Open Access Publishing: When open forums go wrong

Posted by ERV on March 7, 2011
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As a scientist and a blogger and a science communicator, I luvs me some open access publishing! I can link to a paper everyone can read, people can leave questions or comments or ideas in my comment section– its interactive and educational and a lot more fun for everyone (I end up learning a lot answering peoples Qs, or by others answers myself).

I also love the idea of open comments on papers. I dont have to hunt down an email and hope an author responds to a technical question or point– post your question/comment, and either someone on the paper or someone else can answer it for you! Super easy clarifications– and like I tell commentors here, if you have a question, ASK. If you are wondering about something, odds are lots of people have that same question too. Authors dont have to answer the same Q a billion times– its in their papers ‘comments’ section. Huzzah!

But something Ive noticed is that on public access papers with comment sections… anyone can leave a comment. Anyone. Including people who have very strong opinions, but dont have a *clue* what they are talking about. I do not mean people in a field arguing over a point of contention. I mean someone 1) not in the field, with no working understanding of the topic, 2) not understanding a paper, 3) leaving ignorant, even hateful comments on open access papers.

They treat open access papers like an internet forum.

Case in point: the ‘XMRV is def a lab contaminant‘ paper, over at Retrovirology. A commenter by the name of ‘Gerwyn Morris’ left a long, obnoxious, stupid comment on the paper.

Now, there is nothing wrong with stupid questions. I find myself asking stupid questions all the time.

This was a stupid comment, where Gandalfrodo vociferously argued a stupid point, which he didnt know what stupid because he has no idea what he is talking about. But boy howdy, hesagunna tell that hoidy-toity SCIENTIST whats up, though!

A PI attempted to humor her/him, and was rewarded with somehow even stupider responses, escalating in tone, shrillness, and frequency. Its obvious to even the most casual observer hes just making up shit as he goes along, and is coo-coo-bananas.

Apparently Gryffindore thinks he is ‘taking Dusty Miller to task‘.

PRO-TIP: If you are using the same arguments as Creationists, you are not ‘taking anyone to task’. You are annoying people and making an ass of yourself.

I mean, this is not a difficult concept to grasp. Casual readers of ERVs understand the implications of finding two retroviruses integrated in the same location in experimentally infected cell lines and ‘human samples’, not once, but twice. They understand the implications of these viruses not only being in identical locations, but the viruses themselves being identical. One, from cell lines infected with a functionally clonal stock of viruses (lab grown) in the lab, and the other from a wild-type, pathogenic, found in nature with all of the accompanying selective pressures.

Its not just the integration sites that are identical. Its the viruses.

Its contamination.

Casual readers of ERV are (mostly) not professional retrovirologists. They ‘get it’. Bob Silverman is a professional retrovirologist. He gets it.

But Brave Sir Gyreynyory thinks he is talking all of us ‘to task’ with papers that have nothing to do with the topic at hand, and declaring we dont understand ‘the scientific method’. In the comments section of a real, PubMed listed publication.

Its ridiculous.

It completely inappropriate. Gyyyyyyyn is not paying me or Miller or any of the articles authors tuition to teach him the basics of our field. And even if he were, the comment section of a paper is an inappropriate location for such a discussion.

There is a place on the internet where everyone and anyone can leave stupid, insightful, humorous, or annoying comments. Hell, sometimes the stupid/annoying ones are actively encouraged. Its called the blogosphere. There are any number of virology blags on the internet, run by professional virologists, who love to talk about and teach their readers about virology. There is no damn reason why an Average Artard needs to be acting up in the comment section of a professional publication, any more than I need to be throwing a temper tantrum about X-wing flight in the cockpit of the 7.30 am OKC to Dallas flight, or bitching to a Michelin Star chef about how she doesnt understand French cooking like I do (I read about it on the Google Machine!).

It would be nice if these pro-internet, pro-technology open access publications would allow some kind of links to papers. A side-bar of ‘blog coverage of this paper’ or something. Seems like it wouldnt be too difficult to merge some online publications with the network already built up by ResearchBlogging.org, and it would be a great three-way street. Bloggers would get traffic, authors would get more exposure for their work and be able to see reactions to their work, and readers would easily be able to switch back-and-forth between tabs, having a science blogger tell them the basics, so they understand the publication itself better, and then they have a professional in the field right there on the blog where they can ask questions or leave comments, leaving the paper comment section open for ‘We tried X and couldnt get it to work! What pH was your buffer??’.

Of course, I am under no illusion that this kind of set up would actually dissuade people like Gyyyyyyyyyy from leaving comments on papers. His kind are a dime-a-dozen, Ive seen it a million times. They have no intention of learning anything. Their intention is to get attention from people they think are important. This means they are entirely uninterested in commenting on a science blog (especially a girls blog) and learning something. They are interested in attention from ‘important people’ so they can pretend they too are important. Like how Ray Comfort and Michael Behe wont debate me (or hell, even address me directly, in Behes case), while they pull Dawkins pig-tails and run, hoping he chases them. Or like when I make an argument, an Important Male like Coyne encourages my point, and people argue with him instead of me, because hes Important. Those kinds of people, I dont know what to do with them. Arrogant assholes are going to be arrogant assholes no matter how many more appropriate outlets you give them for their asshollery.

But I think adding links to research blogging on research papers would be a great addition to Open Access papers for normal people.

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Comments

  1. #1 William Wallace
    March 7, 2011

    Public comments directly juxtaposed with internet published peer reviewed research is tacky. It should be moderated, left to blogs, or at least marginalized in a separate sandbox as you sugggest. Even professors in the field can leave stupid comments based on a hasty analysis, which is different than saying a professor who did such a thing is stupid. Private correspondance is slower, perhaps, but probably more productive all the way around.

    In short, I agree on most of what you write here (except 12 should be encouraged because it was intelligent, witty, poignant, and thought provoking. And being skeptical of biologist’s ability to discern or rule out coincidence is not all that unreasonable. Just saying.)

  2. #2 stogoe
    March 7, 2011

    Wee Willy Winky,
    Abby purposefully linked in this very post to your very own sandbox where you could lay down turds without stinking up the neighbors’ places. And here you are, dropping trou in the next door neighbor’s dining room. I am ashamed for you and your family.

  3. #3 The Chimp's Raging Id
    March 7, 2011

    @stogoe

    Ha, you beat me too it. The irony of Limp Willy being the first to comment is rich indeed.

    @ERV

    I think you suggested approach is pretty good. The only alternatives I can think of are inferior:

    1. Active comment moderation
    2. Some form of registration system that vets the commenters’ credentials so as to keep out the folks trying to Dunning-Kruger all over the place.

    (1) will be constant effort for the journals and (2) would be a bureaucratic pain in the ass for all involved.

  4. #4 Alan Dove
    March 7, 2011

    Well, why didn’t someone warn us that open comments would be a dicey proposition? Instead of all this Monday-morning quarterbacking, someone should have said something way back in 2006, when PLoS ONE (the first journal to adopt such a system) geared up.

    Oh, right. I did.

  5. #5 Mary
    March 7, 2011

    Great ideas but not sure if even they would work bacause as you said:

    “Arrogant assholes are going to be arrogant assholes no matter how many more appropriate outlets you give them for their asshollery.”

  6. #6 In Vitro Infidelium
    March 7, 2011

    @TCRId
    1. Active comment moderation
    2. Some form of registration system that vets the commenters’ credentials so as to keep out the folks trying to Dunning-Kruger all over the place.
    (1) will be constant effort for the journals and (2) would be a bureaucratic pain in the ass for all involved.

    Registration is easily automated and qualifying email addresses could be made institution only. To not employ this basic level of discussion ‘quality control’ is simply laziness on the part of the journals.

    The arrogant, the stupid and patently ‘disturbed’ are taking over what could/should be spaces for serious debate. Science can’t be a populist democracy, it requires competences that effectively make it a meritocracy. Flattening out the hierarchies within science is certainly healthy, but turning scientific debate into a witless free for all benefits no one.

  8. #8 W. Kevin Vicklund
    March 7, 2011

    Uh, guys, as much as I enjoy bashing the Limpster, I don’t really see anything worth bashing in his comment, except maybe the parenthetical (which everyone pretty much ignored). It also kinda loses the impact if you attack him for saying the opposite of what he said (looks at stogoe).

  9. #9 Ben
    March 7, 2011

    Germ also did this which he thinks got published as “an original article”. Lol. Noob.

  10. #10 Ken
    March 7, 2011

    Yea but what about Gerwynie taking Miller to task by stating that XMRV is inserted into 472 sites in Prostate DNA. Thus contrary to the assertions made by Miller XMRV is capable of making three insertions within a 100 kilobase region as noted in the following table duplicated from the study;

    Sites of XMRV integration in DU145 cells are indicated as red vertical lines along the top, and XMRV integration sites in prostate cancer tissues are indicated as blue “lollipops” on the bottom. Within each chromosome, the top bar shows the relative densities of RefSeq genes, with higher gene-dense regions shown as a more intense cyan. The second bar shows the chromosome cytobands. The third bar shows the cancer breakpoints, and the frequencies of breakpoints in different chromosomal regions are denoted by different colors (see the key at the bottom right-hand corner). The green shading in the bottom bar denotes the locations of common fragile sites.”

    Thus if two of a possible 470 integrated XMRV sequences were found in DU145, cells which were identical in terms of nucleotide insertion points, then the experimental environment can be the only possible source.In short the DU145 cells were contaminated by human DNA during the experimental procedure.

    Seems to make a valid point here against Miller

    http://www.retrovirology.com/content/8/1/13/comments

  11. #11 Ken
    March 7, 2011

    By the way who is this Gerwyn Morris and what is the PA Institute? I never heard of it? Does anyone know?

  12. #12 W. Kevin Vicklund
    March 7, 2011

    Thus contrary to the assertions made by Miller XMRV is capable of making three insertions within a 100 kilobase region as noted in the following table duplicated from the study

    Where does Dr. Miller make that assertion? I can’t find it in either the article or the comments.

  13. #13 Jules
    March 7, 2011

    Gerwyn Morris is in Wales. (Can’t help you with the P A Institute.)

    He hangs out here:

    http://www.mecfsforums.com

    …Disgruntled people aplenty! Ugh.

  14. #14 Jel
    March 8, 2011

    http://www.ncbi.nlm.nih.gov/pubmed/21377178

    XMRV, a new human retrovirus for disease.

  15. #15 Charl
    March 8, 2011

    The badly translated title of a Spanish review article does not constitute news.

  16. #16 ERV
    March 8, 2011

    LOL!

  17. #17 Mobius
    March 8, 2011

    Sadly, far too many people in the US think that the right to have an opinion means that you MUST have an opinion and that you have the right to shout it to the rooftops (which they do have the right to express any opinion they have). BUT…they also think they have the right to have their opinion taken seriously, which said right does not exist.

  18. #18 Mobius
    March 8, 2011

    Lol. Saw this just after reading your blog post…

    From SMBC…

    http://www.smbc-comics.com/comics/20110308.gif

  19. #19 Jel
    March 9, 2011

    I post a link and the name of the study. There is nothing wrong in doing that.

  20. #20 W. Kevin Vicklund
    March 9, 2011

    What a delightfully snarky title!

    XMRV, un nuevo retrovirus humano en busca de enfermedad

    XMRV, a new human retrovirus for in search of disease.

    Puts a whole ‘nother light on things, doesn’t it?

  21. #21 ERV
    March 9, 2011

    WAY TO RUIN THE JOKE, KEVIN! GAHD!

  22. #22 John
    March 9, 2011

    People have been fussing over a false dichotomy between XMRV being a recombinant vs. XMRV being a contaminant-

    A retrovirus being a recombinant (is calling it a recombinate incorrect?) is not mutually exclusive of it being a contaminant as well. For example HIV is a pathogenic retrovirus which can recombinate with other HIV strains, but if you had a big vat of recombinant HIV (is there even any other kind?) and spilled it all over your lab then that HIV would then likely become a contaminant for whatever experiments you were trying to do. Take that example except substitute less-than-microscopic particles of the retrovirus in question, mouse DNA, etc. in place of a vat and that is how a recombinant could also be a contaminant.

    Just because people who have unknowingly been working with cell lines which contain XMRV are worried that they might have been exposed does not preclude that same XMRV contaminating others’ experiments.

  23. #23 ERV
    March 9, 2011

    You got it, John. Recombination plays a huge role in the life-cycle of retroviruses, because they are essentially diploid organisms. Ive covered it before here at ERV.

    All retroviruses are recombinants. Its neat that they found the exact ERVs that recombined. But its still a contaminant.

  24. #24 Jel
    March 9, 2011

    The cell lines in question have not been used by those finding this virus, and the WPI has not used mice in their lab. The authors of the study presented at CROI contaminated their mice with a human MRV retrovirus. There is still zero evidence that this was MLV contamination.

  25. #25 ERV
    March 9, 2011

    There is still zero evidence that this was MLV contamination.
    And there is ‘zero evidence’ for evolution, according to Creationists.

    Your (and Creationists) inability to understand what these papers mean (in English or Spanish) is not an ‘argument’.

    Its also inexcusable, considering you are commenting on the blog of a professional retrovirologist, who doesnt mind answering your questions.

    *shrug* Whatevs.

  26. #26 ken
    March 9, 2011

    What’s your take ERV, on Emory getting involved with XMRV

    http://whsc.emory.edu/home/publications/medicine/emory-medicine/winter2011/virus-of-interest.html

  27. #27 Just ME
    March 9, 2011

    It really sucks that millions of dollars and thousands of hours of good research time in top-flight labs have been wasted to demonstrate conclusively what most of us recognized when we first compared those WPI genomes with Silverman’s. It was contamination! Who cares if it was a recombinant mouse virus from a xenograft or just a bunch of VP62 plasmid floating around in the PCR room.
    Talking about politics, I there should be an investigation into how politics has interfered with science here. Senators Reid and Ensign, Representatives Heller and Berkley have earmarked the hell out of the US taxpayer to bring the bacon home to Big Donor Daddy Whittemore. I think I laughed almost as hard as ERV at the gels in that Science paper, a real throw-back to 1990. Did a few well placed phone calls from Capitol Hill keep the Science editors from laughing, too? Maybe I’m turning into a conspiracy theorist, but something smells.

  28. #28 Ken
    March 9, 2011

    The Flat Earth forum of Gerwynians are Blasting the sequencing of the VP62, VP35, VP42 and the MLV’s from the Alter/LO paper to take ERV down.

    http://www.mecfsforums.com/index.php/topic,6056.60.html?PHPSESSID=l8baskj2iomuo4salauegtu8a7

  29. #29 John
    March 10, 2011

    I think the big question about the Alter/Lo findings is where did the samples from the patients who were retested end up in the phylogenetic analysis since the original patient samples and those from the healthy controls ended up not even being close to each other?

  30. #30 Jel
    March 12, 2011

    All hyposthesis currently presented to claim contamination have failed to account for all the observations. It’s no more complicated then that. As I am a professional, I think it only right to have highlighted this.

  31. #31 Rebecca
    March 15, 2011

    Have you been to Gerwyn’s CFS forum? Everything he says is taken as “gospel” by the members. No one questions it. It is pretty disturbing.

    I am so tired of Gerwyn and his followers. They harrass everyone who does not agree with them, especially others with CFS on different forums. I didn’t think it was possible to make people think less of us, but thanks to Gerwyn and his peeps, they do.

    Thanks Gerwyn, you are awesome! But then again, you already know that!

  32. #32 ERV
    March 15, 2011

    Rebecca– I cant imagine how frustrating that is. When I first encountered them, I went from being someone who didnt know much (or care) about CFS, to being entirely convinced it was fake, based on their, frankly, obvious psychological issues. I need notes like this as reminders that the ones who are sick arent the ones posting 500 messages a day on message boards/news articles/blog posts/etc.

  33. #33 William Wallace
    March 16, 2011

    Yeah, it’s a good thing nobody here behaves like that, Rebecca. It’s pretty sad when people with different ideas are shouted down on the internet.

  34. #34 SAWells
    March 16, 2011

    Poor willie. He’s been shouted down on the entire internet! Who knew?

  35. #35 Padraig
    March 18, 2011

    Gerwyn Morris is just a patient. I don’t know why he is taken as seriously as he is by both sides of the equation. He’s just one opinionated patient out of, sadly, millions who has a following of maybe a dozen other patients. He’s sick and angry and frustrated, with good reason, and has just enough knowledge to get in over his head. Show a little humanity, people. These are pot shots.

  36. #36 ERV
    March 18, 2011

    “Taken seriously by both sides”? I assure you that no one on the ‘science’ side of things takes him seriously.

    And you must be new here, so Ill give you a pro-tip– I dont feel sorry for anyone. I study dead babies for a living. I havent felt sorry for a human in almost a decade, certainly not one with food to eat, clean water to drink, a climate-controlled house to live in, and round-the-clock computer and internet access.

    I really dont feel sorry for someone who uses a supposed disease as an excuse to be an arrogant asshole, especially when that behavior impedes research for said disease.

  37. #37 RRM
    March 18, 2011

    I must admit that I am also guilty as charged; I (without any training in retrovirology) once engaged with this Gerwyn (and his followers) in the comments section of a PlosOne publication. You can check if those comments make any sense
    here

    I see a sort of collective third person Dunning-Kruger like effect in these communities (or do they have a name for this already?): people just seem to lack the meta-cognitive ability to see that a fellow-patient that is slightly smarter/more knowledgeable than them, is still wayyy dumber than the average scientist in the field.

  38. #38 Kelly
    March 18, 2011

    “Arrogant assholes are going to be arrogant assholes no matter how many more appropriate outlets you give them for their asshollery.”

    Said the pot to the kettle.

  39. #39 William Wallace
    March 19, 2011

    Out of curiosity, how long did it take the scientific establishment to take Dr. Barry Marshall’s ideas about ulcers seriously?

  40. #40 W. Kevin Vicklund
    March 19, 2011

    Almost immediately.

  41. #41 William Wallace
    March 19, 2011

    Reference?

  42. #42 W. Kevin Vicklund
    March 20, 2011

    Keeping in mind that there is a difference between taking an idea seriously and accepting it as true, here’s a good summary. The acceptance of Marshall’s ideas and development of an effective treatment roughly parallels that of HIV->AIDS. If anything, even faster. In fact, aside from the disparity in the severity of the diseases, there are a lot of parallels in the timeline of the major milestones in the development of the diagnosis and treatment of the two diseases.

    The biggest problem Marshall faced was that there was already an effective treatment. In fact, Marshall was able to demonstrate in the initial paper why that treatment was effective (which in itself sped up the acceptance rate). So even if you accepted his idea of the cause of ulcers, he still needed to demonstrate that his treatment would be more effective than the SoC.

  43. #43 William Wallace
    March 20, 2011

    Interesting, I just glanced it, will study the article in more detail, later. From the article, however:

    But it isn’t true. I have no reason to doubt that many physicians scoffed when first faced with the notion of a bacterial basis for peptic ulcer disease (PUD).

    This jives with my experience. I had a good friend who was diagnosed with the type of stomach ulcers under consideration, starting in 1986. Antibiotics were not prescribed.

    Thirteen years from discovery (1984) to CDC recommendation (1997) for a relatively safe treatment using a drug already approved for other uses seems like a long time to me, an medical outsider, no matter how apologists for the scientific establishment spin it.

  44. #44 RRM
    March 20, 2011

    Still, even if Marshall was a good example, would it matter? Everybody can invoke Marshall: the WPI, Wakefield, Duesberg and Bozo the Clown.

    When you fall out of an airplane and are just about to hit to ground, do you think to yourself: “wait, up to this moment, my fall is exactly like that one guy that fell out of a plane and survived! Oh my god, I’m gonna live!”?

    Clinging to the exception is really a foolish way of arguing. Being perceived as being wrong is really very, very strongly correlated with actually being wrong.

  45. #45 W. Kevin Vicklund
    March 20, 2011

    This jives with my experience. I had a good friend who was diagnosed with the type of stomach ulcers under consideration, starting in 1986. Antibiotics were not prescribed.

    The first clinical trial of antibiotics, by Marshall, wasn’t completed until 1988. It was a single antibiotic, and while it had a significant improvement in the relapse rate, the side effects and resistance rate were too severe for approval since there was an existing treatment that was effective.

    Thirteen years from discovery (1984) to CDC recommendation (1997) for a relatively safe treatment using a drug already approved for other uses seems like a long time to me, an medical outsider, no matter how apologists for the scientific establishment spin it.

    Eight years – the three-drug regimen trial was completed and approved in 1992. By 1994, 90% of physicians, not just medical researchers, recognized it as the primary treatment. 1997 was the year the CDC promoted it to the public – it was already well-accepted in the medical community.

  46. #46 RRM
    March 21, 2011

    I just visited the forums for my daily dose of true XMRV Science. I couldn’t help noticing that our misunderstood genius now has the following signature:

    John Coffin asserts, “I think a causal role for HIV is not really on the table anymore in a serious way.
    [sic]

    It seemed odd for obvious reasons, so I googled it.
    Here     is the actual Coffin quote in the proper context. He is saying exactly the opposite of what this idiot is thinking. Yet those sheep on the forums probably now think it is proven that this Coffin guy, presently one of the most respected retrovirologists in the world, was a crazy HIV denialist back in the mid-nineties….

    Is this guy for real? Nobody can be that stupid?

  47. #47 RRM
    March 21, 2011

    I just visited the forums for my daily dose of true XMRV Science. I couldn’t help noticing that our misunderstood genius now has the following signature:

    John Coffin asserts, “I think a causal role for HIV is not really on the table anymore in a serious way.
    [sic]

    It seemed odd for obvious reasons, so I googled it.
    Here     is the actual Coffin quote in the proper context. He is saying exactly the opposite of what this idiot is thinking. Yet those sheep on the forums probably now think it is proven that this Coffin guy, presently one of the most respected retrovirologists in the world, was a crazy HIV denialist back in the mid-nineties….

    Is this guy for real? Nobody can be that stupid?

  48. #48 JKR
    December 23, 2011

    RRM, from what I have read… yes, he is really that stupid.

    Wow. I’m shocked. If they know anything about HIV research, they would have known that early in the research, causal link between HIV and AIDS was a cause-celebre for many for both legitimate and snarky/non-kosher reasons (I have some very strong opinions about Gallo’s disruptive role in all this, but that’s another story.) The article is just highlighting the whole debate, and like RRM says, Coffin is saying the debate is over at this point.

    I’ve come to the conclusion that this misunderstood genius is willing to use any and all means to gather any shred of “evidence” to somehow give the impression that he is on a crusade that will prove right at the end.

  49. #49 Smurfette
    June 25, 2012

    Gerwyn Morris has published a paper on CFS in the journal Metabolic Brain Disease!
    http://www.springerlink.com/content/c11431ku6005jh26/

  50. #50 Tony Mach
    June 25, 2012

    Thank you Smurfette, I have only seen Michael Maes and stopped reading – that Maes has written a paper together with Gerwyn consolidates my low opinion of him.