User talk:James D. MacAllister

Welcome!

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Reference errors on 30 June

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Conflict of interest in Wikipedia

Hi James I work on conflict of interest issues here in Wikipedia and am also active at WikiProject Medicine. Thanks for disclosing your role at the Margulis Digital Archive. I am providing you with notice of Wikipedia's Conflict of Interest guideline and Terms of Use and will have some comments and requests for you below.

Hello, James D. MacAllister. We welcome your contributions to Wikipedia, but if you have an external relationship with some of the people, places or things you have written about on Wikipedia, you may have a conflict of interest or close connection to the subject.

All editors are required to comply with Wikipedia's neutral point of view content policy. People who are very close to a subject often have a distorted view of it, which may cause them to inadvertently edit in ways that make the article either too flattering or too disparaging. People with a close connection to a subject are not absolutely prohibited from editing about that subject, but they need to be especially careful about ensuring their edits are verified by reliable sources and writing with as little bias as possible.

If you are very close to a subject, here are some ways you can reduce the risk of problems:

Avoid or exercise great caution when editing or creating articles related to you, your organization, or its competitors, as well as projects and products they are involved with.
Avoid linking to the Wikipedia article or website of your organization in other articles (see Wikipedia:Spam).
Exercise great caution so that you do not accidentally breach Wikipedia's content policies.

Please familiarize yourself with relevant content policies and guidelines, especially those pertaining to neutral point of view, verifiability of information, and autobiographies. Note that Wikipedia's terms of use require disclosure of your employer, client, and affiliation with respect to any contribution for which you receive, or expect to receive, compensation.

For information on how to contribute to Wikipedia when you have a conflict of interest, please see our frequently asked questions for organizations. Thank you.

Comments and requests

Wikipedia highly values contributions by subject matter experts; at the same time, experts have some special challenges when they first start editing here. Please see the essay with advice for experts, WP:EXPERTS, which discusses both sides of that coin.

One of the challenges is related to conflicts of interest (COI). You may be familiar with that concept from your real world work, but it has some interesting twists here in Wikipedia, since Wikipedia's structure allows editors to instantly publish, with no prior peer review. Please do read WP:COI, especially the section on Writing about yourself and your work.

Wikipedia is a scholarly project, and like all scholarly endeavors, managing COI is essential for ensuring the integrity of Wikipedia and retaining the public's trust in it. As in academia, COI is managed here in two steps - disclosure and a form of peer review.

Disclosure: You have already disclosed the relationship with Margulis on your User page, so the first part is partly done. I have also added a tag to the Talk page of the Margulis article so your relationship is disclosed there.

Peer review: Going forward, please do not edit the article directly, but rather offer suggestions for content changes at the article's Talk page. You can do that easily - and provide notice to the community of your request - by using the "edit request" function as described in the conflict of interest guideline. I made that easy for you by adding a section to the beige box at the top of the Talk page - there is a link at "click here" in that section -- if you click that, the Wikipedia software will automatically format a section in which you can make your request. The reason for this, is that it allows peer review of proposed changes before they become part of the encyclopedia. We have gotten great contributions that way, and were able to protect the integrity of WP at the same time. Would you please do that going forward?

You can reply here if you have any questions or want to discuss anything, or you can ask at the article Talk page. Jytdog (talk) 13:47, 8 July 2015 (UTC)[reply]

copied here from response left at my Talk page Jytdog (talk) 00:45, 9 July 2015 (UTC) [reply]

Hello Jytdog,

I am not sure if my reply to your multiple emails got delivered so I am trying this. I am new to Wikipedia so bear with me. First, let me say that I am not sure why I am singled out as being engaged in an "edit war" when my (actually three of us) careful contribution was replaced wholesale by the previous version which tells Wikipedia users nothing about what Lynn Margulis thought about the subject of AIDS except to include a story about a professor of psychology who could not understand her concerns--without any description of what those concerns were! Dr. Hunter has commented, "Biography of scientist who questioned HIV–AIDS link Lynn Margulis --

I've raised concerns at Talk:Lynn_Margulis#HIV_and_AIDS that recent edits lend undue validity to a fringe viewpoint. Courtesy-pinging James D. MacAllister; also pinging WLU and MastCell who are experienced in this area. Adrian J. Hunter -- This article did not call Margulis an "AIDS denialist", but quoted a source that referred to her "endorsement of HIV/AIDS denialism". It appears the source was both justified in this wording and accurately represented by Wikipedia[39]..i concur with this opinion--Ozzie10aaaa (talk) 14:38, 8 July 2015 (UTC)"

I would like to bring to your attention the irony in Dr. Hunter's complaint that Lynn Margulis was representing a "fringe idea". Most of Lynn Margulis' ideas were considered "fringe ideas" for her entire 50-year career. That is until most were proven correct. I must assume that Dr. Hunter's claim is that "HIV is the cause of AIDS" and that is the consensus view-end of story. He certainly isn't claiming that Lynn Margulis was not an expert in spirochetes. He isn't claiming that symbiosis and symbiogenesis (in the form of the Human Microbiome Project, etc.) is a fringe idea. He should take note of the co-authors of the McFall-Ngai paper. Does he claim that these authors represent the fringe of science? The Tauber, Sapp and Gilbert paper--are these three folks fringe thinkers? The attendees at the small meeting in Berlin were a who's who of experts on spirochetoses from all over the world. Surely, some discussion of what came out of that meeting merits mention on Wikipedia if a neutral voice is what you are after. What is there now is basically an attack on Margulis without any details or facts. I don't think that is my being "sympathetic". It is evident that the entry is just some name calling by someone who believes HIV causes AIDS and no one should question that. But that is what Lynn Margulis did. Is the entry about her ideas or some psychologist's who just believes what he's been told and how could the consensus be wrong. Look at all the papers written about the Modern Synthesis and the "gene-centered" view of evolution and biology. All overstated, incomplete, or completely wrong. 70 years of consensus. That is science self-correcting (albeit too slowly). There is no doubt that "HIV positivity" is generally not good news for anyone, but there is a difference between correlation and causation. Even Luc Montagnier does not consider HIV alone sufficient to cause immune collapse. Is he fringe? Yes he is because he holds that view. Questioning hypotheses is not "denialism". It is what thinking scientists do. Does Dr. Hunter believe that Lynn Marulis was not good at thinking?

I have to question Wikipedia's idea of scholarly when someone thinks that stating facts with references "lend undue validity" to a subject and should be replaced by name calling and innuendo. Certainly, a good editor would not have to replace everything we contributed with an entry that is worthless to a user who is probably interested in what Lynn Margulis thought--not what her detractors would have users believe absent any facts.

I would point to your own policies which I would hope apply to Dr, Hunter as well as me.

General

3. Experts, of course, can be wrong; and different experts can reasonably disagree on the same topic. (We disagree, but I am presenting what Lynn Margulis thought, not what her opposition thought--it is after all, her entry not theirs)

Advice for expert editors

2. Editing an article in Wikipedia is not like writing an original research article for an academic journal, nor it is like writing a literature review article where you synthesize a story from original research papers; instead, it should be a solid review of the subject as a whole, summarizing what published reviews say. Wikipedia is not a place to publish original research, nor your own synthesis of the research literature, even if it is brilliant. The genre here is "encyclopedia" - each articles is meant to provide "a summary of accepted knowledge regarding its subject". (I believe that Dr. Hunter is making his own case not the case that Lynn Margulis was making.)

5. Experts do not have any privileges in resolving conflicts in their favor: in a content dispute between a (supposed) expert and a non-expert, it is not permissible for the expert to "pull rank" and declare victory. "Because I say so" is never an acceptable justification for a claim in Wikipedia, regardless of expertise. Likewise, expert contributions are not protected from subsequent revisions from non-experts. Ideally, if not always in practice, it is the quality of the edits that counts. :(I get the very distinct feeling that rank is being pulled by someone who is not an expert on the science of Lynn Margulis.)

6. Expert editors are cautioned to be mindful of the potential conflict of interest that may arise if editing articles which concern an expert's own research, writings, or discoveries. Wikipedia's conflict of interest policy does allow an editor to include information from his or her own publications in Wikipedia articles and to cite them. This may only be done when the editors are sure that the Wikipedia article maintains a neutral point of view and their material has been published in a reliable source by a third party. If the neutrality or reliability are questioned, it is Wikipedia consensus, rather than the expert editor, that decides what is to be done. When in doubt, it is good practice for a person who may have a conflict of interest to disclose it on the relevant article's talk page and to suggest changes there rather than in the article. Transparency is essential to the workings of Wikipedia. (arguments that are settled by authority or consensus are classic examples of "misplaced concreteness". Neither is a substitute for evidence.) James D. MacAllister (talk) 00:39, 9 July 2015 (UTC)[reply]

Thanks for replying. (I cut your message from my Talk page and pasted it here to keep the thread together. Please do reply here.) So many things, in that long message. Most important things.

1) Wikipedia is not a wild west. This is "the encyclopedia that anyone can edit" and to prevent this place from self-destructing into a garbage dump of content over which people argue in ugly Mad Max fashion, over the years the community built a whole body of policies and guidelines that govern content and editor behavior on Talk pages. At the same time, the bottom line for all decisions here, is "consensus" - editors discuss disagreements, based on the policies and guidelines and try to agree. And we have a whole system of dispute resolution here too. It is all sane, and can even be beautiful. But there is a lot to learn, if you want to really engage here. There is a foundation to this place.

2) Almost everything you wrote above, makes no sense, here in Wikipedia. That is not surprising, as you just arrived here, and don't understand how this place works. How we make decisions about content, etc.

3) What is worse, you have started out by doing what we call "wikilawyering" - you grabbed bits of the guidance documents I told you about so far (which are not even the most important ones here), and are throwing those bits at me to try to "win". This is typical behavior of new editors, and if you stick around and read what you wrote above in a year or so, you will wince. I am wincing for you.

4) So first and foremost, slow down and work on other articles, until you understand Wikipedia - -not just the letter of our policies and guidelines, but their spirit. If you press forward as you have been on the Margulis article, you are going to either a) get thrown out of here (editing Wikipedia is a privilege, not a right, and editors who cause disruption get blocked or banned); or b) storm away from here angry. Neither is necessary, but new, passionate editors often storm ahead anyway, and one of those two things is generally what happens.

5) You wrote above that this account is shared by 3 people. This is a violation of the username policy, which says "one account, one person". If other people have been using this account, please do not let them use it anymore.

6) Most importantly, what I wrote to you about, is conflict of interest. You ignored that. Please acknowledge that you have a COI with regard to the Margulis article. That is the #1 reason why I came to your page. I am happy to try to help you get oriented in other ways, but I am not going to get involved in content disputes you are having, as that makes things too messy. I am here to discuss your COI. Please respond to that. Thanks. Jytdog (talk) 01:11, 9 July 2015 (UTC)[reply]

I'm just Adrian, not Dr. Hunter (but give me a few more months!). In addition to what Jytdog has written, please see WP:RIGHTGREATWRONGS. Wikipedia is not the place to show that Margulis was correct about AIDS, nor the place to critically analyse the evidence. Wikipedia just reports what reliable sources say, and must accurately reflect the mainstream position that HIV is the cause of AIDS. If that position turns out to be incorrect, that will need to be reported in conventional sources first, and only then can Wikipedia follow suit. Adrian J. Hunter^{(talk•contribs)} 04:47, 9 July 2015 (UTC)[reply]

cut/pasted here from response left at my Talk page Jytdog (talk) 12:58, 9 July 2015 (UTC)[reply]

Jytdog,

Ouch! That was quite a scolding. In my defense, I would offer that if all new users are alike then I am no worse and also it would seem that the system of educating new editors needs improvement. It was my intention to improve the entry, which is really uninformative as to anything of substance about Lynn Margulis or am I confused about who the page is about? So what do I do to make amends for being new and making all the newbie gaffs? What do I need to do about my COI (sounds almost like an STD)? It does make me knowledgeable on the subject of the section. Is that a bad thing? Sorry about involving others in my contribution--scientists collaborate--so it is just a habit. I know--ignorance of the Wiki rules is no excuse! Really, no one ever has anyone proof read or suggest a better word or revision in sentence structure ? There was nothing in what was written that did not represent my views so, in that sense, it was my contribution and I was making it under my own name. I wasn't presenting information that I am not expert in or trying to front for anyone. But I will obey the do-it-all-yourself rule from here on out.

If there is little possibility of making a contribution to the entry, given that I do disagree with the content as it stands, it would save everyone's time just to know that up front. I am not fond of beating my head against a stone wall if I don't have to. There is the Lynn Margulis Archive after all for scholars. James D. MacAllister (talk) 02:36, 9 July 2015 (UTC)[reply]

Hi James... I have seen lots of people enter Wikipedia and watched their trajectories. Different people enter Wikipedia in different ways. Some come gently, tentatively, knowing that they have a lot to learn; some come in at full roar and are more busy arguing than they are learning. You have come in on the "busy arguing" end of that spectrum. I am just telling you that, and telling you what ~typically~ happens when people come in that way. No one's trajectory is predetermined; I am just telling you what is typical. You can do with that, as you will. (people always do!)

Thanks for asking how to "make amends"... there really is no need to make amends per se - just change your tack! Instead of making demands for changes and arguing hard for them, ask for changes, and if people write back to you that those changes are not OK under Wikipedia's policies and guidelines, ask why (really ask - that is how you learn), and go read the links to the relevant policies and guidelines that you are given in reply, and think about them - try to put together in your head, what Wikipedia is all about... learn! Go back and read what you asked for, read the reply again in light of what you know now, and if you still don't understand, ask whatever it is. This is the way to proceed when you are learning. Take it slow. Become part of the community, be here to build an encyclopedia (what we call WP:HERE) as opposed to WP:NOTHERE. If you want (and only if you want) I have developed a mini-essay to orient users to how Wikipedia works. I can place it below, here on your talk page if you want to read it. (it is a bit long, but as i said there is a lot to learn, and tries to cover the important things in one bite) Just let me know.

About your COI. First, I am a bit surprised that you act as though you are not familiar with this concept. Your userpage says you have published in the scientific literature, and every reputable journal that I know requires authors to understand what a COI is, and to disclose any COI they have. Federal grant applications also require disclosure of COI. It is a common thing. So... surprising. Here is U Mass Amhert's website discussing it.

As in academia, we manage COI in Wikipedia in two ways. Disclosure and peer review. I discussed this above... would you please have a look at that again, and let me know if it makes more sense to you now? Thanks. Jytdog (talk) 13:16, 9 July 2015 (UTC)[reply]

cut/pasted here from response left at my Talk page Jytdog (talk) 12:58, 9 July 2015 (UTC)[reply]

Jytdog,

I do not understand "You ignored that."

6) Most importantly, what I wrote to you about, is conflict of interest. You ignored that. Please acknowledge that you have a COI with regard to the Margulis article. That is the #1 reason why I came to your page. I am happy to try to help you get oriented in other ways, but I am not going to get involved in content disputes you are having, as that makes things too messy. I am here to discuss your COI. Please respond to that. Thanks. Jytdog (talk) 01:11, 9 July 2015 (UTC)

How do I "acknowledge" that I have a "COI" in the Margulis et al paper? I have stated that I am one of the co-authors and my name is given on the reference. I am unclear about what else or where else I am to do something. I have read the COI guidelines but have to admit, other than the self-citing COI I am not sure which others apply to me. I am a volunteer archivist. I am not paid. I was making an improvement to the Wiki entry which has no reward attached to it -- I am retired so I am not trying to promote myself.

Please explain. James D. MacAllister (talk) 03:28, 9 July 2015 (UTC)[reply]

Hi. Above, at the top of this "comments and requests" I explained that you have a COI and advised you how we manage COI in Wikipedia. What I was looking for from you, was something like. "I see what you are saying about my COI with regard to the Margulis article. I will agree to follow Wikipedia's COI management process - thanks for letting me know about it!" That's all. :) Jytdog (talk) 13:18, 9 July 2015 (UTC)[reply]

James, I would like to wrap up this COI part of the discussion. Would you please reply on this? Thanks. Jytdog (talk) 19:56, 9 July 2015 (UTC)[reply]

Jytdog, I did not intend to act as though I was not familiar with this [COI] concept. I did not realize that you were expecting a statement. I thought there was something like a box I had to check that I had failed to do. Yes, I am quite familiar with conflict of interest. I see what you are saying about my COI with regard to the Margulis article. I will agree to follow Wikipedia's COI management process - thanks for letting me know about it! Below is how you mentioned COI and Peer review and I have added my comments in bold.

"One of the challenges is related to conflicts of interest (COI). You may be familiar with that concept from your real world work, but it has some interesting twists here in Wikipedia, since Wikipedia's structure allows editors to instantly publish, with no prior peer review. Please do read WP:COI, especially the section on Writing about yourself and your work." I did that but I think when you said there were "twists" it made me think there was something more complicated to be done.

"Wikipedia is a scholarly project, and like all scholarly endeavors, managing COI is essential for ensuring the integrity of Wikipedia and retaining the public's trust in it. As in academia, COI is managed here in two steps - disclosure and a form of peer review." I am assuming that we have wrapped up the disclosure portion.

"Disclosure: You have already disclosed the relationship with Margulis on your User page, so the first part is partly done. I have also added a tag to the Talk page of the Margulis article so your relationship is disclosed there." I read this originally as the COI business was complete.

"Peer review: Going forward, please do not edit the article directly, but rather offer suggestions for content changes at the article's Talk page." I still do not know how to access the article's talk page. "You can do that easily - and provide notice to the community of your request - by using the "edit request" function as described in the conflict of interest guideline. I made that easy for you by adding a section to the beige box at the top of the Talk page - there is a link at "click here" in that section -- if you click that, the Wikipedia software will automatically format a section in which you can make your request. The reason for this, is that it allows peer review of proposed changes before they become part of the encyclopedia. We have gotten great contributions that way, and were able to protect the integrity of WP at the same time. Would you please do that going forward?" I did not connect this question which seemed related to Peer review to acknowledging my COI--I assumed it was rhetorical. I have not located the article's talk page or the beige box or click it link-- sometimes navigation is not intuitive.James D. MacAllister (talk) 21:57, 9 July 2015 (UTC)[reply]

(you have the hang of the colon/indenting thing - wonderful!) OK, the foundation of Wikipedia is WP:CONSENSUS (our most important policy) and we reach consensus by talking. So.. every article in Wikipedia has an associated "Talk" page which is where editors discuss edits to the article. Likewise, every policy, and guideline, and essay...and every User page. This page, where we are writing, is the Talk page that goes with your User page. There are "tabs" (not the indenting kind, but the file folder kind) at the top of every page in Wikipedia, near the top left corner. If you look at the top left corner of this page, you will see "User page" and next to that, "Talk". Likewise, if you look at the Lynn Margulis article, you will see "Article" and next to that, "Talk" - if you click on the Talk tab, it takes you to the associated Talk page, which your can go directly by clicking here Talk:Lynn Margulis. There, you will see the beige box I mentioned. Hopefully that makes sense. (and maybe you just caught, that you can create a hyperlink to an article by surrounding it with double square brackets, and to its talk page by just sticking "Talk:" in front of it, and surrounding that with double square brackets)

I mentioned that there are policies/guidelines that govern content as well as behavior. The guideline for behavior in discussions at all Talk pages, is here: talk page guidelines. On article Talk pages, people discuss the actual article, based on sources and policies/guidelines - not each other, and not the topic in general. On User talk pages, like this one, we talk about each other, or general issues. The conversation we have been having, about your COI and how Wikipedia works - that is all very appropriate User Talk page discussion.

So, unless you have more questions about COI or anything else we've discussed, that about wraps this up. I offered somewhere in this page, to provide you with my "orientation" essay. If you want that, let me know. If you have any further questions, feel free to drop me a note at my Talk page (which you have already found). I wish you well! Jytdog (talk) 23:37, 9 July 2015 (UTC)[reply]

Thank you Jytdog for all the help and patience. It is a BIG beige box. I will poke about the Lynn Margulis talk page and read whatever is there. Yes please send link to your orientation essay. I will read the talk page guidelines and make edit requests when I think I've got the guidelines for talk down.James D. MacAllister (talk) 01:32, 10 July 2015 (UTC)[reply]

Edit warring warning

Hi James - I am also providing you notice of our policy on edit warring, as you are new here. Please keep this in mind going forward. Thanks!

You currently appear to be engaged in an edit war according to the reverts you have made on Lynn Margulis. Users are expected to collaborate with others, to avoid editing disruptively, and to try to reach a consensus rather than repeatedly undoing other users' edits once it is known that there is a disagreement.

Please be particularly aware that Wikipedia's policy on edit warring states:

Edit warring is disruptive regardless of how many reverts you have made.
Do not edit war even if you believe you are right.

If you find yourself in an editing dispute, use the article's talk page to discuss controversial changes; work towards a version that represents consensus among editors. You can post a request for help at an appropriate noticeboard or seek dispute resolution. In some cases it may be appropriate to request temporary page protection. If you engage in an edit war, you may be blocked from editing. Jytdog (talk) 14:29, 8 July 2015 (UTC)[reply]

How does messaging or talk work?

Jytdog and Adrian,

How does talk work? Do I talk here and somehow my message gets to you? It seems counterintuitive--like I am talking to myself.

James D. MacAllister (talk) 13:12, 9 July 2015 (UTC)[reply]

Just reply here. Every editor in Wikipedia has a "Watchlist". You can add any article (and its talk page too - they "travel" together) in multiple ways. You can click on the "star" shape that is next to the search box above. Or, you will notice when you edit any page, that just under the "Edit summary" box there are two checkboxes - "This is a minor edit" and "Watch this page". You can check the box there, too. You can see your Watchlist by clicking "Watchlist" at the very top of every page that Wikipedia displays to you, near the right side. You see it? People put articles they are interested in, on their Watchlist - this lets you track changes made to that article, so you can react to the change, if you want to. This Talk page is on my watchlist, so if you reply here, I will see it on my watchlist, and respond. We talk back and forth on Talk pages throughout Wikipedia. We also "thread" comments. When you reply to me, look at the start of my comment. You will see a colon there. The Wikipedia software turns that colon, into a tab or indentation in the displayed text. When you reply to me, put two colons there, and after you save, you will see two tabs/indentations. You have threaded your comment, showing that you are replying to me. Adrian might reply to me too, and if he does, he will also put two colons - that shows he is replying to me, not to you. If he puts three colons, it will indent three times, showing that he is responding to you, not to me. That is how threading works here. Hope that makes sense. Jytdog (talk) 13:24, 9 July 2015 (UTC)[reply]

I was halfway through replying when I say Jytdog had already beaten me to it! One colon for me for now, since I'm really replying to you and not to Jytdog.

You're absolutely right that starting to edit Wikipedia is far more difficult than it ought to be. It's something I think the community has been aware of for a long time, but for some reason there doesn't seem to be much will to address the problem. I do hope we haven't put you off editing and that you'll continue and become a productive contributor. I think retired scientists are an excellent and underutilised resource for Wikipedia. Adrian J. Hunter^{(talk•contribs)} 13:33, 9 July 2015 (UTC)[reply]

James, another way of communicating is called "pinging". If you write [[User:user's name]] in your message, so for you it would be [[User:James D. MacAllister]], a message is automatically sent to the user that you have mentioned them. This appears as a little red square at the top of your page. Welcome, and best of luck in the editing.DrChrissy ^(talk) 13:44, 9 July 2015 (UTC)[reply]

Still fuzzy on how to use colons and have comments go where intended. Question: Is the primary peer reviewed science literature considered publication in "mainstream" "reliable sources"? This just in from ResearchGate: Cited article: Spirochete round bodies Syphilis, Lyme disease & AIDS: Resurgence of “the great imitator”? Citation: "...When exposed to unfavorable conditions such as osmotic and heat shock, B. burgdorferi produces atypical forms (e.g., Brorson and Brorson 1998, 2004; Singh and Girschick 2004; Miklossy et al. 2008; Margulis et al. 2009). The extracellular and intracellular presence of these atypical forms has been demonstrated in brain tissue of humans with confirmed neuroborreliosis, and atypical forms can exist in the absence of spirochetal forms (Miklossy et al. 2008). ..." Article: Lyme borreliosis in Canada: biological diversity and diagnostic complexity from an entomological perspective. The Canadian Entomologist 12/2009; 141(6):521-549. DOI:10.4039/n08-CPA04James D. MacAllister (talk) 14:47, 9 July 2015 (UTC)[reply]

James, you might care to read an essay I have been working on hereWikipedia:Identifying primary and secondary sources for biology articles. Please note this is only an essay, not guidelines or policy, but it might help and it does have related links. The reliability of sources differs between subjects, however, due to a topic ban imposed on me I am unable to discuss these with you, however, I am sure other editors will let you know about these. By the way, when you change to a completely different question, it helps both you and other editors to start a new section.DrChrissy ^(talk) 15:10, 9 July 2015 (UTC)[reply]

James, the editor who just messaged you above, DrChrissy, is currently topic-banned from discussing anything related to Wikipedia's guideline for content about health or other biomedical information (WP:MEDRS) anywhere in Wikipedia, so I suggest to you that he is probably not the ideal model to learn from, with regard to editing about health related content in Wikipedia. You will of course do as you will. Jytdog (talk) 17:51, 9 July 2015 (UTC)[reply]

That is really a pretty cheap shot. I have been trying to help James with biology and science sources in general. I have not offered any advice whatsoever on the subject I am not allowed to talk about. Your edit seems simply an attempt to try and discredit me in the eyes of a newcomer to the project. James, there is also a policy that editors should comment on edits, not the editors. Above is a prime example of that policy being broken.DrChrissy ^(talk) 22:09, 9 July 2015 (UTC)[reply]

Oy! Your info arrived a little late. I assumed Dr. Chrissy was another Wiki person like Adrian Hunter.

DrChrissy is indeed another Wikipedia person, like me and like Adrian. There are all kinds of people here, with all kinds of perspectives and with various privileges, some with more privileges, and some less, and most with just standard levels. Remember when I wrote above that editing Wikipedia is a privilege that can be lost in whole or in part? DrChrissy lost part of his privileges here - he cannot discuss anything related to our MEDRS guide. That's all. Jytdog (talk) 18:32, 9 July 2015 (UTC)[reply]

Not sure exactly what topic-banned means or should mean to me. He did mention that he could not discuss guidelines and that his essay was just that and not Wiki policy or guideline. Thanks for the link to (WP:MEDRS). Perhaps you or Adrian would comment on my remarks under the new heading below which deals with the fact that textbooks, books, and other third party sources present obsolete ideas--especially in science and medicine.2601:180:8100:35DF:99F5:414F:1272:AD61 (talk) 18:45, 9 July 2015 (UTC)[reply]

Source material --what is considered mainstream reliable sources?

Question: Is the primary peer reviewed science literature considered publication in "mainstream" "reliable sources"? This just in from ResearchGate: Cited article: Spirochete round bodies Syphilis, Lyme disease & AIDS: Resurgence of “the great imitator”? Citation: "...When exposed to unfavorable conditions such as osmotic and heat shock, B. burgdorferi produces atypical forms (e.g., Brorson and Brorson 1998, 2004; Singh and Girschick 2004; Miklossy et al. 2008; Margulis et al. 2009). The extracellular and intracellular presence of these atypical forms has been demonstrated in brain tissue of humans with confirmed neuroborreliosis, and atypical forms can exist in the absence of spirochetal forms (Miklossy et al. 2008). ..." Article: Lyme borreliosis in Canada: biological diversity and diagnostic complexity from an entomological perspective. The Canadian Entomologist 12/2009; 141(6):521-549. DOI:10.4039/n08-CPA04James D. MacAllister (talk) 14:47, 9 July 2015 (UTC)[reply]

James, you might care to read an essay I have been working on hereWikipedia:Identifying primary and secondary sources for biology articles. Please note this is only an essay, not guidelines or policy, but it might help and it does have related links. The reliability of sources differs between subjects, however, due to a topic ban imposed on me I am unable to discuss these with you, however, I am sure other editors will let you know about these. By the way, when you change to a completely different question, it helps both you and other editors to start a new section.DrChrissy ^(talk) 15:10, 9 July 2015 (UTC)So[reply]

Dr. Chrissy, Thanks for pointing me to your essay. I was using the term "primary" to include all peer-reviewed papers, primary, secondary and literature reviews as opposed to science reporting. So if I want to reference McFall-Ngai, Margaret, Hadfield, Michael G., Bosch, Thomas C. G., Carey, Hannah V., Domazet-Loso, Tomislav, Douglas, Angela E., Dubilier, Nicole, Eberl, Gerard, Fukami, Tadashi, Gilbert, Scott F., Hentschel, Ute, King, Nicole, Kjelleberg, Staffan, Knoll, Andrew H., Kremer, Natacha, Mazmanian, Sarkis K., Metcalf, Jessica L., Nealson, Kenneth, Pierce, Naomi E., Rawls, John F., Reid, Ann, Ruby, Edward G., Rumpho, Mary, Sanders, Jon G., Diethard Tautz, and Jennifer J. Wernegreen (2013) "Animals in a bacterial world, a new imperative for the life sciences." Proceedings of the National Academy of Sciences of the United States of America, I would first have to reference “I, Ecosystem” ScienceNews magazine feature cover story on microbiomes that was based on the McFall-Ngai et al paper? Even the SN article which won an honorable mention for best consumer full issue in science and technology at Eddie & Ozzie Awards did not really get the story right. (e.g., The cover tag line was "How microbes have infiltrated every niche of multicellular life." That puts the cart before the horse: microbes have always been present in multi-cellular life and mediated multi-cellular evolution--a crucial distinction.) The November 2014 issue of National Geographic magazine features a story, "Mindsuckers: Meet Nature's Nightmare" written by science reporter Carl Zimmer based on Richard Dawkin's book "The Extended Phenotype". However, Dawkins bases his book in neo-Darwinism that, according to Denis Noble, the president of the Union of Physiological Sciences (citing multiple peer reviewed papers and also books) in his presidential address to the IUPS states and demonstrates that "All of the rules and assumptions of the Modern Synthesis have been broken." So the article by Zimmer or the neo-Darwinist explanation given in the remake of the "Cosmos" series on television present material that is out-of-date. Would those still be mainstream and reliable? I am asking because so much mainstream and supposedly reliable sources get things wrong. I am sure the New York Times still considers Richard Dawkins the go-to guy for questions about evolution, even if his ideas have been repeatedly demonstrated not to square with many studies and with books in print. (e.g, James A. Shapiro's book, "Evolution: A view from the 21st century" gives chapter and verse on why neo-Darwinism is at best incomplete and at worse demonstrably wrong in great detail and is abundantly referenced, but Shapiro's view, being new, could easily be called "fringe" because the majority of folks in biology, medicine and evolution are from the neo-Darwinist school. I would appreciate your comments on this as I am happy to request edits and base the requests on reliable sources, but even after reading your essay, I am not sure what makes a source reliable. Not sure why tildes do not sign my name. James D. MacAllister

I doubt this answer is going to satisfy you all that much, but it is consensus which makes a source reliable. First of all, the reliability of a source is related to context. The reliability of a source depends on what you want to say. If you are unsure, you can ask at the talk page of the article, or be bold, make the edit and be prepared to discuss it if your edit is reverted.

This primary and secondary business can be confusing, especially for scientists like us. Newspaper reports are considered to be secondary sources whereas scientific articles reporting novel findings are primary. It is usual for secondary sources to be preferred to primary sources, so in many cases, a newspaper report is more preferred to a scientific report! If you have ever dealt with the press about any of your papers you will probably know how "differently" they report/distort science, but that is what WP have decided. By the way, I have very recently run into the issue that SOME newspapers are considered to be RS whereas others are not - again, it is consensus that matters.

An issue that you raised above I think is whether you need to cite the original source of a concept or data. In science, we would always do this, but on WP, it is not necessary. Edits must be verifiable. This means that if you were to read a reliable newspaper (e.g. in the UK perhaps The Independent) and this stated that in an interview with a scientist they reported the discovery that 99% of ginger tom-cats are sterile, you could edit the cat page with this information and cite only the newspaper article. No need to mention the researcher. Not fair on scientific notability I know, but unfortunately that is the way it is. Happy to help more if you need it.

DrChrissy ^(talk) 18:38, 9 July 2015 (UTC)[reply]

For content about health what DrChrissy writes is incorrect. Please read WP:MEDRS for information about that, James. Secondary sources for content about health are reviews in the biomedical literature (not primary sources reporting research), and statements by major medical and scientific bodies (things like AAAS, WHO, or say Infectious Diseases Society of America or the American Heart Association. DrChrissy's essay is not widely accepted. Even out side of biomedical/health content, reviews in the scientific literature are miles better than reports in the media. Jytdog (talk) 19:56, 9 July 2015 (UTC)[reply]

I'm not sure why you felt the need to write that the essay is not widely accepted - I have received no negative comments about it, then again, I have no idea how many people have read it. Why do you feel it is not widely accepted? By the way, I totally agree that reviews in the scientific literature are considerably better than newspaper reports, but the reality is that it can easily take 3 to 5 years for a primary scientific report to appear in a review article.DrChrissy ^(talk) 21:34, 9 July 2015 (UTC)[reply]

how frequently reviews are done varies across topics/fields. Jytdog (talk) 21:44, 9 July 2015 (UTC)[reply]

Yes it does - I forgot to add "depending on the subject".DrChrissy ^(talk) 21:46, 9 July 2015 (UTC)[reply]

Infectious Disease Society guidelines for spirochetoses are "misinformed". The group that does them has its own COI issues which unfortunately explain why the group is not interested in patient health. One of that group from the CDC recently co-authored a literature review that failed to find hundreds of references in the medical literature in English and did not bother with publications in other languages (Russian literature on the subject is extensive) on the subject of round bodies. I found more peer reviewed papers covering a longer time span in 5 minutes on Google! They did cite a paper on which I am a co-author and then came to a totally inexplicable conclusion that there was no evidence that round bodies required treatment! A recent paper from Johns Hopkins just came to the opposite conclusion. Papers in fields away from medicine easily find that round bodies are viable--for example in biomass conversion to ethanol where there is no controversy about these pleomorphic forms of bacteria being viable and described in detail. Last year I had a tick bite. The tick was on me for at least 18 hours. I had the tick examined for pathogens at UMass Amherst and it was positive for Lyme. This year, I had a PCR test for Lyme. The test results stated as definitive that I have never been exposed to Lyme. The fact that these facts contradict one another is not a surprise to me. Spirochetes are very good at hiding out in red blood cells.James D. MacAllister (talk) 22:32, 9 July 2015 (UTC)[reply]

Quick note

I saw your post at the article. Thanks so much for using the edit request function!

You'll see I marked the edit request as "declined" for not being specific. I don't think your intention was to ask for specific changes to the article, so I hope that makes sense to you.

Some more stuff about how Talk pages at articles work... I don't know if you read WP:TPG but there is an emphasis there on using the talk page to make concise, actionable comments. This is even more so when making an "edit request" -- the purpose that tool is to request an actual, concrete change to the article - like "please change "asdasdfasd" to "asdfgasdfadsfafd" - requesting an edit.

What you wrote is what we call a WP:Wall of text. What that essay, and the stuff at "Be concise" in WP:TPG try to explain is part of how Wikipedia works. To say a bit more, we are all volunteers here, and few people have the time to read very long Talk page posts. More importantly - generally if the long post is used well and many specific issues are raised in it (I say that because we do get new editors who make very long posts on Talk pages that are just rambling messes.. yours is not like that!), it is really hard to figure out how to response. Where do you start? If an editor tries to respond to everything, and then the original poster replies, the written discussion becomes unmanageable. A very kind editor will guess as to what is most important to the original poster, and will respond to just that, but that doesn't happen too often. Most times long posts are just not responded to.... as it is impossible.

What I suggest that you do, is pick one chunk of content in the actual article, and suggest a change to it on the Talk page (including the sources that support the proposed new content) and provide the reason for the change. And please do that in a way that communicates that you are looking for a discussion, not making a demand. ("requesting" an edit!) And please be ready to listen to responses and to understand why those responses are being made. I hope that all makes sense. If you want help formatting or setting it up, I would be glad to help you with that Jytdog (talk) 12:57, 13 July 2015 (UTC)[reply]

Jytdog,

I was being concise given the subject matter and the apparent ignorance of what the paper actually says. I had to answer Adrian Hunter's points particularly where I thought he erred in his logic or presented arguments that neither I nor the paper make. I have no objection to your declining my edit as I was not asking for a specific edit, but responding to Adrian Hunter's reasoning and presenting an examination of the paper as to what it actually says as opposed to what Professor Kalichman claims or how Adrian Hunter sees it. It should be a given that editors have read the paper itself if they are going to make judgements about it. From Adrian Hunters comments I had to assume that he had not read the paper, so in replying to his points I must concisely pull out those parts of the paper that mention AIDS or HIV and describe what is actually being said and why. It is also a scientific position paper written from 2009 so it has a historic context which also has to be understood and editors also need to understand why a position paper is written. I thought that posting this would be a good starting point for then making specific edit requests which Adrian Hunter and others will weigh. I would hope that you, Adrian Hunter and other editors read what I wrote and not simply dismiss it as a "Wall of Text". I think that is too easy a cop-out given the charges made and endorsed on Wikipedia that the paper is an example of "HIV/AIDS denialism" and "AIDS denialism". The paper is about spirochetoses and questions whether "tunnel vision" may have AIDS researchers not investigating a highly likely possibility of a co-factor that is well-known to compromise immunity. Co-factors in discussions of AIDS are not a "fringe" topic. It is easy and short to label something "denialism" or "fringe" or "wall of text". I have the more difficult task, which is to refute the personal and professional accusation. I am happy to follow your advice (which I greatly appreciate) about making edit requests for specific edits and using the paper and other references to support them. It is much easier to do that if the editors are informed what the paper in question presents and why. If Wikipedia is going to present scholarship then volunteer editors should be willing to read either the source material or, in this case, a summary of that material from another editor (even if I have a conflict of interest and will be making edit requests.)

Just to clarify a point you made. Is it not allowed to make any comment on the talk page unless it is in the form of an edit reguest? I was under the impression from another posting that some discussion regarding edits, edits being declined, being reverted or edit requests would be proper.James D. MacAllister (talk) 14:10, 13 July 2015 (UTC)[reply]

Your reply makes sense, thanks! The "edit request" function is really just for making requests to change the article - if all you want to do is discuss things, there is no need to use it. Thanks for asking - apt question! :) In general, things are more efficient and productive if discussion on Talk focuses on specific proposals to change content that is in the article, or proposals for new content. And it is best to do that bit by bit.... Thanks again for talking. Jytdog (talk) 14:21, 13 July 2015 (UTC)[reply]

Thank you for the clarification. I thought that the only way I could contribute was by using the edit request function so I would be identified as having a COI. So how do I make comments and identify myself as having a conflict of interest? Or is that done automatically? I did not answer your question about whether or not I read WP:TPG. Yes, I did and I even went back just now to read it again because I thought you were saying I had missed something important in "being concise"--like an word count that could not be exceeded. Thank you for reading and understanding what I was attempting to do, including being as concise as possible. Someone once said, "If I had enough time, I would have written a shorter note." I am sure I could have been even more concise but there is a limit to how long I want to spend editing my comments. I will attempt to be as concise as possible in the future. Is it possible for you to "correct" my use of the edit request function and simply make my Wall of Text as comment or discussion? I think that will be less confusing to other editors. I look forward to knowing the proper way to make a comment or discuss an issue.James D. MacAllister (talk) 14:33, 13 July 2015 (UTC)[reply]

I appreciate the care you are taking! By now it is pretty clear at the Talk page that you have a COI, so please just feel free to Talk now. (this is a community and we get to "know" each other - you can count on some continuity in people working on a given article) If somebody new shows up who seems unaware of your COI, you can just pop them a note at their Talk page or at the article Talk page. It is never meant to be a bludgeon or muzzle - just reasonable disclosure to the other people discussing things. I hear you on the difficulty of being concise! everybody is a volunteer here (well, except for paid editors and they are not that common) Jytdog (talk) 14:54, 13 July 2015 (UTC)[reply]

follow up - two things:

first, you may have seen that I added "reflists" to the talk page. The formmatting looks like this: {{reflist-talk}} - it is no big deal, but if you are going to cite a ref on the talk page, it is useful to include that so that people talking with you have easy access to the ref. Without that, refs pile up at the bottom of the article which is harder for your respondants to find and also creates clutter. Again, no big deal.

more importantly, about this comment, please try to remain focused on actual article content, and on sources that can actually be used in the article. Talking about your discussions with Margulis and things she has said to you, explaining why she did X or Y based on your experiences... none of that is good on a Wikipedia article Talk page, as none of it can actually be used in the article. (we can only base Wikipedia articles on what reliable sources say - and reliable sources are defined in WP:MEDRS and WP:RS.) If you keep doing that, you are going to end up frustrating the folks who are talking with you... and that will not help you get you what you want. I hope that makes sense! Jytdog (talk) 16:21, 16 July 2015 (UTC)[reply]

Where do I enter the "realists"? Before I sign? I will check WP:MEDRS and WP:RS. Thanks. I will reign in my desire to clarify--the curse of a technical writer. Thanks for your changes, suggestions and reminder.James D. MacAllister (talk) 16:44, 16 July 2015 (UTC)[reply]

You can add {{reflist-talk}} wherever you want references to appear. It's just for convenience. Adrian J. Hunter^{(talk•contribs)} 15:39, 17 July 2015 (UTC)[reply]