to tell you the painful truth. Crick wanted Rodley, author of the first non-helical DNA structure, “dead in the water”, so he publicly called for the Rodley structure to be created and discredited. These authors jumped at the chance.

This publication was garbage. If you don’t believe me, ask the authors. They cannot defend this work, and they know it. They claim that they separated the strands of a circular chromosome, then reannealed those strands at pH 8, to give a base-paired duplex, i.e. to give the Rodley structure. They then demonstrated that this “thing” they created had a different electrophoretic mobility than native DNA.

I hate to pop your bubble, but it was conclusively proven, by earlier published research from much more careful workers than these, that it is PATENTLY IMPOSSIBLE to reanneal circular DNA at pH 8 in any finite amount of time. Linear DNA, yes. Circular DNA, no! The structure that Stettler et al therefore created was most likely form IV, or in any event a NON-BASE-PAIRED anomalous structure with no biological relevance.

How about a control experiment? To “prove” that their anomalous structure was base paired (which is impossible, because it wasn’t), they did a control experiment using DNA from one strand of a virus chromosome only, where no base pairing would be possible. Would it form the duplex “thing” structure also? If so, then the whole experiment is invalidated. If not, then the “thing” they created really was base-paired, and side-by-side DNA is indeed “dead in the water”.

I would be very impressed by this control experiment, except that they didn’t do it. UNLESS, that is, you consider the following garbage to constitute a valid “control” experiment”. This farce of a pseudo-control experiment employed the following:

A different DNA… …in a different solvent… …at a different pH… …at a different ionic strength… …at a different temperature, and for …a different time of incubation.

WHAT THE HELL SORT OF “CONTROL” IS THIS? IS THIS THE “MOUNTAIN OF EVIDENCE” YOU WANT YOUR LIVES AND CAREERS TO REST UPON?

Moreover, the pseudo-reannealed product showed no cooperativity upon melting. WHAT? Where’s the “base pairing”? WHAT’S THE MATTER WITH YOU PEOPLE?

Look at that control experiment again, and THINK ABOUT IT. You have to think, no matter how painful it is. Your entire DNA science rests upon a control experiment employing a different DNA in a different solvent at a different pH, ionic strength and temperature, incubated for a different period of time.

Your move.

Now let’s look at the second article:

2. Crick FHC, Wang JC & Bauer WR (1979). Is DNA really a double helix? J. Mol. Biol. 129, 449-461. DOI:10.1016/0022-2836(79)90506-0. PDF: http://profiles.nlm.nih.gov/ps/access/SCBCDD.pdf

This was very possibly the most thought-destroying article in the history of DNA science. These authors, scrambling to justify their twisted structure in the face of increasing evidence that it’s a laboratory artifact, turned to topoisomer experiments. This they did because they knew – and so admitted -- that crystallography and NMR cannot prove the structure. This is not my statement, but Crick’s. To quote him, we “must turn to evidence of quite a different type”. So he turned to topoisomers.

The treatment of DNA with topoisomerase produces topoisomers. Duh. The authors state that the topoisomers differ by one in their superhelicity. No one disputes that.

SO WHAT? WHO CARES?

Have you all forgotten what the question was, which the article purportedly asked? The question was “WHAT IS THE STRUCTURE OF THE NATIVE COMPOUND?” Not the topoisomers.

By cleverly manipulating the conditions of electrophoresis, it is possible to create the illusion that the native band is exactly 1 twist more tightly-twisted than the most dense topoisomer, but that still doesn’t tell you the structure of the native form of DNA, because it’s well-known and openly-admitted that heavier topoisomers tend to band in about the same place. The exact linking number, Lk, of the parental duplex is NOT revealed by this experiment.

In other words, this, as “proof” of the Watson-Crick structure in the native chromosome, is smoke-and-mirrors. In reality, the article didn’t even address the question, much less answer it. Oh, it can surely be alleged that the article addressed the question of helicity in the artifactual topoisomers, but I don’t care about that. I want to know what the structure of DNA is in your body and mine. I don’t care about laboratory topoisomers. This article did NOT answer the question.

In conclusion, all we learn from this waste of ink is that native DNA has an electrophoretic mobility greater than the topoisomers. What does that tell you about the structure of native DNA? NOTHING.

Let me repeat that for emphasis, because you don’t listen, and you don’t think: The fact that native DNA has a higher electrophoretic mobility than the topoisomers teaches exactly and precisely NOTHING about the native structure.

It’s been satisfactorily demonstrated that a side-by-side native structure would do the same thing (i.e., band ahead of the densest topoisomer), but you won’t look. Don’t strain yourselves looking now. You might get a headache.

Let all you wise men and women not waste any more of your precious time attacking me; nay, not a single minute. If you’re really as smart as you say you are, you should be readily able to discredit me by producing, NOW, a published article which asks the question “Is DNA really a helix?” and ALSO ANSWERS THE QUESTION. PLEASE:

No more uncontrolled and wretchedly-designed pseudo-experiments. No more hot-air discussions of topoisomers or other laboratory artifacts.

You can’t produce any such article, can you? I didn’t think so.

Well I’m 62 years old. I’ve wasted my entire life talking to people like you, which was like talking to a wall. I have no money, so you can’t take anything from me. I have no job. I have no assets. Unlike you, I don’t own a home, or drive a Lexus, Nexus, or Plexus, or whatever you call those fancy cars you all drive.

But I have one thing you don’t have. I have a respect for the truth, and a willingness to sacrifice my life, my career, and my happiness for it. I stake my truths against all your useless awards, against all your pharmaceutical-juggernaut sponsorships, and against all your prestigious academic appointments, any day of the week. Like today.

Yours truly,

Ken Biegeleisen, MD, PhD


WELL, HERE WE GO AGAIN. I took my article down, and Wikipedia put it back up, with the crudely-inserted lies fully intact. I can see that I'm going to have to spend the rest of my life arguing with ignorant fools on the pharmaceutical payroll, who fancy themselves "scientists" because they have a grant to do "research" on phony cancer cures, and because they live in a nice house and drive an expensive car. All right, the battle lines are drawn. First of all, to the liar and fraud who posted the following: --- "Such side-by-side models of DNA were proposed early in the history of molecular biology" --- YOU, SIR, ARE A LIAR AND A FOOL. The first non-helical structure was proposed in 1976. Do NOT go on my web page with lies, unless you provide a reference. I have given citations for everything I said, you have provided NOTHING (except your undocumented lies). Either learn the subject, or get the hell off the page. Oh, let's not forget your other "brilliant" comment: --- "The more recent solution of the single crystal X-ray structure of the nucleosome core particle showed nearly 150 base pairs of the DNA (i.e. about 15 complete turns), with a structure that is in all essential respects the same as the Watson–Crick model. This dealt a death blow to the idea that other forms of DNA" --- You, sir, may have fooled yourself and your golf buddies, but you didn't fool me. You're referring to Luger et al, Nature 389, 251-260 (1997), which you imagine, in your twisted, whirling helical delusions, I haven't seen. The person who hasn't seen it is YOU. Oh, sure, you read the summary, and you looked at the pretty pictures, but you never examined the structure, which is not correct. Why do I say it's not correct? Because there are exactly and precisely 146 basic, positively-charged amino acid residues in the DNA-binding regions of the histone octamer (excluding the part of the structure known as Helix II, which is not believed to bind DNA), and there also exactly and precisely 146 DNA negatively-charged DNA base pairs in the structure. This is not "good news" for your point of view. I'm sure you'd just love it if I dismiss equivalence of positive and negative charges as pure "coincidence", wouldn't you? For if it is NOT "coincidence", then it must be explained, must it not? And how are YOU going to explain it? It is not disputed by any authority I've every heard of, that the nature of the interaction between nucleic acid and nucleoprotein is CHARGE, yet there is not a single proper electrostatic bond in this structure. I define "proper" as being 3 angstroms. I'd settle for 4 angstroms --- what the hell, "nobody's perfect" --- but there are NONE OF THOSE either! I looked high and low and finally found a single 5 angstrom contact between DNA and protein, but the vast majority of positive and negative charges are 10, 20 or more angstroms apart, and, as I hope and pray you still remember from your undergraduate days, the strength of the salt bridge decreases exponentially with the length. In other words, this structure is INCORRECT. We have a structure with two fundamental components united by charge interactions, and THERE ARE NO CHARGE INTERACTIONS! Ah, but we have that hypnotic, whirling double-helix joke, wrapped around the laboratory-reconstituted histone-octamer artifact like a scarf. Sweet. And sooo "PC". Please note that I mean no disrespect to Lugar et al, whose work is well-intentioned and well-executed; but it's artifact. I suspect that this structure may someday be of great importance in having created a framework for the correct structure to be deduced, but in its current form it is WRONG. You doubt this? Don't just stand there moaning like a lost boy. Go to the literature and show me a single important discovery which couldn't have been made unless this structure, IN ALL ITS DETAILS, was correct. Is there, for example, a drug which was specifically designed to take advantage of its particular structure pecularities, and which cures people of illness? I think we know the answer to that already. Is there an enzyme whose active site only binds to this awkward and unlikely structure because of the peculiar NON-alignment of charged groups (which is all we can speak of, since there are no aligned ones)? I think we already know the answer to this also. But "the ball is in your court" now. You think you're smart, and you think you're knowledgeable. Stop your insufferably vague references to the non-existent, fanciful and delusional, and present some hard data, or else GET THE HELL OFF MY PAGE. --- And as for you, Wikipedia, I asked you to remove this page. You apparently intend to condemn me to spending the rest of my life defending obvious truth against the ignorant onslaughts of the modern equivalent of the Catholic medieval inquisition, which imprisoned Galileo for insulting the Tychonian error, even though the Pope himself knew it was wrong. Our new molecular-biological pope-equivalent, namely Crick, said, way way back in 1953, "The ... difficulty involves the necessity for the two complementary chains to unwind in order to serve as a template for a new chain. This is a very fundamental difficulty when the two chains are interlaced as in our model (etc etc)" (Watson & Crick, 1953, CSHSQB 18:123-132). Crick was smarter than the rest of you, because HE KNEW his structure was flawed (which you do NOT know), but, like the 17th century Pope Urban iii, he proceeded with it anyway for the benefit therein. YES, WE'VE ALL BENEFITED, NOT JUST CRICK. But some of us have chosen to not be complete "Emperor's New Clothes" fools, worshipping every nuance of the structure, both the correct and the incorrect parts of it, as if it was some sort of molecular biological "god". I therefore again invite you to take this page down. Wikipedia is not ready for serious science, but must, by it's nature, be limited to that which is popular, financially profitable, and polically correct. This is NOT consistent with the Encyclopedia Britannica's own definition of "Encyclopedia", which defines it as a "reference work that contains information on ALL (emphasis added) branches of knowledge or that treats a particular branch of knowledge in a comprehensive manner"; likewise for the online Merriam-Webster definition, "A work that contains information on all branches of knowledge or treats comprehensively a particular branch of knowledge". Whoever wrote these definitions did not contemplate an encyclopedia whose content was ruled by men who, to quote Goldfinger, "love only gold", and who kill anything which interferes with the flow of their godamned grant money. Ugh.Notahelix (talk) 12:12, 28 May 2012 (UTC)

The article is not being sabotaged, it is that the style of the article does not fit Wikipedia. Wikipedia is to disseminate knowledge, in a neutral tone and from a neutral point of view, admittedly the status quo is on double helical DNA but your accusations against other editors are over the top. No one here has any ulterior motive. The article is written like an essay and littered with bias. I would say if you want to make easier accessible this knowledge that you think is ignored, Wikipedia is the best place to do it, it just needs to be written in a more neutral tone that would allow the reader to come to the same conclusion as you have without persuasive language or inherent bias. Just the facts, not the conclusions -129.234.93.194 (talk) 16:30, 28 May 2012 (UTC)
I'm sorry about the confusion over the fair use policy. As I said, Wikipedia's policy is far more restrictive than elsewhere; even if a use is legally fair use, we have extra guidelines that must be followed due to our policy of releasing our work under a free content license. When you submit an article to a journal, in most cases you lose the copyright of the article to the journal publisher, and thus you no longer have the legal right to release it into the public domain. You cannot copy and paste a figure from a journal, even if you are the author, but if you recreate the image from scratch you then own the copyright to the new image and can contribute it to Commons.
That being said, your uncivil behavior and use of name-calling is disruptive to the project and also against our policies. See Wikipedia:Civility and Wikipedia:No personal attacks. We take these policies seriously, and repeated violation of them could lead to consequences such as being banned from Wikipedia. If you intend to continue here, I suggest that you focus on learning our content policies and helping us ensure that your contributions are in line with them.
Keep in mind our policy that "Verifiability, and not truth, is one of the fundamental requirements for inclusion in Wikipedia.... No matter how convinced you are that something is true, do not add it to an article unless it is verifiable." Wikipedia must reflect what the published literature says in a neutral, balanced way. Antony–22 (talk⁄contribs) 18:19, 28 May 2012 (UTC)

This is my last note here, unless something changes. That ignoramous "N. Gautham" has put his garbage back on the page. I told him NOT to come back without documentation. For God's sake, man, you guys are torturing me over documentation, documentation, documentation...and this fool just keeps putting up the same DUMB remark about non-helical structures having been proposed and discarded in 1953, which is a lie, and for which had gives no documentation. HAVE YOU COMPLAINED TO HIM? I bet you haven't. No, I'm sorry, you're not the kind of publication I wish to be associated with. I spent over 2 months preparing this page, and it was a complete waste of time, because YOU HAVE MADE IT SO. You removed all my figures, which were legally posted, except the single example of animated gif, fig. 7A. which I was going to re-submit with credit to the Bulletin of Mathematical Biology, but I cannot upload any figures, because you have blocked my ability to do so. It's enough already. I've wasted the ENTIRE DAY on this crap, and I'm not putting up with any more. Either put my figures back -- because every one of them is essential, and every one (including the new version of fig. 7A) is being used with the full and unrestricted consent of the journals from which they are taken. If your policy excluded even that which the journal permits, then I can't use you, and you can't use me. Please note that my work too is copyrighted -- I NEVER submit anything to anyone without first registering it with the US Copyright Office. I've never had to use any of these "backup" copyrights before, but if you do not take this article down, I shall consult with a lawyer. This is a very sick game you're playing, and two can play it. Alternatively, put my figures back (except fig. 7), and show me some evidence of good faith. "Good faith" means some sign that you respect a field in which at least a dozen men have labored for nearly 50 years without reward, compiling a body of knowledge that cannot be ignored except by extreme intellectual recklessness. You have to decide which side you're on, and I don't care what decision you make. Are you going to use your editorial powers to disseminate this knowledge, or are you going to use them to uphold a depraved and frightfully ignorant status quo? It can't go both ways -- you can't just keep sitting on the fence. I am demanding that you either return my figures today, and remove the block to me uploading new ones, or else, if you just can't do that, then make damned sure this page - WHICH I OWN -- is down tomorrow. I don't care at this point whether you ban me from Wikipedia -- I don't want to be on Wikipedia; the thought of it turns my stomach. I need to disseminate knowledge to the ignorant, and your hands are tied to the very ignorance I'm fighting against.Notahelix (talk) 19:32, 28 May 2012 (UTC)

I think you are misunderstanding Wikipedia's copyright considerations. When you contribute material to Wikipedia, you agree to irrevocably grant a licence for its use under the Creative Commons and the GNU Free Documentation licences, which allow anybody to use and edit your contributions for any purpose. This agreement is displayed right below the edit window. See Wikipedia:Copyrights. If you didn't mean to do this, there are channels that can be used to resolve this, and I can contact other editors who can help to a greater extent than I can.
Furthermore, keep in mind that we have a policy mandating no legal threats. We have conflict resolution procedures that can be used to deal with any issues we may come up with, and legal threats will only hinder your ability to come to an agreeable resolution. Antony–22 (talk⁄contribs) 21:03, 28 May 2012 (UTC)
I have posted a note on the Administrator's Noticeboard here to recruit other editors with more experience in these issues. Antony–22 (talk⁄contribs) 21:28, 28 May 2012 (UTC)

Dear Antony: I happen to be a physician, and I would like to acquaint you a with a legal doctrine which you quite apparently know nothing about, namely "informed consent". The Wikipedia method of teaching prospective contributors how to prepare and submit an article, and what the "rules" of doing so are, are so vague as to border on a joke. The number of Wikepedia web sites alleging themselves to be "instructional" cannot be counted for multiplicity. Each one is woefully incomplete, and to get the missing instructions requires hours of frustrating searching. Any disinterested 3rd party would be forced to the conclusion that you are a gang of wise guys who delight in tormenting newcomers, as a college fraternity house delights in torturing and occasionally seriously injuring new "pledges". No competent court will uphold your so-called "agreement to irrevocably grant a licence...under the Creative Commons and the GNU Free Documentation licences" because you don't raise a finger to explain your dirty tricks to prospective writers. Besides, that which is already copyrighted cannot be transferred to another party without full disclosure, and that little tiny small-print "warning" you alluded to is like classic "small print" on a deceptive contract, which may or may not hold up to legal scrutiny, depending upon what the courts believe the intentions of the parties are. I think your intentions are consummately evil. I wrote an article about the likelihood, nay virtual certainty that non-helical DNA exists and is important. Your intention has now become crystal-clear, enough to subject to x-ray crystallography. You and your associates intend to turn this article into yet another monument to the whirling, twirling and ultimately defunct "Watson-Crick double-helix", by taking every statement on the page, and bringing in a liar to twist it around so it appears to say the opposite of what it really says. I can already see that, while you hypocritically demand full documentation for everything I say, your lies and deceptions will never require a shred of documentation. That Gautham guy has been up 2 or 3 times already, and he still has provided no documentation for his lies. His so-called "reference" is a complete farce -- a letter to the editor disputing a non-helical DNA article which apparently hurt his feelings. It's HIS UNDOCUMENTED OPINION, unsupported by any evidence. I'm not going to let you get away with this. I intend to fight you until this page is taken down, and if I've stuck to my theory of DNA structure for 40 years, don't think I'm going to give up quickly. Therefore, I hereby request that you expeditiously advise me as to how to speak directly to your "conflict resolution" department, because this article MUST COME DOWN. It's painfully clear that you think you know more about DNA than I do. Why, then, don't you get off your lazy butt and write your own article? Why do you have to expropriate my intellectual property for your own perceived benefit? SEND ME THE CONTACT INFORMATION FOR THE "CONFLICT RESOLUTION" DEPARTMENT IMMEDIATELY.Notahelix (talk) 00:45, 29 May 2012 (UTC)

I'm communicating with the administrators to determine the proper course of action. I'm not a lawyer, but you did agree to grant a binding license for your submitted content, and this fact was prominently displayed every time you made an edit, whether you took the time to investigate what it meant or not. I doubt this license can be overturned based on your own request, but it's possible that you'll get the benefit of the doubt as a newcomer, and the deletion of this article will be allowed regardless. Antony–22 (talk⁄contribs) 01:38, 29 May 2012 (UTC)

While we're waiting for the Decision of the Secret Administrators, could someone please explain to me, without Wikipedia Standard Obfuscation, exactly and precisely why it is that if a journal's published copyright policy allows useage, you still don't. Case in point: You cavalierly removed Fig. 8, without which the entire section is hamstrung. I created that figure. I created the ordinate, the abscissa, all the pictures in it, and all the labels. I drew the box. The data points were taken from the published data, but I added the dots and drew the lines. So please don't talk to me about "creating your own". The publisher says: "Other parties [i.e., other than original article author(s)] are welcome to copy, distribute, transmit and ADAPT (emphasis added) the work — at no cost and without permission — for noncommercial use as long as they attribute the work to the original source using the citation above.” The "citation above" reads: "This research was originally published in Journal Name. Author(s). Title. Journal Name. Year; Vol:pp-pp. © the American Society for Biochemistry and Molecular Biology." All this was, and still is, in the figure. What exactly is your problem with this figure? I've asked before and gotten no cogent answer. Please just answer the question plainly, or, if you don't intend to answer it, just say so. Please also, don't refer me to one of those Wikipedias pseudo-explanatory pages on this subject, which are written in an incomprehensible English-like language; as murky as a swamp for uncertainty.Notahelix (talk) 10:39, 29 May 2012 (UTC)

Alright, I'll break this down since you're unwilling to take the time to learn the site rules.
First, you do not have sole control of this page. Once a contribution is made to Wikipedia, anyone may edit it.
Second, all material on Wikipedia may be freely re-used for any purpose, including commercial ones. This is incompatible with your publishers' "noncommercial use" clause.
Third, Wikipedia is not the place to promote your personal projects or hypotheses. We report what reliable, third-party publications have stated about the subject. We do not simply reprint your paper, nor take your word for it that your conjectures are correct. — The Hand That Feeds You:Bite 13:08, 29 May 2012 (UTC)

It was kind of you to explain the part about "all material on Wikipedia [being re-usuable} for any purpose". You may think this is self-evident, but I certainly didn't know it. While you were writing the above, I added a new figure 8. It is 100% my own work. The data are typical of at least a half-dozen and maybe more papers by various authors, and are therefore not attributable to any journal. There are no data points whatsoever. The curves were hand-drawn by me, and the little pictures of chromosomes were always by me -- none have ever appeared in any publication. If this is acceptable to you, maybe there's hope that this can be done with hand-drawn figures.Notahelix (talk) 15:50, 29 May 2012 (UTC)

I wonder if you could continue your kind provision of explanations of the exceedingly complex Wikipedia rules for images, and explain to me why former Fig. 10 (DNA B vs Z 400.jpg) was removed. This was a slight modification of a Wikimedia Commons image. I contacted the author in advance, to resolve a slight ambiguity in the manner of attribution he desired, and I complied with his request. The caption of the image accurately depicted his name, his Wikimedia username, and the filename, and it correctly identified both English Language Wikipedia and Wikimedia Commons as the source. This too is not acceptable? What did I do wrong? (I just read 4 different Wikipedia image instruction pages, and I remain clueless).Notahelix (talk) 16:55, 29 May 2012 (UTC)

Regarding Fig. 10, you should be able to edit something that was already on Commons and then re-upload it. It looks like you may have used the fair use banner rather than the banner that releases your changes under the free content license, which might have confused someone into thinking that it wasn't free content and was copied from somewhere else. (There's a drop-down box on the upload page that allows you to select a license.) You should try contacting the administrator who deleted it on their talk page. Tell them that you edited a file from Commons and that you meant to release it under a free license but you used the wrong banner. You can see the deletion information by clicking on this redlink: File:DNA B vs Z 400.jpg. Antony–22 (talk⁄contribs) 17:25, 29 May 2012 (UTC)

Why was this article title changed? The subject matter deals only with duplex circular DNA.Voice of 5-23 (talk) 19:37, 29 May 2012 (UTC)

Dear Antony-22 aka "Committed Identity": Wikipedia continuously talks of its "impartiality". It has just unexpectedly come to my attention that you are in no way impartial to the Non-helical DNA page, but in fact have been prejudiced against it all along, and with a track record to prove it. I suppose in the "best of all possible worlds" you would do well to recuse yourself, but I actually don't care. I don't need your help. I'm 62 and I've survived the causeless hatred of hostile journal editors since I was younger than you are now. Moreover, I'm too old to benefit from any of this. If I won the Nobel Prize tomorrow, what would I do with it? I'm not going to start a new career in academia at this late stage, and I have nothing to spend the money on. But you're a different story. You're just a little kid in graduate school, who maybe thinks that the world means well for you. Well, it doesn't. The world means to grind you underfoot. But maybe, just maybe I can help a little bit. You purport to be interested in such fields as DNA nanotechnology, and you don't know the structure of DNA -- I've been around A LOT longer than you, and you can bank on what I just said. Who knows, if you stopped jerking around with idiotic whirling helices, you just might get a critical edge on your competition. What? You don't think you're competing with anyone? Good luck! My advice to you is to go to my web site (www.NotAHelix.com), and spend a little over an hour watching the PowerPoint presentation "The Double Non-Helix Part 2: Probable Structure of the Protamine-DNA Complex". Can't spare an hour? Little boy, before you die, the number of hours of your precious time which you will know, in retrospect, were totally wasted, is beyond all reckoning. You can bank on that too. Let me tell you a little story. I once spent an entire hour on the phone with Steven Mayo at your grad school -- I strongly suspect you know the guy -- and he spent that entire hour telling me, over and over in a hundred different ways, that he didn't have 5 minutes to review the materials I sent him. One hour to say he didn't have 5 minutes? Really - you can't make this stuff up. In the course of that hour he attempted to prove he was so much smarter than me that he could disprove decades of my hard work in a few minutes on the phone. He proposed that the DNA-protamine structure -- which has never been published or even proposed by anyone in the world except me -- could in fact be solved with W-C double-helical DNA. In 5 minutes on the phone. All you have to do, the smart-alec said, was to take the protamine beta sheet and change the phi and psi angles so as to turn it into a helix, then wrap it around the DNA! Man, that's the stupidest, dumb-ass idea I've ever heard. But I incorporated the idea, copiously illustrated, into the PowerPoint presentation I referred to above, and showed why it's ridiculously wrong. I did NOT mention his name -- I'm not out to do such things. If you really love science, and if you really love DNA science, and if you do not watch "Probable Structure of the Protamine-DNA Complex" (bring popcorn if you must), I'll forever question your substance as a scientist. Don't be a fool like Mayo, and say "I don't have a spare hour". I said it before and I'll say it again: Before our miserable lives end, we shall all waste thousands and thousands of hours on things that don't help. You owe it to yourself to watch something that might not only help, but might change you entire life direction for the better, and give you a critical advantage over your pathetically dumbed-down "helicist" colleagues. Yes, I am writing this for my benefit, but it is MUCH more for your benefit than mine, because my life is over, and yours hasn't begun.Voice of 5-23 (talk) 20:39, 29 May 2012 (UTC)

Alright, that's enough right there. You're getting far too emotional about this. It's just a damn article on Wikipedia, not worth this crusade. We have strict rules against personal attacks: WP:NPA. Stop with the insults. — The Hand That Feeds You:Bite 20:51, 29 May 2012 (UTC)
Ken, "Hand" is right. Passion is a good thing, but not when it makes you act like a zealot who can't or won't deal respectfully with others who either don't understand, or do understand, but simply disagree. It's of no value if it just alienates you from everyone else, or makes them want to leave the room when you start talking.
And, for the second time, you have to break up what you write into small paragraphs. No one is going to bug out their eyes to try to read a solid wall of text on a computer screen. That said, I've responded at some length to your earlier comments on the talk page for your "Voice of 5-23" user account. --OhioStandard (talk) 21:28, 29 May 2012 (UTC)

Sorry if I offended anyone. This was a personal message to Antony-22, whom I cannot contact any other way. Perhaps that's forbidden? Anyway ask Antony-22 if he was offended. The answer might surprise you. If he too was offended, I'll apologize to him on this page. I certainly meant no offense.Voice of 5-23 (talk) 21:44, 29 May 2012 (UTC)

You can communicate with any editor on their Talk page, which is linked in their signature. Antony's is here. That said, whether or not he was offended is tangential; Wikipedia requires a collegial environment to work, as we're all collaborating. Vitriol and insults are not conducive to such. Remember, this is not the place to defend your papers or argue your theory. This is an encyclopedia, not a debate forum. — The Hand That Feeds You:Bite 22:03, 29 May 2012 (UTC)

Voice, don't address your arguments to me personally. I am no more the judge of your contributions than anyone else here. Antony–22 (talk⁄contribs) 01:32, 30 May 2012 (UTC)

Quality and recency of sources

Latest comment: 12 years ago13 comments5 people in discussion

I think that everyone here agrees that (right or wrong, fairly or unfairly) the idea of non-helical DNA is a decidedly non-mainstream idea. That doesn't necessarily mean that Wikipedia should not cover the topic, but it does require us to be careful in how we approach this subject. How much weight is it appropriate for us to give this material, and which information should be presented in 'Wikipedia's voice', versus attributed to individual advocates? Is this material that would be covered in a more balanced manner if incorporated into another article?

Editors newer to Wikipedia may find the following policy and guideline pages useful in understanding how Wikipedia editors try to approach these sorts of questions:

In order to present the idea of non-helical DNA structures as an active area of research or as a significant minority viewpoint, we need to be able to show that it is handled that way be experts in the field, in relatively recent publications, preferably through the use of suitable secondary sources (review articles) rather than just on the basis of primary literature.

At the moment, our article contains 8 references dated to the year 2000 or later [1]:

  • 1. Biegeleisen, K (2002). Topologically non-linked circular duplex DNA. Bull Math Biol 64, 589-609. doi:10.1006/bulm.2002.0288.
  • 4. Biegeleisen, K., 2005. Rodley Side-By-Side Structure. Protein Data Bank, http://www.rcsb.org/, accession number 2AW8.
  • 9. Lehninger, Principles of Biochemistry, 4th Edition. Ed. Nelson DL & Cox MM. Springer 2004, p. 962. ISBN 978-0716743392.
  • 14. Xu YC (2009). Finding of a zero linking number topoisomer. Biochim Biophys Acta, 1790, 126–133. doi:10.1016/j.bbagen.2008.10.012.
  • 23. Biegeleisen K (2006). The probable structure of the protamine-DNA complex. J Theoret Biol, 241(3):533-540 (2006). doi:10.1016/j.jtbi.2005.12.015.
  • 24. Biegeleisen, K., 2005. Protein Data Bank, http://www.rcsb.org/, accession numbers 2AWR and 2AWS.
  • 25. Delmonte C & Mann L (2003). Variety in DNA secondary structure. Curr Sci 85, 1564-1570. Current Science home page: http://cs-test.ias.ac.in/cs/index.php. Free PDF download at: http://cs-test.ias.ac.in/cs/php/toc.php?vol=085&issue=11.
  • 26. Delmonte C. http://www.notahelix.com/delmonte/index_delmonte.htm.

Reference 4 is a recent theoretical structure created by K. Biegeleisen based on Rodley et al. 1976.

Reference 9 doesn't have anything to do with non-helical DNA structures.

Reference 24 is to two theoretical structures created by K. Biegeleisen for his publication in Ref. 23.

Reference 26 is to a non-peer-reviewed web page, hosted by K. Biegeleisen.

That leaves 4 peer-reviewed publications from this century:

Reference 1 is a review article by K. Biegeleisen, advocating non-helical DNA structures. It cites only 4 papers published later than 1980, and only one of which (Wu and Wu, 1996) which arguably relates to non-helical DNA.

Reference 14 is a primary study which presents some evidence for non-standard DNA conformations. The author suggests that his results may be explained by left-handed DNA helices coexisting with right-handed; non-helical DNA is not presented as a credible explanation.

Reference 23 is an entirely theoretical paper by K. Biegelstein.

Reference 25 is a review by Delmonte and Mann, published in the low-impact Current Science (2010 impact factor 0.897; journal worryingly not indexed by PubMed/Medline). In nine years this review has been cited just four times by other publications—though one of those citations was in a subsequent rebuttal in a later issue of the journal.

Who supports this model of DNA? Taking the three article that actually embrace non-helical models of DNA, we have three unique authors:

  • Ken Biegeleisen: While Dr. Biegeleisen holds both an MD and a PhD, his work has focused primarily on the clinical treatment of vascular diseases: [2]. Of his eight PubMed-indexed publications [3], only two refer to DNA, the remainder deal with vascular disease. He does not appear to have conducted any laboratory work related to DNA structure.
  • Clive Delmonte: Delmonte appears to be a chemical engineer, with no PubMed-indexed publications to his credit. (A PubMed search for C. Delmonte will find publications by Brazilian forensic pathologist Carlos Delmonte.)
  • L.R.B. Mann: I was unable to identify other science publications (if any) by this author, given that Mann is a very common surname. On the web, he seems most often cited for his editorship of the compilation Science and Christianity, published while he was affiliated with the University of Auckland, Centre for Continuing Education.

Problematically, then, we have a very small number of non-experts (in either DNA or in structural biology) advancing a fringe theory.

Are we missing any recent publications by experts?

If we are, then please, please, list them here. If not, then it would appear that this article is offering an extremely generous, credulous treatment of a theory that (at the moment) occupies the far, far fringe of scientific thought. TenOfAllTrades(talk) 17:47, 30 May 2012 (UTC)

I was about to raise the same issues, but Ten has done a wonderfully thorough job at analyzing them. The proposals from the 1970s, which are all in the History section, were taken seriously enough that Crick published a paper refuting them. I believe that those proposals are encyclopedic for their historical interest, and I've already taken a first pass at copyediting that section.
Those proposals were rejected due to later discoveries. This letter, which is a direct response to one of Delmote's papers, summarizes the situation well. It says that "the discovery of topoisomerases took 'the sting' out of the topological objection to the plectonaemic double helix. The more recent solution of the single crystal X-ray structure of the nucleosome core particle showed nearly 150 base pairs of the DNA (i.e. about 15 complete turns), with a structure that is in all essential respects the same as the Watson–Crick model. This dealt a death blow to the idea that other forms of DNA, particularly double helical DNA, exist as anything other than local or transient structures." I have a good textbook on nucleic acid chemistry that I can mine for further references if needed.
All the sections following the History section are overly-detailed descriptions of the work of Wu, Biegeleisen, and Delmonte (with the exception of the first half of "Topology of circular DNA explained by a non-helical model", which is more or less a review of accepted experimental data). Solely on style grounds, of these sections should be condensed into one or two paragraphs each. Whether they should remain at all on due weight ground is questionable. Antony–22 (talk⁄contribs) 20:57, 30 May 2012 (UTC)
Antony raises an excellent point, that I didn't (but should have) touched on in my initial post. Non-helical DNA conformations were taken seriously as a legitimate minority viewpoint thirty and forty years ago. It would certainly be appropriate for Wikipedia to cover the legitimate, historical scientific controversy; stripped of polemic and placed in context, there is lots of material in the current version of this article that could potentially be adapted to that end. In the absence of substantive evidence that any active, credible researchers are working with non-helical models of DNA, we are obliged to make it clear that this is not a current area of study. TenOfAllTrades(talk) 21:43, 30 May 2012 (UTC)
The question in my mind is whether Wu, 1996  is worth mentioning. Oddly, it's an experimental paper in a mathematical biology journal, but the author is a professor at Northwestern. Nevertheless, it has been thinly cited, with the six citing works being three of the articles listed above, two non-peer-reviewed papers, and a doctoral thesis. At maximum, it would get a paragraph in the "Experimental attempts" subsection. Does it warrant even that much mention?
As an aside, "non-helical" is being used to mean non-linked here, so proposed structures with equal numbers of right- and left-handed twists would come within the scope of this article. Antony–22 (talk⁄contribs) 00:10, 31 May 2012 (UTC)
Fair enough, though we should probably be careful in our use of non-standard terminology—to my naive reader's mind, I would be very reluctant to treat 'non-helical' and 'paranemic' as synonyms. (And of course one can have non-linked circular stands with non-equal numbers of right- and left-handed twists if there is also supercoiling...but that's another can of worms.) While the article sometimes purports to be about structures with no net twists, the bulk of the content (and pretty much all of the figures) seem to be about non-helical structures: the side-by-side models and more exotic creatures like linear tetraplexes.
As to Wu, well—I give him credit for sticking to his guns. He first posited paranemic, non-helical DNA structures in the 1960s, and he's kept at it ever since. Unfortunately, his 1996 paper has had a very tepid reception. I'm inclined to apply the guidance from WP:MEDRS, and note how little attention the paper or its concepts have garnered in other scholarly sources (primary or secondary) over the last sixteen years. There aren't any good review articles that evaluate and support his conclusions. In contrast, Luger's 1997 crystal structure of the nucleosome (showing right-handed DNA helices on core histones) has drawn extensive citation; Web of Science finds roughly 3200 cites of her original Nature paper. While it's always possible that the current thinking in the field is horribly wrong, it's not the place of Wikipedia's editors to make that determination on our own. TenOfAllTrades(talk) 01:10, 31 May 2012 (UTC)
Okay, then I'd support cutting everything currently in the "More recent proposals" section. The "Background on DNA supercoiling" section seems (I think) more or less okay, though it needs copyediting, and I have a source I can check it against and use as a ref. I think that section would be best moved to DNA supercoil.
As for the "History" section, I do think it's notable and long enough to be a standalone article; there's some opportunity for modest expansion, though it also still needs some copyediting for OR and tone. The alternative would be to condense it and move it to History of molecular biology or Nucleic acid double helix#History. Antony–22 (talk⁄contribs) 02:26, 31 May 2012 (UTC)
Also, regarding the "Alkali denaturation" section, there seems to be a considerable body of work on topological stress forcing comformational changes such as the formation of Z-DNA and other forms such as H-DNA, cruciforms, or even local denaturation. The one theoretical paper the section is based on is by no means the only word or the last word on the subject. Antony–22 (talk⁄contribs) 17:43, 2 June 2012 (UTC)

Response from the author

I don’t suppose you folks would object if I put a word in. First of all, it has not, for some time, mattered to me what you do with this article. But I think it matters to you. You call yourselves an encyclopedia, which the Encyclopedia Britannica defines as a “reference work that contains information on all branches of knowledge or that treats a particular branch of knowledge in a comprehensive manner”. Note the word “comprehensive”. You have not attained to that level, at least certainly not in this matter. There are exactly and precisely two papers, and two alone, which directly address the question “Does DNA have a helical structure, or not?”, and which conclude that it does. This is the so-called “mountain of evidence” (to quote one hostile journal referee) upon which you base your hostility to this article. One of those papers is Crick et al, which you yourselves are currently batting around on this page. If you read that paper carefully, which I know you won’t, because I don’t think you really care in the first place, you will see that it only deals with topoisomers. Yes, the paper provides reasonably good evidence that topoisomers are helical, and differ by 1 in the linking number Lk. Who cares? What I want to know, and what you OUGHT TO want to know, is what is Lk of the un-nicked parental chromosome. Crick does not even address the question, much less answer it, wherefore the question remains unanswered. All we know from Crick et all is that the parental structure is denser than the topoisomers. What does that tell you? Nothing. The second paper is Stettler et all, quoted on this Wiki page. Stettler et all is the work of Charles Weissmann, and it’s garbage. I will not back off from saying this, and I will not be intimidated, by people purporting to have validity because of academic position, to white wash or any more condone this monstrosity of a pseudo-scientific "work". You can’t know this unless you know the science, and you don’t. He DIDN’T re-anneal DNA as he said he did, because previous publications proved that impossible. He DIDN’T do a control experiment – his “control” was a blatant, unabashed outrageous FRAUD. If you have any other papers which DIRECTLY ask the question “Is DNA really a helix, or not?”, and conclude affirmatively, produce them now. The comments by Gautham, who makes the incredible suggestion that non-helical structure were examined BEFORE 1953 and rejected, is an out-and-out lie. If you think otherwise, PRODUCE THE PAPERS. Why do you object to everything I say, and swallow the lies of others? On the other hand, this Wiki page has about 10 references, all well-designed, well thought out, and in the case where experimental work was done, presented along with IRONCLAD CONTROLS. So, as I see it, it’s 10-papers-against-2 in favor of non-helical structure. If you think otherwise, PRESENT THE EVIDENCE. You keep insisting on documentation from me, how about some from you? Gautham presented no evidence, just lies, and you printed it. How about printing the truth? If you leave this Wikipedia page there, and God-forbid it turns out to be wrong, you will lose nothing. If you erase it, and it proves to be right – which is a near-certainty – you will be greatly ashamed later. The choice is yours.Voice of 5-23 (talk) 22:08, 30 May 2012 (UTC)

No. As I stated above this is not the place to argue your preferred theory. We are not required to debate the subject with you, nor prove the scientifically accepted model. You are approaching this from an aggressive position, one which does you no service. Wikipedia relies on third-party reliable sources (WP:RS), not arguments from authority. If it can be demonstrated that this is a notable minority view on DNA, the article may be appropriate, but in a reduced size.
This isn't meant as intimidation; you simply misunderstand the rules and guidelines Wikipedia operates by. I and others are willing to work with you to make the article conform to Wikipedia's standards. However, you're going to have to reign in your emotions to do so. Things will likely be cut, as the sources do not appear to satisfy Wikipedia's rules. If you take such cuts so personally every time, this will not work well. — The Hand That Feeds You:Bite 22:23, 30 May 2012 (UTC)
Ken, the problem is that we have a lot less discretion than you seem to think we do. It's not remotely personal on anyone's part, here, but a host of policies we all agree to abide by make it extremely difficult for any article that's not very well-supported by mainstream publications to "stick", especially if it contradicts accepted canon. Just one of them is our policy on due weight; you should take a look. Wikipedia isn't going to be the place that readers can come to learn about very thinly supported scientific theories, even if any group of contributors here think they're right.
That doesn't mean those theories are wrong, of course, they might very well be right. It's just that we really can't operate any other way; we can't put up articles based on our own opinions of research; we can only parrot what others say, in reliable sources, and can only do so in proportion to how heavily represented in those sources competing ideas happen to be. We also have to have a lot of bureaucratic rules, simply from an organisational standpoint, if thousands of random strangers from all over the world are going to be able collaborate at all, let alone effectively.
Does that mean we pay a price in losing out on novel ideas, better ideas, even more correct ideas? Of course, yes. But despite what you think of the academic publishers, we're not one of them; and we're not trying to be. In fact, we're trying not to be. I'm sorry that's not consistent with your goals, truly. Best, --OhioStandard (talk) 22:39, 30 May 2012 (UTC)
In summary, all we really do is compile information written elsewhere (although in our own words) in proportion to how heavily or thinly it's represented in mainstream sources. We don't really "publish" anything, at least nothing that hasn't already been published elsewhere by some reliable source. Wikipedia isn't a "primary source", nor even a "secondary one", really. As an encyclopaedia, we're a "tertiary source", a compilation, essentially. If you recognise that this would have meant that we wouldn't have given space to Galileo or Copernicus or Lavoisier or Newton, had Wikipedia been around at that time, perhaps you can feel a little better about this, being in the same shoes as they would have been in, too. You're in good company that way, in other words. --OhioStandard (talk) 23:05, 30 May 2012 (UTC)

Gentlemen: I'm not going to look at this page anymore, because you all annoy the hell out of me, except Ohiostandard, who says the same things the rest of you do, without sounding elitist and condescending. I'm going to continue upgrading my pictures (which, thank God, are apparently not being torn down anymore) and working on this page, and if you overwrite what I do, so be it. Thanks Ohiostandard for explaining things to me with clarity. So long, folks. Oh -- one more thing -- I almost forgot -- I made very appropriately rude and abusive remarks about Gautham's undocumented fiction about non-helical structures having been long-since considered and rejected -- one of the most incredible examples of historical revisionism I have ever seen from a "helicist", but I neglected to comment on his better-SOUNDING story of the histone octamer and the 150 DNA base pairs (actually 146) somehow proving that DNA is helical. What I wanted to tell you was that if you're really interested in that subject, and if you want to know why it's certain that Karen Lugar's in-vitro reconstituted x-ray-crystallography-based structure proposal for the histone octamer cannot possibly be correct, you can learn this subject in somewhere between 5-10 minutes, by going to www.notahelix.com, starting the "Protamine-DNA structure" slide show, and looking at slides 12-30 (which, on the average, run about 30 seconds each). These slides will take you right into the structure, IF YOU'RE INTERESTED, and show you, atom-by-atom, why this structure, however meritorious it may be, simply cannot be entirely correct. Mind you, a great deal of it may turn out to be correct (and please do not forget that this is an in-vitro laboratory-reconstituted product, not the real thing extracted whole from cells), but to offer it as "proof" of the DH in the nucleosome is really, really far-fetched. I don't expect any of you to devote even 5-10 minutes to this, but if you just can't bring yourselves to look at this very entertaining audiovisual presentation, if nothing else, at least be wary of the undocumented claims of people like Gautham -- you demand documentation from me, demand it from him also! And before you accept his undocumented allegations arising from his misunderstanding of nucleosome structure, why not go to the movies at NotAHelix? Bring some popcorn -- you'll have a ball. Bye-bye.Voice of 5-23 (talk) 23:29, 30 May 2012 (UTC)

without sounding elitist and condescending
That's the pot calling the kettle black, I'm afraid. Ah well, we tried. — The Hand That Feeds You:Bite 01:13, 31 May 2012 (UTC)

Latest edits

Latest comment: 12 years ago4 comments3 people in discussion

These latest edits do not seem to show an improvement in tone. The text still reads like if it belongs in a research paper. Voice of 5-23, honestly, you're just wasting your time if you continue down this path as most of the text will be stubbed or deleted. --NeilN talk to me 14:38, 1 June 2012 (UTC)

I have done some preliminary copyediting for original research and synthesis. Voice, I have tried to mark problematic paragraphs with "citation needed" markers rather than removing them immediately. When you see those, you should replace them with a reference the published source that the text is based on. Keep in mind that you can't post your own evaluation of published sources, you can only use evaluations that have also been published. Text that isn't supported by a source can be removed, but you now have a chance to provide the citations. Antony–22 (talk⁄contribs) 23:41, 1 June 2012 (UTC)
I shall review the text with your admonitions in mind. But I can't do it tonight, so I hope it's still there later in the weekend. Thank you for your advice.Voice of 5-23 (talk) 00:13, 2 June 2012 (UTC)
No rush.
I have another couple of things to keep in mind. One is to avoid writing up overly detailed descriptions of single research articles. As an encyclopedia, only the main conclusions of the paper should be presented, in a concise fashion, allowing the reader to refer to the cited article itself if they are interested in the details. While there are exceptions, I'd say a good rule of thumb is that if you're writing more than one or two paragraphs about a single article, you're providing too much detail.
It is also a good idea to use reviews rather than primary research articles as the basis for writing new material, and to use them as a guide to which research articles to include. This is so that the Wikipedia article accurately reflects the balance of published viewpoints. The scientific citation guidelines are the official guidelines, and I also have an unofficial essay containing my own guidance on the subject. Antony–22 (talk⁄contribs) 23:29, 2 June 2012 (UTC)


Voice response

Latest comment: 12 years ago2 comments2 people in discussion

This turned out to be long, long, long, and I have been warned about that. But there are multiple flags which have now been raised, and I presume I'm expected to respond to them, which I'll gladly do. I'm not in a hurry, and I'm not expecting any editor to drop everything and address all this anytime soon.

From the top: The first "[citation needed]" was easy. This was for the sentence reading "Early studies quickly revealed that the strands of duplex circular chromosomes do not separate when subjected to conditions which readily denature linear DNA". The 1965 reference, from the work of Vinograd, who might be called the "father of circular DNA research" (I just made that title up), has been added.

The rest gets more difficult. With respect to the section that begins "However, it has not been possible, to date, to firmly establish an exact time and place of action for the topologically active enzymes presumed to be involved in DNA replication", CANNOT be referenced, because it states an absence, and a reference is a presence. The actual "reference" might be regarded as Lehninger's textbook description of DNA replication, which minutely describes the activities of all the enzymes except the topoloigically-active ones (i.e. topoisomerase and gyrase), which are indicated as working outside the replicative fork, but not in any timed fashion (at least not any timing which was noted). I can say, with complete humility, that I, for one, do not know exactly where and when they act, but I'm confident that no one else knows either. I can only think of 2 ways to deal with this: One way is to remove the sentence; the other way is to leave it with the flag, and see whether anyone else will knock it out of the water by showing that the timing IS, in fact known. I sincerely doubt, however, that anyone knows that. (If they do, I suppose I'M "knocked out of the water"!)(That's OK - I don't know everything).

Next: The sentence "The problem with the study was that these workers ignored several published papers on the subject of the re-annealing of denatured circular DNA, the most important of which were by Robert Warner and his associates", which has been flagged as "Improper synthesis". I have now read the definition of "improper synthesis", and I see that it's quite true. The problem here is that much, much more -- more than anyone not familiar with this aspect of DNA science could possibly imagine -- hinges on this single, thin paper. As I have pointed out, this is -- and I stand by this rather confidently -- the ONLY paper ever published which directly asks the question. There simply aren't any others -- the entire world of molecular biology was thoroughly-satisfied with this study, which was almost literally commissioned by Crick himself, and which therefore was held to be beyond reproach. The work with which I "synthesized" it was by Warner, whom Weissmann knew well -- they were both part of a group that emanated from Vinograd's CalTech lab, and which, at the time I arrived at NYU, had branches at UC Irvine (Bob Warner) and NYU (Weissmann and Rush, the latter having been my thesis adviser). The fact that Weissmann didn't know about Warner's research on reannealing is rather surprising, since Warner's main postdoc, Bill Strider -- the one doing most of his work -- was at NYU, only a few feet from Weissmann's own lab. This oversight on Weissmann's part is, of course, forgiveable, as is every sin potentially forgiveable, but when a mistake is made -- especially when this much depends upon the conclusion -- it ought to be acknowledged. I'm old enough now, and experienced enough in this area, that I am able to address questions to people who were once my "superiors"; not to be questioned. Thus, a year or two, I wrote to Weissmann, whom I didn't know personally, because he had left NYU to found the Swiss company Biogen about a year or two before I arrived. He knew my name, because he knew Rush, my advisor. At first he was friendly, but when I inquired about his experimental design in this paper, his tone changed. I'd like to quote his email response directly, but I think that would be inappropriate, perhaps even illegal. I can, however, paraphrase. He made the incredible statement that, in performing and publishing this work, they weren't trying to prove anything (????? !!!!!). Then he said something about it being a long time ago, etc etc, (i.e., all the details lost in the "sands of time"), and I understand that and cannot deny its validity as an excuse. But when you realize that this was a crossroads of history of sorts, and that this man, at this critical time, single-handedly murdered non-helical DNA science, you might also consider that there is no statute of limitation on murder (although I doubt the courts would agree with my use of the word "murder" here; it's just how I feel about the whole thing). So you're absolutely right; this is "synthesis". The question will then be "is this ever justifed?". If not, I guess the sentence has to go.

NEXT: Another "[citation needed]": The sentence "The green curve in the figure at right illustrates this principle for a typical re-annealing of alkali-denatured circular DNA in 1M NaCl, at 60º, for 20 minutes at the indicated pH". This was a figure which Wikipedia editors deep-sixed (copyright issues) because it came from J Biol Chem. I spent the better part of a day re-creating the critical part of the data (reducing it to one curve without data points), and adding the Weissmann arrow, making everything look a bit cartoonish so it couldn't be attributed to any particular copyrighted journal article. This was originally from the work of the above-referenced "improper synthesis" author, Bob Warner, and he had three publications, all showing similar data. I don't know which one to reference, and if I reference any, will that mean that there was again be copyright issues? I need your help on this one. Thanks in advance.

NEXT: The sentence "It would certainly appear more probable that they created an anomalous duplex of some sort which, however, lacked normal base pairing". The only reference for this is the Weissmann article itself, which, on p.36 (Fig. 13) shows a melting curve for nicked native DNA ("Form II") and his new species, "Form V". He says Form V is base-paired. We are taught, in biochemisty school, that a base-paired nucleic acid structure denatures according to the rules of cooperativity. Well, the Form II shows cooperativity. The Form V melting curve, in rather stark contrast, is virtually linear, which would appear to rule out any significant base pairing. But this is my unpublished conclusion. This line must either be removed, or perhaps I can re-write it in a less controversial language, so that the sentence merely points at the data without drawing undocumented conclusions. I'm open to advice.

NEXT (and last): Another "[citation needed]": "But since the outcome of direct and deliberate experimental investigations, into the question of whether or not DNA has a net helical twist in circular chromosomes, appears to rest upon a single questionably-controlled study, it would be highly-desirable if more work could be done in this area." I'm not sure which part is being asked for citation. The absence of published experiments which directly test the helicity vs non-helicity of native DNA (I think I've already blabbered about this above) cannot be referenced, because it's an absence -- something which doesn't exist. Only that which is exists can be referenced. This is another spot where it would seem to me to be desirable to leave it for a while, and see whether anyone proves me wrong. If, on the other hand, the citation requested is for the latter part of the sentence, to paraphrase, "more work would be desirable", I can't reference that either, because it's my opinion, although I think it far from controversial. What area of science doesn't need more research?

OH, SORRY -- ONE MORE THING: I see that Gautham is back. I've been expecting him. Now he's in the middle of the article totally out-of-context. Above and beyond the scientific content of his insertion, it just doesn't fit where it is. I've already removed this comment twice, because its purpose seems to me to be to make the article read as if it denies itself. What's the point of that? As for his statement about the nucleosome, he means well (there's not doubt in my mind that he believes in the correctness and appropriatness of what he is saying), but I don't think he's ever examined the Lugar et al structure with virtual modeling software himself. It's got problems, and no matter what one's opinion is of it, the ultimate fact about it (as far as its relevance here) is that it is a structure made from laboratory-reconstituted protein subunits and added DNA. Even if the structure is 100% correct, which I most sincerely doubt (and I have an extensive review of it on my web site), I emphatically deny that it has any great relevance to DNA structure in the nucleosome in living, unprocessed cells, because Lugar et als added DNA was already right-handed helical before it was added to the test tube. I REALLY REALLY WISH that Gautham would look at the protamine-DNA structure described on this very Wikipedia page. The virtual structure files are all published and readily available, and if he actually looked at them, and didn't profoundly change his point of view about the nucleosome, I'll eat my hat -- and you can bank on that (I'm not too worried -- I'm a doctor, and if I get "hat poisoning", I can probably think of a remedy).Voice of 5-23 (talk) 03:16, 3 June 2012 (UTC)

Oh, Voice, I didn't mean to make you write out a long response to each and every tag. The point is that you need to find someone, somewhere, anywhere that has said something in a peer-reviewed reputable source, that supports the text . (In the specific cases that you noted that we were asking to reference an absence of something, you don't need to prove that it doesn't exist in the literature, you just need to find one source that says that it is absent.) If you can't find anyone in all the literature who has advocated a certain viewpoint, then it just doesn't belong in Wikipedia. Antony–22 (talk⁄contribs) 05:18, 3 June 2012 (UTC)

Moved section

Latest comment: 12 years ago1 comment1 person in discussion

I have moved one of the sections from this article to DNA supercoil, as it is a pretty thorough description of that topic and seems more relevant than here. If an introduction to the topic is deemed necessary in this article we can add a few paragraphs back at the beginning of the article. Antony–22 (talk⁄contribs) 05:18, 3 June 2012 (UTC)

Article trashed

Latest comment: 12 years ago3 comments3 people in discussion

Antony-22, you have hamstrung and castrated this article. There's nothing left of value, and it no longer serves any purpose. You may actually believe that you have, I think you call it "NPOV", but this is a bias to heavy to be measured. I asked you to take the article down weeks ago, and you insist on leaving it up. For what purpose? You killed it. I'm not coming back to either the article or the talk page. There simply isn't any point. If you have anything to say email me at [redacted].Voice of 5-23 (talk) 12:24, 3 June 2012 (UTC)

Again, you have refused to educate yourself regarding Wikipedia's rules, then complain when the article is edited to conform to those rules. You do not own the article. — The Hand That Feeds You:Bite 11:45, 4 June 2012 (UTC)
In my (reasonably informed) view, this article has put forward (aggressively and inappropriately) a flat-earth-style take on the relevant science. There were indeed originally grounds for serious doubt about how tight double-helical DNA could possibly function biologically and avoid becoming an impossible tangle. But it was fairly soon discovered that the universal biological solution to this problem is the topoisomerase/gyrase family of enzymes whose function is to relieve the torsional strain and disentangle DNA supercoils and catenanes. On one hand, the catalytic mechanisms, structures, subtypes and their specific functions and actions, and distribution across the kingdoms of life have now been very thoroughly studied. Because their action is essential to replication (among many other processes), topoisomerase inhibitors are the basis of successful drugs that target rapidly-replicating cells such as bacterial invasions and cancer cells. On the other hand, the B-form double-helical structure has been absolutely clearly shown to be overwhelmingly the preferred structure of DNA: Z-form, Holliday junctions, etc exist also but are rare, and single-stranded DNA usually must be protected by a string of single-strand binding proteins to keep it from either being digested or from re-pairing. Karolin (not Karen) Luger has done not just one but about 30 different nucleosome structures by crystallography, and is now using SAXS and other techniques to study dynamic forms that open up partly for histone exchange, which still have curved double-helix DNA wrapped around them. Nucleosomes can apparently also slide along the DNA when pushed, but maintain their arrangement. The double helix and its canonical base-pairing properties are the basis of the entire fields of molecular biology, DNA nanotechnology, and many successful commercial products - so there is practical as well as scientific evidence for the basic truth of this totally accepted, fundamental and important aspect of biology. The possibly non-helical nature of DNA is suitable content for a history of science note, but has no place in explication of current science because there is no longer any doubt or controversy. - Dcrjsr (talk) 12:37, 15 June 2012 (UTC)


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