How a Valentine’s Editorial about Chocolate & Semen Lead to the Resignation of Top Surgeon Greenfield

27 04 2011
Children's Valentine in somewhat questionable ...

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Dr. Lazar Greenfield, recently won the election as the new President of  ACS (American College of Surgeons). This position would crown his achievements. For Greenfield was a truly pre-eminent surgeon. He is best known for his development of an intracaval filter bearing his name. This device probably has saved many lives by preventing blood clots from going into the lungs. He has been highly productive having authored more than 360 scientific articles in peer-reviewed journals, 128 book chapters as well as 2 textbooks.

Greenfield also happened to have a minor side job as the editor-in-chief of Elsevier’s Surgery News. Surgery News is not a peer-reviewed journal, but what Greenfield later defines as a monthly throw-away newspaper (of the kind Elsevier produces a lot).

As an-editor-in chief Greenfield wrote open editorials (opinion pieces) for Surgery News. He found a very suitable theme for the February issue: Valentine’s day.

Valentine’s Day is about love, and the editorial was about romantic gut feeling possibly having a physiological basis. In other words, the world of  sexual chemical signals that give you butterflies-feelings. The editorial jumps from mating preferences of fruit flies, stressed female rotifers turning into males and synchronization of menstrual cycles of women who live together, to a study suggesting that “exposure” to semen makes female college students less depressed. All 4 topics are based on scientific research, published in peer review papers.

Valentines Day asks for giving this “scientific” story a twist, so he concludes the editorial as follows:

“So there’s a deeper bond between men and women than St. Valentine would have suspected, and now we know there’s a better gift for that day than chocolates.”

Now, everybody knows that that conclusion ain’t supported by the data.
This would have required at least a double-blind randomized trial, comparing the mood-enhancing effects of chocolate compared to …….  (yikes!).

Just joking, of course…., similar as dear Lazar was trying to be funny….

No, the editorial wasn’t particularly funny.

And somehow it isn’t pleasant to think of a man’s love fluid wrapped in a ribbon and a box with hearts, while you expect some chocolates. Furthermore it suggests that sperm is something a man just gives/donates/injects, not a resultant of mutual love.

However this was the opposite of what Greenfield had in mind:

The biochemical properties of semen that were reviewed have been documented in peer-reviewed journals and represent the remarkable way that Nature promotes bonding between men and women, not something demeaning.”

Thus the man just tried to “Amuse his readers” and highlight research on “some fascinating new findings related to semen.”

I would have appreciated a more subtle ending of the editorial, but I would take no offense.

….Unlike many of his fellow female surgeons.  The Women in Surgery Committee and the Association of Women Surgeons considered his editorial as “demeaning to women” (NY-Times).

He offered his sincere apologies and resigned as Editor-in-Chief of the paper. The publication was retracted. As a matter of fact the entire February issue of Surgery News was taken off the ACS-website. Luckily, Retraction Watch published the editorial in its entirety.

Greenfield’s apologies weren’t enough, women surgeons brought the issue to the Board of Regents, who asked him to resign, which he eventually did.

A few weeks later he wrote a resentful letter. This is not a smart thing to do, but is understandable for several reasons. First, he didn’t he mean to be offensive and made his apologies. Second, he has an exemplary career as a longtime mentor and advocate of women in surgery. Third, true reason for his resign wasn’t the implicit plead for unprotected sex, but rather that the editorial reflected “a macho culture in surgery that needed to change.” Fourth, his life is ruined over something trivial.

Why can’t one write a lighthearted opinion-piece at Valentine’s day without getting resigned? Is it because admitting that “the “bond between men and women” is natural and runs deep” is one of those truths you cannot utter (Paul Rahe).

Is this perhaps typically American?

Elmar Veerman (Dutch Journalist, science editor at VPRO) comments at at Retraction Watch:

(…) Frankly, I don’t see the problem. I find it rather funny and harmless. Perhaps because I’m from Europe, where most people have a more relaxed attitude towards sex. Something like ‘nipplegate’ could never happen here (a nipple on tv, so what).  (…) I have been wondering for years why so many Americans seem to think violence is fine and sex is scary.

Not only female surgeons  object to the editorial. Well-known male (US) surgeons “fillet” the editorial at their blogs: Jeffrey Parks at Buckeye Surgeon ( 1 and 2), Orac Knows at Respectful Insolence (1 and 2) and Skeptical Scalpel (the latter quite mildly).

Jeffrey and Orac do not only think the man is humorless and a sexist, but also that the science behind the mood-enhancing aspects of semen is crap.

Although Jeffrey only regards “The “science” a little suspect as per Orac.”…. Because of course: “Orac knows.”

Orac exaggerates what Greenfield has said in the “breathtakingly inappropriate and embarrassing article  for Surgery News”, as he calls it. [1]:  “Mood-enhancing effects of semen” becomes in Orac’s words  the cure for female depression and  “a woman needs a man to inject his seed into her in order to be truly happy“.
Of course, it is not fair to twist words this way.

The criticism of Orac against the science that supports Dr. Greenfield’s joke is as follows: The first two studies are not related to human biology and the semen study” is “about as lame a study as can be imagined. Not only is it a study in which causation is implied by correlation, but to me the evidence of correlation is not even that compelling.”  

Orac is right about that. In his second post Orac continues (in response to the authors of the semen paper, who defend Greenfield and suggest they had obtained “more evidence”):

(..)so I was curious about where they had published their “replication.” PubMed has a wonderful feature in which it pops up “related citations” in the right sidebar of any citation you look up. I didn’t recall seeing any related citations presenting confirmatory data for Gallup et al’s study. I searched PubMed using the names of all three authors of the original “semen” study and found no publications regarding the antidepressant properties of semen since the original 2002 study cited by Dr. Greenfield. I found a lot of publications about yawning and mental states, but no followup study or replication of the infamous “semen” study. color me unimpressed” [2](..)

Again, I agree with Orac: the authors didn’t publish any confirmatory data.
But looking at related articles is not a good way to check if related articles have been published: PubMed creates this set by comparing words from the title, abstract, and MeSH terms using a word-weighted algorithm. It is goal is mainly to increase serendipity.

I didn’t have time to do a proper Pubmed search, which should include all kinds of synonyms for sperm and mood/depression. I just checked the papers citing Gallups original article in Google Scholar and found 29 hits (no Gallop papers indeed), including various articles by Costa & Brody i.e. the freely available letter (discussing their research): Greater Frequency of Penile–Vaginal Intercourse Without Condoms is Associated with Better Mental Health. This letter was a response to an opposite finding by the way.

I didn’t look at the original articles and I don’t really expect much of it. However, it just shows the Gallop study is not the only study, linking semen to positive health effects.

Assuming Greenfield had more than a joke in mind, and wanted to reflect on the state of art of health aspects of semen, it surprises me that he didn’t dig any further than this article from 2002.

Is it because he really based his editorial on a review in Scientific American from 2010, called “An ode to the many evolved virtues of human semen” [3,4], which describes Gallup’s study and, strikingly, also starts with discussing menstrual synchrony.

Greenfield could have discussed other, better documented, properties of semen, like its putative protection from pre-eclampsia (see references in Wikipedia)[5]

Or even better, he could have cited other sexual chemical signals that give you butterflies-feelings, like smell!

In stead of “Gut Feelings” the title could have been “In the nose of the beholder” or “The Smell of Love” [6].

And Greenfield could have concluded:

“So there’s more in the air than St. Valentine would have suspected, and now we know there’s a better gift for that day than chocolates: perfume.

And no one would have bothered and would have done with the paper as one usually does with throwaways.

Notes

  1. Coincidentally, while reading Orac’s post I saw a Research Blogging post mentioned in the side bar: masturbation-and-restless-leg-syndrome. …Admittedly, this was a friday-weird-science post and a thorough review of a case study.
  2. It would probably have been easier to check their website with an overview of publications
  3. Mentioned in a comment somewhere, but I can’t track it down.
  4. If Greenfield used Scientific American as a source he should have read it all to the end, where the author states: I bid adieu, please accept, in all sincerity, my humblest apologies for what is likely to be a flood of bad, off-color jokes—men saying, “I’m not a medical doctor, but my testicles are licensed pharmaceutical suppliers” and so on—tracing its origins back to this innocent little article. Ladies, forgive me for what I have done.”
  5. Elmar Veerman has written a review on this topic in 2000 at Kennislink: http://www.kennislink.nl/publicaties/sperma-als-natuurlijke-bescherming (Dutch)
  6. As a matter of fact these are actual titles of scientific papers.
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Friday Foolery #39. Peer Review LOL, How to Write a Comment & The Best Rejection Letter Evvah!

15 04 2011

LOL? Peer review?! Comments?

Peer review is never funny, you think.
It is hard to review papers, especially when they are poorly written. From the author’s point of view, it is annoying and frustrating to see a paper rejected on basis of comments of peer reviewers, who either don’t understand the paper or thwart you in your attempts to get the paper published, for instance because you are a competitor in the field.

Still, from a (great) distance the peer review process can be funny… in some respects.

Read for instance a collection of memorable quotes from peer review critiques of the past year in Environmental Microbiology (EM does this each December). Here are some excerpts:

  • Done! Difficult task, I don’t wish to think about constipation and faecal flora during my holidays!
  • This paper is desperate. Please reject it completely and then block the author’s email ID so they can’t use the online system in future.
  • It is sad to see so much enthusiasm and effort go into analyzing a dataset that is just not big enough.
  • The abstract and results read much like a laundry list.
  • .. I would suggest that EM is setting up a fund that pays for the red wine reviewers may need to digest manuscripts like this one.
  • I have to admit that I would have liked to reject this paper because I found the tone in the Reply to the Reviewers so annoying.
  • I started to review this but could not get much past the abstract.
  • This paper is awfully written. There is no adequate objective and no reasonable conclusion. The literature is quoted at random and not in the context of argument…
  • Stating that the study is confirmative is not a good start for the Discussion.
  • I suppose that I should be happy that I don’t have to spend a lot of time reviewing this dreadful paper; however I am depressed that people are performing such bad science.
  • Preliminary and intriguing results that should be published elsewhere.
  • Reject – More holes than my grandad’s string vest!
  • The writing and data presentation are so bad that I had to leave work and go home early and then spend time to wonder what life is about.
  • Very much enjoyed reading this one, and do not have any significant comments. Wish I had thought of this one.
  • This is a long, but excellent report. […] It hurts me a little to have so little criticism of a manuscript.

More seriously, the Top 20 Reasons (Negative Comments) Written by the Reviewers Recommending Rejection of 123 Medical Education Manuscripts can be found at Academic Medicine (vol 76, no . 9 / 2 0 0 1). The top 5 is:

  1. Statistics: inappropriate, incomplete, or insufficiently described, etc.  11.2 %
  2. Overinterpretation of the results 8.7 %
  3. Inappropriate, suboptimal, insufficiently described instrument 7.3%
  4. Sample too small or biased  5.6 %
  5. Text difficult to follow, to understand 3.9%

Neuroskeptic describes 9 types of review decisions in the The Wheel of Peer Review. Was your paper reviewed by “Bee-in-your-Bonnet” or by “Cite Me, Me, Me!”

Rejections are of all times. Perhaps the best rejection letter ever is written by Sir David Brewster editor of The Edinburgh Journal of Science to Charles Babbage on July 3, 1821. Noted in James Gleick’s, The Information. A History, a Theory, a Flood

Excerpt at Marginal Revolution (HT @TwistedBacteria):

The subjects you propose for a series of Mathematical and Metaphysical Essays are so very profound, that there is perhaps not a single subscriber to our Journal who could follow them. 

Responses to a rejection are also of all ages. See this video anno 1945 (yes this scene has been used tons of times for other purposes)

Need tips?

Read How to Publish a Scientific Comment in 1 2 3 Easy Steps (well literally 123 steps) by Prof. Rick Trebino. Based on real life. It is Hilarious!

PhD comics made a paper review worksheet (you don’t even have to read the manuscript!) and gives you advise how NOT to address reviewer comments. LOL.

And here is a Sample Cover Letter for Journal Manuscript Resubmissions. Ain’t that easy?

Yet if you are still unsuccessful and want a definitive decision rendered within hours of submission you can always send your paper to the Journal of Universal Rejection.





Kaleidoscope 2: 2010 wk 31

8 08 2010

Almost a year ago I started a new series Kaleidoscope, with a “kaleidoscope” of facts, findings, views and news gathered over the last 1-2 weeks.
It never got beyond the first edition. Perhaps the introduction of this Kaleidoscope was to overwhelming & dazzling: lets say it was very rich in content. Or as
Andrew Spong tweeted: “Part cornucopia, part cabinet of wonders, it’s @laikas Kaleidoscope 2009 wk 47”

This is  a reprise in a (somewhat) “shorter” format. Lets see how it turns out.

This edition will concentrate on Social Media (Blogging, Twitter Google Wave). I fear that I won’t keep my promise, if I deal with more topics.

Medical Grand Rounds and News from the Blogosphere

Life in the Fast Lane is the host of this weeks Grand Rounds. This edition is truly terrific, if not terrifying. Not only does it contain “killer posts”, each medblogger has also been coupled to its preferred deadly Aussie critter.
Want to know how a full time ER-doctor/educator/textbook author/blogger/editor /health search engine director manages to complete work-related tasks …when the kids are either at school or asleep(!), then read this recent interview with Mike Cadogan, the founder of Life in the Fast Lane.

Don’t forget to submit your medical blog post to next weeks Grand Rounds over at Dispatch From Second Base. Instructions and theme details can be found on the post “You are invited to Grand Rounds!“ (update here).

And certainly don’t forget to submit your post related to medical information to the MedLibs Round (about medical information) here. More details can be found at Laika’s MedLibLog and at Highlight Health, the host of the upcoming Edition.
(sorry, writing this post took longer than I thought: you have one day left for submission)

Dr Shock of the blog with the same name advises us to submit good quality, easy-to-understand posts dealing with science, environment or medicine to Scientia Pro Publica via the blog carnival submission form.

There is a new on-line science blogging community – Scientopia, till now mostly consisting of bloggers who left Scienceblogs after (but not because of) Pepsigate. New members can only be added to the collective by invitation (?). Obviously, pepsi-researchers will not be invited, but it remains to be seen who will…  Hopefully it doesn’t become an elitist club.
Virginia Heffernan (NY-Times) has an outspoken opinion about the (ex-) sciencebloggers, illustrated by this one-liner

“ScienceBlogs has become Fox News for the religion-baiting, peak-oil crowd.”

Although I don’t appreciate the ranting-style of some of the blogs myself (the sub-“South Park” blasphemy style of PZ Myers, as Virginia puts it). I don’t think most Scienceblogs deserve to be labelled as “preoccupied with trivia, name-calling and saber rattling”.
See balanced responses at: NeurodojoNeuron Culture & Neuroanthropology (anything with neuro– makes sense, I guess).
Want to understand more about ScienceBlogs and why it was such a terrific community, then read Bora Z’s (rather long) ScienceBlog farewell post.

Oh.. and there is yet another new science blogging platform: http://www.labspaces.net/, that has evolved from a science news aggregator . It looks slick.

Social Media

Speaking about Twitter, did you know that  Twitter reached its 20 billionth tweet over the weekend, a milestone that came just a few months after hitting the 10 billion tweet mark!? (read more in the Guardian)

Well and if you have no idea WHAT THE FUCK IS MY SOCIAL MEDIA “STRATEGY”? you might click the link to get some (new) ideas. You probably need to refresh the site a couple of times to find the right answer.

First-year medical school and master’s of medicine students of Stanford University will receive an i-pad at the start of the year. The extremely tech-savvy Students do appreciate the gift:

“Especially in medicine, we’re using so many different resources, including all the syllabuses and slides. I’m able to pull them up and search them whenever I need to. It’s a fantastic idea.”

Good news for Facebook friends: VoIP giant Vonage has just introduced a new iPhone, iPod touch and Android app that allows users to call their Facebook friends for free (Mashable).

It was a shock – or wasn’t it – that Google pulled the plug on Google Wave (RRW), after being available to the general public for only 78 days?  The unparalleled tool that “could change the web”, but was too complex to be understood. Here are some thoughts why Google wave failed.  Since much of the Code is open source, ambitious developers may pick up where Google left.

Votes down for the social media site Digg.com: an undercover investigation has exposed that a group of influential conservative members were involved in censorship, deliberately trying to ban progressives, by “burying them” (voting down), which effectively means these progressives don’t get enough “digs” to reach the front page where most users spend their time.

Votes up for Healthcare Social Media Europe (#HCSMEU), which just celebrated its first birthday.

Miscellanous

A very strange move: a journal has changed a previously stated conclusion of a previously published paper after a Reuters Health story about serious shortcomings in the report. Read more about it at Gary Schwitzer’s HealthNewsReview Blog.

Finally for the EBM-addicts among us: The Center of Evidence Based Medicine released a new (downloadable) Levels of Evidence Table. At the CEBM-blog they stress that hierarchies of evidence have been somewhat inflexibly used, but are essentially a heuristic, or short-cut to finding the likely best evidence. At first sight the new Table looks simpler, and more easy to use.

Are you a Twitter user? Tweet this!





MedLibs Round 2.6

11 07 2010

Welcome to this months edition of MedLib’s Round, a blog carnival of “excellent blog posts in the field of medical information”.

This round is a little belated, because of late submissions and my absence earlier this week.
But lets wait no longer …..!

Peer Review, Impact Factors & Conflict of Interest

Walter Jessen at Highlight HEALTH writes about the NIH Peer Review process. Included is an interesting video, that provides an inside look at how scientists from across the US review NIH grant applications for scientific and technical merit. These scientists do seem take their job seriously.

But what about peer review of scientific papers? Richard Smith, doctor, former editor of the BMJ and a proponent of open access publishing, wrote a controversial post at the BMJ Groups Blog called scrap peer review and beware of “top journals. Indeed  the “top journals” publish the sexy stuff, whereas evidence comprises both the glamorous and the unglamorous. But is prepublication peer review really that bad and should we only filter afterwards?

In a thoughtful post at his Nature blog Confessions of a (former) Lab Rat another Richard (Grant) argues that although peer review suffers terribly from several shortcomings it is still required. Richard Grant also clears up one misconception:

Peer review, done properly, might guarantee that work is done correctly and to the best of our ability and best intentions, but it will not tell you if a particular finding is right–that’s the job of other experimenters everywhere; to repeat the experiments and to build on them.

At Scholarly Kitchen (about what is hot and cooking in scholarly publishing) they don’t think peer review is a clear concept, since the list of ingredients differ per journal and article. Read their critical analysis and suggestions for improvement of the standard recipe here.

The science blogosphere was buzzing in outrage about the adding a corporate nutrition blog sponsored by PepsiCo to ScienceBlog (i.e see this post at the Guardian Science Blog). ScienceBlogs is the platform of eminent science bloggers, like OracPharyngula and Molecule of the Day. After some bloggers left ScienceBlog and others threatened to do so, the Pepsico Blog was retracted.

An interesting view is presented by David Crotty at Scholarly Kitchen. He states that it is “hypocritical for ScienceBlog’s bloggers to have objected so strenuously: ScienceBlogs has never been a temple of purity, free of bias or agenda.” Furthermore the bloggers enjoy more traffic and a fee for being a scienceblogger, and promote their “own business” too. David finds it particularly ironic that these complaints come from the science blogosphere, which has regularly been a bastion of support for the post-publication review philosophy. Read more here.

Indeed according to a note of Scienceblog at the disappeared blog their intention was “to engage industry in pursuit of science-driven social change”, although it was clearly not the right way.

The partiality of business, including pharma, makes it’s presence in and use of Social Media somewhat tricky. Still it is important for pharma to get involved in web2.0. Interested in a discussion on this topic? Than follow the tags #HCSM (HealthCare Social Media) and #HCSMEU (Europe) on Twitter.
Andrew Spong, has launched an open wiki, where you can read all about #HCSMEU.

The value of journal impact factors is also debatable. In the third part of the series “Show me the evidence” Kathleen Crea at EBM and Clinical Support Librarians @ UCHC starts with an excerpt of an article with the intriguing title “The Top-Ten in Journal Impact Factor Manipulation”:

The assumption that Impact Factor (IF) is a number absolutely proportional to science quality has led to misuses beyond the index’s original scope, even in the opinion of its devisor.”

The post itself (Teaching & Learning in Medicine, Research Methodology, Biostatistics: Show Me the Evidence (Part 3)b) is not so much about evidence, but offers a wealth of information about  journal impact factors, comparisons of sites for citation analysis, and some educational materials for teaching others about citation analysis. Not only are Journal Citation Reports and SCOPUS discussed, but also the Eigenfactor, h-index and JANE.

Perhaps we need another system of publishing and peer review? Will the future be to publish triplets and peer review these via Twitter by as many reviewers as possible? Read about this proposal of Barend Mons (of the same group that created JANE) at this blog. Here you can also find a critical review of an article comparing Google Scholar and PubMed for retrieving evidence.

Social Media, Blogs & Web 2.0 tools

There are several tools to manage the scientific articles, like CiteULike and Mendeley. At his blog Gobbledygook Martin Fenner discusses the pros and cons of a new web-based tool specifically for discussing papers in Journal Clubs: JournalFire

At the The Health Informaticists they found an interesting new feature of Skype:  screen sharing. Here you can read all about it.

Andrew Sprong explains at his blog STweM how to create a PDF archive of hashtagged tweets using whatthehashtag?! and Google DocsScribd or Slideshare. A tweet archive is very useful in case of  live tweet or stream sessions at conferences. (each tweet is then labeled with a # or hashtag, but tweets are lost after a few days if not archived)

L1010201At Cool Toy of the DayPatricia Anderson posts a lot about healthcare tools. She submitted Cool Toys Pic of the day – Eyewriter“, a tool for allowing persons with ALS and paralysis to draw artwork with their eyes. But you find a lot more readworthy posts at this blog and her main blog Emerging Technologies Librarian.

Heidi Allen at Heidi Allen Digital Strategy started a discussion on the meaning of social-medicine for Physicians. The link to the original submission doesn’t work right now, but if you follow this link you see several posts on social-medicine, including “Physicians in Social Media”, where 3 well-known physicians give their view on the meaning of social-medicine.

Dr Shock at Dr Shock MD PhD, wonders whether “the information on postpartum depression in popular lay magazines correspond to scientific knowledge?” Would it surprise you that this is not the case for many articles on this topic?

The post of Guus van den Brekel at DigiCMB with the inspiring title Discovering new seas of knowledge partly goes about the seas of knowledge gained at the EAHIL2010 (European Association for Health Information and Libraries) meeting, with an overview of many sessions, and materials when possible. And I should stress when possible, because the other  part of the post is about the difficulty of obtaining access to this sea of knowledge. Guus wonders:

In this age of Open Access, web 2.0 and the expectancy of the “users” -being us librarians (…) one would assume that much (if not all) is freely available via Conferences websites and/or social media. Why then do I find it hard to find the extra info about those events, including papers and slides and possibly even webcasts? Are we still not into the share-mode and overprotective to one’s own achievements(….)

Guus makes a good point,especially in this era, when not all of us are able to go and visit far away places. Luckily we have Guus who did a good job of compiling as much material as possible.

Wondering about the evidence for the usefulness of web 2.0, then have a look at this excellent wiki by Dean Giustini: http://hlwiki.slais.ubc.ca/index.php/Evidence-based_web_2.0.
The Health Librarianship Wiki Canada (the mother wiki) has a great new design and is a very rich source of information for medical librarians.

Another good source for recent peer reviewed papers about using social media in medicine and healthcare is a new series by Bertalan Mesko at Science Roll. First it was called Evidence Based Social Media News and now Social media journal club.

EHR and the clinical librarian.

Nikki Dettmar presents two posts on Electronic Health Records at Eagledawg.net, inspired by a recent Medical Library Association meeting that included a lot about electronic health records (EHRs). In the first part “Electronic Health Records: Not All About the Machine” she mentions the launch of an OpenNotes study that “evaluates the impact on both patients and physicians of sharing, through online medical record portals, the comments and observations made by physicians after each patient encounter.” The second post is entitled “a snapshot of ephemeral chaos“. And yes the title says it all.

Bertalan Mesko at Science Roll describes a try out of a Cardiology Resident and Research Fellow in Google Wave to see whether that platform is suitable for creating a database of the electronic records of a virtual patient. The database looks fine at first glance, but is it safe?

Alisha764’s Blog celebrated its 1 year anniversary in February. Alisha Miles aim for the next year is to not only post more but to focus on hospital libraries including her experience as a hospital librarian. Excellent idea, Alisha! I liked the post Rounding: A solo medical librarian’s perspective with several practical tips if you join the round as a librarian. I hope you can find time to write more like this, Alisha!

Our next host is Walter Jessen at Highlight HEALTH. You can already start submitting the link to a (relevant) post you have written here.

See the MedLibs Archive for more information.

Photo Credits:





Will Nano-Publications & Triplets Replace The Classic Journal Articles?

23 06 2010

ResearchBlogging.org“Libraries and journals articles as we know them will cease to exists” said Barend Mons at the symposium in honor of our Library 25th Anniversary (June 3rd). “Possibly we will have another kind of party in another 25 years”…. he continued, grinning.

What he had to say the next half hour intrigued me. And although I had no pen with me (it was our party, remember), I thought it was interesting enough to devote a post to it.

I’m basing this post not only on my memory (we had a lot of Italian wine at the buffet), but on an article Mons referred to [1], a Dutch newspaper article [2]), other articles [3-6] and Powerpoints [7-9] on the topic.

This is a field I know little about, so I will try to keep it simple (also for my sake).

Mons started by touching on a problem that is very familiar to doctors, scientists and librarians: information overload by a growing web of linked data.  He showed a picture that looked like the one at the right (though I’m sure those are Twitter Networks).

As he said elsewhere [3]:

(..) the feeling that we are drowning in information is widespread (..) we often feel that we have no satisfactory mechanisms in place to make sense of the data generated at such a daunting speed. Some pharmaceutical companies are apparently seriously considering refraining from performing any further genome-wide association studies (… whole genome association –…) as the world is likely to produce many more data than these companies will ever be able to analyze with currently available methods .

With the current search engines we have to do a lot of digging to get the answers [8]. Computers are central to this digging, because there is no way people can stay updated, even in their own field.

However,  computers can’t deal with the current web and the scientific  information as produced in the classic articles (even the electronic versions), because of the following reasons:

  1. Homonyms. Words that sound or are the same but have a different meaning. Acronyms are notorious in this respect. Barend gave PSA as an example, but, without realizing it, he used a better example: PPI. This means Protein Pump Inhibitor to me, but apparently Protein Protein Interactions to him.
  2. Redundancy. To keep journal articles readable we often use different words to denote the same. These do not add to the real new findings in a paper. In fact the majority of digital information is duplicated repeatedly. For example “Mosquitoes transfer malaria”, is a factual statement repeated in many consecutive papers on the subject.
  3. The connection between words is not immediately clear (for a computer). For instance, anti-TNF inhibitors can be used to treat skin disorders, but the same drugs can also cause it.
  4. Data are not structured beforehand.
  5. Weight: some “facts” are “harder” than others.
  6. Not all data are available or accessible. Many data are either not published (e.g. negative studies), not freely available or not easy to find.  Some portals (GoPubmed, NCBI) provide structural information (fields, including keywords), but do not enable searching full text.
  7. Data are spread. Data are kept in “data silos” not meant for sharing [8](ppt2). One would like to simultaneously query 1000 databases, but this would require semantic web standards for publishing, sharing and querying knowledge from diverse sources…..

In a nutshell, the problem is as Barend put it: “Why bury data first and then mine it again?” [9]

Homonyms, redundancy and connection can be tackled, at least in the field Barend is working in (bioinformatics).

Different terms denoting the same concept (i.e. synonyms) can be mapped to a single concept identifier (i.e. a list of synonyms), whereas identical terms used to indicate different concepts (i.e. homonyms) can be resolved by a disambiguation algorithm.

The shortest meaningful sentence is a triplet: a combination of subject, predicate and object. A triplet indicates the connection and direction.  “Mosquitoes cause/transfer malaria”  is such a triplet, where mosquitoes and malaria are concepts. In the field of proteins: “UNIPROT 05067 is a protein” is a triplet (where UNIPROT 05067 and protein are concepts), as are: “UNIprotein 05067 is located in the membrane” and “UNIprotein 0506 interacts with UNIprotein 0506″[8].  Since these triplets  (statements)  derive from different databases, consistent naming and availability of  information is crucial to find them. Barend and colleagues are the people behind Wikiproteins, an open, collaborative wiki  focusing on proteins and their role in biology and medicine [4-6].

Concepts and triplets are widely accepted in the world of bio-informatics. To have an idea what this means for searching, see the search engine Quertle, which allows semantic search of PubMed & full-text biomedical literature, automatic extraction of key concepts; Searching for ESR1 $BiologicalProcess will search abstracts mentioning all kind of processes where ESR1 (aka ERα, ERalpha, EStrogen Receptor 1) are involved. The search can be refined by choosing ‘narrower terms’ like “proliferation” or “transcription”.

The new aspects is that Mons wants to turn those triplets into (what he calls) nano-publications. Because not every statement is as ‘hard’, nano-publications are weighted by assigning numbers from 0 (uncertain) to 1 (very certain). The nano-publication “mosquitoes transfer malaria” will get a number approaching 1.

Such nano-publications offer little shading and possibility for interpretation and discussion. Mons does not propose to entirely replace traditional articles by nano-publications. Quote [3]:

While arguing that research results should be available in the form of nano-publications, are emphatically not saying that traditional, classical papers should not be published any longer. But their role is now chiefly for the official record, the “minutes of science” , and not so much as the principle medium for the exchange of scientific results. That exchange, which increasingly needs the assistance of computers to be done properly and comprehensively, is best done with machine-readable, semantically consistent nano-publications.

According to Mons, authors and their funders should start requesting and expecting the papers that they have written and funded to be semantically coded when published, preferably by the publisher and otherwise by libraries: the technology exists to provide Web browsers with the functionality for users to identify nano-publications, and annotate them.

Like the wikiprotein-wiki, nano-publications will be entirely open access. It will suffice to properly cite the original finding/publication.

In addition there is a new kind of “peer review”. An expert network is set up to immediately assess a twittered nano-publication when it comes out, so that  the publication is assessed by perhaps 1000 experts instead of 2 or 3 reviewers.

On a small-scale, this is already happening. Nano-publications are send as tweets to people like Gert Jan van Ommen (past president of HUGO and co-author of 5 of my publications (or v.v.)) who then gives a red (don’t believe) or a green light (believe) via one click on his blackberry.

As  Mons put it, it looks like a subjective event, quite similar to “dislike” and “like” in social media platforms like Facebook.

Barend often referred to a PLOS ONE paper by van Haagen et al [1], showing the superiority of the concept-profile based approach not only in detecting explicitly described PPI’s, but also in inferring new PPI’s.

[You can skip the part below if you’re not interested in details of this paper]

Van Haagen et al first established a set of a set of 61,807 known human PPIs and of many more probable Non-Interacting Protein Pairs (NIPPs) from online human-curated databases (and NIPPs also from the IntAct database).

For the concept-based approach they used the concept-recognition software Peregrine, which includes synonyms and spelling variations  of concepts and uses simple heuristics to resolve homonyms.

This concept-profile based approach was compared with several other approaches, all depending on co-occurrence (of words or concepts):

  • Word-based direct relation. This approach uses direct PubMed queries (words) to detect if proteins co-occur in the same abstract (thus the names of two proteins are combined with the boolean ‘AND’). This is the simplest approach and represents how biologists might use PubMed to search for information.
  • Concept-based direct relation (CDR). This approach uses concept-recognition software to find PPIs, taking synonyms into account, and resolving homonyms. Here two concepts (h.l. two proteins) are detected if they co-occur in the same abstract.
  • STRING. The STRING database contains a text mining score which is based on direct co-occurrences in literature.

The results show that, using concept profiles, 43% of the known PPIs were detected, with a specificity of 99%, and 66% of all known PPIs with a specificity of 95%. In contrast, the direct relations methods and STRING show much lower scores:

Word-based CDR Concept profiles STRING
Sensitivity at spec = 99% 28% 37% 43% 39%
Sensitivity at spec = 95% 33% 41% 66% 41%
Area under Curve 0.62 0.69 0.90 0.69

These findings suggested that not all proteins with high similarity scores are known to interact but may be related in another way, e.g.they could be involved in the same pathway or be part of the same protein complex, but do not physically interact. Indeed concept-based profiling was superior in predicting relationships between proteins potentially present in the same complex or pathway (thus A-C inferred from concurrence protein pairs A-B and B-C).

Since there is often a substantial time lag between the first publication of a finding, and the time the PPI is entered in a database, a retrospective study was performed to examine how many of the PPIs that would have been predicted by the different methods in 2005 were confirmed in 2007. Indeed, using concept profiles, PPIs could be efficiently predicted before they enter PPI databases and before their interaction was explicitly described in the literature.

The practical value of the method for discovery of novel PPIs is illustrated by the experimental confirmation of the inferred physical interaction between CAPN3 and PARVB, which was based on frequent co-occurrence of both proteins with concepts like Z-disc, dysferlin, and alpha-actinin. The relationships between proteins predicted are broader than PPIs, and include proteins in the same complex or pathway. Dependent on the type of relationships deemed useful, the precision of the method can be as high as 90%.

In line with their open access policy, they have made the full set of predicted interactions available in a downloadable matrix and through the webtool Nermal, which lists the most likely interaction partners for a given protein.

According to Mons, this framework will be a very rich source for new discoveries, as it will enable scientists to prioritize potential interaction partners for further testing.

Barend Mons started with the statement that nano-publications will replace the classic articles (and the need for libraries). However, things are never as black as they seem.
Mons showed that a nano-publication is basically a “peer-reviewed, openly available” triplet. Triplets can be effectively retrieved ànd inferred from available databases/papers using a
concept-based approach.
Nevertheless, effectivity needs to be enhanced by semantically coding triplets when published.

What will this mean for clinical medicine? Bioinformatics is quite another discipline, with better structured and more straightforward data (interaction, identity, place). Interestingly, Mons and van Haage plan to do further studies, in which they will evaluate whether the use of concept profiles can also be applied in the prediction of other types of relations, for instance between drugs or genes and diseases. The future will tell whether the above-mentioned approach is also useful in clinical medicine.

Implementation of the following (implicit) recommendations would be advisable, independent of the possible success of nano-publications:

  • Less emphasis on “publish or perish” (thus more on the data themselves, whether positive, negative, trendy or not)
  • Better structured data, partly by structuring articles. This has already improved over the years by introducing structured abstracts, availability of extra material (appendices, data) online and by guidelines, such as STARD (The Standards for Reporting of Diagnostic Accuracy)
  • Open Access
  • Availability of full text
  • Availability of raw data

One might argue that disclosing data is unlikely when pharma is involved. It is very hopeful therefore, that a group of major pharmaceutical companies have announced that they will share pooled data from failed clinical trials in an attempt to figure out what is going wrong in the studies and what can be done to improve drug development (10).

Unfortunately I don’t dispose of Mons presentation. Therefore two other presentations about triplets, concepts and the semantic web.

&

References

  1. van Haagen HH, ‘t Hoen PA, Botelho Bovo A, de Morrée A, van Mulligen EM, Chichester C, Kors JA, den Dunnen JT, van Ommen GJ, van der Maarel SM, Kern VM, Mons B, & Schuemie MJ (2009). Novel protein-protein interactions inferred from literature context. PloS one, 4 (11) PMID: 19924298
  2. Twitteren voor de wetenschap, Maartje Bakker, Volskrant (2010-06-05) (Twittering for Science)
  3. Barend Mons and Jan Velterop (?) Nano-Publication in the e-science era (Concept Web Alliance, Netherlands BioInformatics Centre, Leiden University Medical Center.) http://www.nbic.nl/uploads/media/Nano-Publication_BarendMons-JanVelterop.pdf, assessed June 20th, 2010.
  4. Mons, B., Ashburner, M., Chichester, C., van Mulligen, E., Weeber, M., den Dunnen, J., van Ommen, G., Musen, M., Cockerill, M., Hermjakob, H., Mons, A., Packer, A., Pacheco, R., Lewis, S., Berkeley, A., Melton, W., Barris, N., Wales, J., Meijssen, G., Moeller, E., Roes, P., Borner, K., & Bairoch, A. (2008). Calling on a million minds for community annotation in WikiProteins Genome Biology, 9 (5) DOI: 10.1186/gb-2008-9-5-r89
  5. Science Daily (2008/05/08) Large-Scale Community Protein Annotation — WikiProteins
  6. Boing Boing: (2008/05/28) WikiProteins: a collaborative space for biologists to annotate proteins
  7. (ppt1) SWAT4LS 2009Semantic Web Applications and Tools for Life Sciences http://www.swat4ls.org/
    Amsterdam, Science Park, Friday, 20th of November 2009
  8. (ppt2) Michel Dumontier: triples for the people scientists liberating biological knowledge with the semantic web
  9. (ppt3, only slide shown): Bibliography 2.0: A citeulike case study from the Wellcome Trust Genome Campus – by Duncan Hill (EMBL-EBI)
  10. WSJ (2010/06/11) Drug Makers Will Share Data From Failed Alzheimer’s Trials




The Trouble with Wikipedia as a Source for Medical Information

14 09 2009

This post was chosen as an Editor's Selection for ResearchBlogging.org

Do you ever use Wikipedia? I do and so do many other people. It is for free, easy to use, and covers many subjects.

But do you ever use Wikipedia to look up scientific or medical information? Probably everyone does so once in a while. Dave Munger (Researchblogging) concluded a discussion on Twitter as follows:

Logo of the English Wikipedia
Image via Wikipedia

“Wikipedia’s information quality is better than any encyclopedia, online or off. And, yes, it’s also easy to use”.

Wikipedia is an admirable initiative. It is a large online collaborative, multilingual encyclopedia written by contributors around the world.
But the key question is whether you can rely on Wikipedia as the sole source for medical, scientific or even popular information.

Well, you simply can’t and here are a few examples/findings to substantiate this point.

RANKING AND USE

E-patients

When you search  for diabetes in Google (EN), Wikipedia’s entry about diabetes ranks second, below the American Diabetes Association Home Page. A recent study published in the J Am Med Inform Assoc [1] confirms what you would expect: that the English Wikipedia is a prominent source of online health information. Wikipedia ranked among the first ten results in more than 70% of search engines and health-keywords tested, and outranked other sources in case of rare disease-related keywords. Wikipedia’s articles were viewed more frequently than the corresponding MedlinePlus Topic pages. This corroborates another study that can be downloaded from the internet here [10]. This study by Envision Solutions, LLC, licensed under the Creative Commons License, concluded that the exposure of Internet user’s to health-related user-generated media (UGM) is significant, Wikipedia being the most reference resource on Google and Yahoo.

The following (also from envisionsolutionsnow.com, from 2007 [10]) illustrates the impact of this finding:

According to the Pew Internet & American Life Project*, 10 million US adults search online for information on health each day [1]. Most (66%) begin their research on a search engine like Yahoo or Google. In addition, Americans are saying that the information they find on the Internet is having an impact. According to Pew, “53% of health seekers report that their most recent health information session [influenced] how they take care of themselves or care for someone else.” In addition, 56% say the information they find online has boosted their confidence in their healthcare decision-making abilities.

And according to an update from the Pew Internet & American Life Project (2009) [11]:

In 2000, 46% of American adults had access to the internet, 5% of U.S. households had broadband connections, and 25% of American adults looked online for health information. Now, 74% of American adults go online, 57% of American households have broadband connections, and 61% of adults look online for health information.

Thus a lot of people look online for health care questions and are more inclined to use highly ranked sources.
This is not unique for Health topics but is a general phenomenon, i.e. see this mini-study performed by a curious individual: 96.6% of Wikipedia Pages Rank in Google’s Top 10 [12]. The extreme high traffic to Wikipedia due to search referrals has  even been been denounced by SEO-people (see here) [13]: if you type “holiday” Wikipedia provides little value when ranking in the top 10: everybody knows what a holiday is 😉

Medical students use it too.

A nightmare for most educators in the curriculum is that students rely on UGM or Web 2.0 sites as a source  of medical information. Just walk along medical students as they work behind their computers and take a quick glance at the pages they are consulting. These webpages often belong to the above category.

AnneMarie Cunningham, GP and Clinical Lecturer in the UK, did a little informal “survey” on the subject. She asked 31 first year medical students about their early clinical attachments in primary and secondary care and summerized the results on her blog Wishful Thinking in Medical Education [14]. By far and away Wikipedia was the most common choice to look up unfamiliar clinical topics.

AnneMarie:

‘Many students said I know I shouldn’t but….’ and then qualified that they used Wikipedia first because it was easy to understand, they felt it was reasonably reliable, and accessible. One student used it to search directly from her phone when on placement..

50% of the doctors use it!

But these are only medical students. Practicing doctors won’t use Wikipedia to solve their clinical questions, because they know where to find reliable medical information.

Wrong!

The New Scientist cites a report [15] of US healthcare consultancy Manhattan Research (April 2009), stating that that 50 percent of the doctors turn to Wikipedia for medical information.

A recent qualitative study published in Int J Med Inform [2] examined the “Web 2.0” use by 35 junior physicians in the UK. Diaries and interviews encompassing 177 days of internet use or 444 search incidents, analyzed via thematic analysis. Although concepts are loosely defined (Web 2.0, internet and UMG are not properly defined, i.e. Google is seen as a web 2.0 tool (!) [see Annemarie’s critical review [16] the results clearly show that 89% of these young physicians use at least one “Web 2.0 tool” (including Google!) in their medical practice, with 80% (28/35) reporting the use of wikis. The visit of wiki’s is largely accounted for by visits to Wikipedia: this was the second most commonly visited site, used in 26% (115/44) of cases and by 70% (25/35) of all physicians. Notably, only one respondent made regular contribution to a medical wiki site.

The main motivation for using the Internet for information seeking was the accessibility and ease of use over other tools (like textbooks), the uptodateness, the broad coverage and the extras such as interactive immages. On the other hand most clinicians realized that there was a limitation in the quality or usefulness of information found. It is reassuring that most doctors used UGM like Wikipedia for background or open questions, to fulfill the need for more in depth knowledge on a subject, or to find information for patients, not for immediate solving of clinical questions.

The Int J Med Inform article has been widely covered by blogs: i.e. see Wishful Thinking in Medical Education [16], Dr Shock, MD, PhD [17], Life in the Fast Lane [18], Clinical Cases and Images Blog [19] and Scienceroll [20].

Apparently some doctors also heavily rely on Wikipedia that they refer to Wikipedia articles in publications (see the Int. J Cardiol. PubMed [3] abstract below)!!

8-9-2009 14-03-15 Int J cardiol wikipedia references 2

WHY WIKIPEDIA IS NOT (YET) A TRUSTWORTHY AND HIGH QUALITY HEALTH SITE

Whether the common use of Wikipedia by e-patient, medical students and doctors is disadvantageous depends on the quality and the trustworthiness of the Wikipedia articles, and that is in its turn dependent on who writes the articles.

Basically, the strength of Wikipedia is it weakness: anyone can write anything on any subject, and anyone can edit it, anonymously.

Negative aspects include its coverage (choice of subjects but also the depth of coverage), the “overlinking”, the sometimes frustating interactions between authors and editors, regularly leading to (often polite) “revision wars“, but above all the lack of ‘expert’ authors or peer review. This may result in incomplete, wrong or distorted information.

Positive aspects are its accessibility, currency, availability in many languages, and the collective “authorship” (which is an admirable concept).

The following humorist video shows how the wisdom of the crowds can lead to chaos, incorrect and variable information.

SCOPE AND ACCURACY (What has been covered, how deep and how good) :

Too much, too little, too ….

With respect to its coverage one study in the Journal of Computer-Mediated Communication (2008) [4] concludes:

Differences in the interests and attention of Wikipedia’s editors mean that some areas, in the traditional sciences, for example, are better covered than others. (…)
Overall, we found that the degree to which Wikipedia is lacking depends heavily on one’s perspective. Even in the least covered areas, because of its sheer size, Wikipedia does well, but since a collection that is meant to represent general knowledge is likely to be judged by the areas in which it is weakest, it is important to identify these areas and determine why they are not more fully elaborated. It cannot be a coincidence that two areas that are particularly lacking on Wikipedia—law and medicine—are also the purview of licensed experts.

It is not unexpected though that Wikipedia’s topical coverage is driven by the interests of its users.

Sometimes data are added to Wikipedia, that are in itself correct, but controversial. Recently, Wikipedia published the 10 inkblots (Scienceroll, [21]) of the Rorschach test, along with common responses for each. This had led to complaints by Psychologists , who argue that the site is jeopardizing one of the oldest continuously used psychological assessment tests (NY Times [22]).

The actual coverage of medical subjects may vary greatly. In one study [5], abstract-format, 2007) Wikipedia entries were screened for the most commonly performed inpatient surgical procedures in the U.S. Of the 39 procedures, 35 were indexed on Wikipedia. 85.7% of these articles were deemed appropriate for patients. All 35 articles presented accurate content, although only 62.9% (n=22) were free of critical omissions. Risks of the procedures were significantly underreported. There was a correlation between an entry’s quality and how often it was edited.

Wikipedia may even be less suitable for drug information questions, questions that one-third of all Internet health-seekers search for. A study in Annals of Pharmacotherapy [6] comparing the scope, completeness, and accuracy of drug information in Wikipedia to a free, online, traditionally edited database (Medscape Drug Reference [MDR]) showed that  Wikipedia answered significantly fewer drug information questions (40.0%) compared with MDR (82.5%; p < 0.001) and that Wikipedia answers were less complete. Although no factual errors were found, errors of omission were higher in Wikipedia (n = 48) than in MDR (n = 14). The authors did notice a marked improvement in Wikipedia over time. The authors conclude:

This study suggests that Wikipedia may be a useful point of engagement for consumers looking for drug information, but that it should be supplementary to, rather than the sole source of, drug information. This is due, in part, to our findings that Wikipedia has a more narrow scope, is less complete, and has more errors of omission versus the comparator database. Consumers relying on incomplete entries for drug information risk being ill-informed with respect to important safety features such as adverse drug events, contraindications, drug interactions, and use in pregnancy.
These errors of omission may prove to be a substantial and largely hidden danger associated with exclusive use of
user-edited drug information sources.

Alternatively, user-edited sites may serve as an effective means of disseminating drug information and are promising as a means of more actively involving consumers in their own care. However, health professionals should not use user-edited sites as authoritative sources in their clinical practice, nor should they recommend them to patients without knowing the limitations and providing sufficient additional information and counsel…

Not Evidence Based

German researches found [7], not surprisingly, that Wikipedia (as well as two major German statutory health insurances):

“…failed to meet relevant criteria, and key information such as the presentation of probabilities of success on patient-relevant outcomes, probabilities of unwanted effects, and unbiased risk communication was missing. On average items related to the objectives of interventions, the natural course of disease and treatment options were only rated as “partially fulfilled”. (..)  In addition, the Wikipedia information tended to achieve lower comprehensibility. In conclusion(..) Wikipedia (..) does not meet important criteria of evidence-based patient and consumer information though…”

Wrong, misleading, inaccurate

All above studies point at the incompleteness of Wikipedia. Even more serious is the fact that some of the Wikipedia addings are wrong or misleading. Sometimes on purpose. The 15 biggest wikipedia blunders [23] include the death announcements of Ted Kennedy (when he was still alive),  Robert Byrd and others. Almost hilarious are the real time Wikipedia revisions after the presumed death of Kennedy and the death of Ken Lay (suicide, murde, heart attack? [24).

In the field of medicine, several drug companies have been caught altering Wikipedia entries. The first drug company messing with Wikipedia was AstraZeneca. References claiming that Seroquel allegedly made teenagers “more likely to think about harming or killing themselves” were deleted by a user of a computer registered to the drug company [25], according to Times [26]. Employees of Abbott Laboratories have also been altering entries to Wikipedia to “eliminate information questioning the safety of its top-selling drugs.”(See WSJ-blog [27] , brandweeknrx.com [28], and recently Kevin MD[29])

These are “straightforward” examples of fraudulent material. But sometimes the Wikipedia articles are more subtly colored by positive or negative bias.

Take for instance the English entry on Evidence Based Medicine (in fact the reason why I started this post). Totally open-minded I checked the entry, which was automatically generated in one of my posts by Zemanta. First I was surprised by the definition of EBM:

Evidence-based medicine (EBM) aims to apply the best available evidence gained from the scientific method to medical decision making. It seeks to assess the quality of evidence of the risks and benefits of treatments (including lack of treatment).

instead of the usually cited Sacket-definition (this is only cited at the end of the paper):

“the practice of evidence based medicine means integrating individual clinical expertise with the best available external clinical evidence from systematic research”

In short, the whole article lacks cohesion: the definitions of EBM are not correct, there is too much emphasis on not directly relevant information (4 ways to grade the evidence and 3 statistical measures), the limitations are overemphasized (cf. chapter 7 with 6 in the Figure below) and put out of perspective.

Apparently this has also been noted by Wikipedia, because there is a notice on the Evidence Based Medicine Page saying:

This article has been nominated to be checked for its neutrality. Discussion of this nomination can be found on the talk page. (May 2009)

9-9-2009 9-55-04 wikipedia EBM start smal

Much to my surprise the article had been written by Mr-Natural-Health, who’s account seems not to be in use since 2004  and who is currently active as User:John Gohde. Mr Natural Health is a member of WikiProject Alternative medicine.

Now why in earth would some advocate of CAM write the Wikipedia EBM-entry? I can think of 4 (not mutually exclusive) reasons:

  1. When you’re an EBM-nonbeliever or opponent this is THE chance to misinform readers about EBM (to the advantage of CAM).
  2. The author was invited to write this entry.
  3. No EBM-specialist or epidemiologist is willing to write the entry, or to write for Wikipedia in general (perhaps because they find Wikipedia lacks trustworthiness?)
  4. EBM specialists/epidemiologists are not “allowed”/hindered to make major amendments to the text, let alone rewrite it.

According to Mr Naturopath point 2 is THE reason he wrote this article. Now the next question is “exactly by whom was he invited?” But the TALK-page reveals that Mr Naturapath makes it a tough job for other, better qualified writers, to edit the page (point 4). To see how difficult it is for someone to re-edit a page, please see the TALK-page. In fact, one look at this page discourages me from ever trying to make some amendments to any Wikpedia text.

SOLUTIONS?

Changes to Wikipedia’s organization

Wikipedia has long grasped that its Achilles heel is the free editability (see for instance this interview with Wikipedia’s founder [30]). Therefore, “WikiProjects” was initiated to help coordinate and organize the writing and editing of articles on a certain topic, as well as “Citizendium” which is an English-language wiki-based free encyclopedia project aimed to improve the Wikipedia model by providing a “reliable” encyclopedia. “It hopes to achieve this by requiring all contributors to use their real names, by strictly moderating the project for unprofessional behavior, by providing what it calls “gentle expert oversight” of everyday contributors, and also through its “approved articles,” which have undergone a form of peer-review by credentialed topic experts and are closed to real-time editing.”

Starting this fall Wikipedia will launch an optional feature called “WikiTrust” will color code every word of the encyclopedia based on the reliability of its author and the length of time it has persisted on the page: Text from questionable sources starts out with a bright orange background, while text from trusted authors gets a lighter shade.

9-9-2009 15-25-36 wikipedia wikiproject medicine

The Wikipedia EBM article is within the scope of these two projects, and this is good news. However, Wikipedia still clings to the idea that: “Everyone is welcome to join in this endeavor (regardless of medical qualifications!).” In my opinion, it would be better if Wikipedia gave precedence to experts instead of hobbyists/ people from another field, because the former can be expected to know what they are talking about. It is quite off-putting for experts to contribute. See this shout-out:

Who are these so-called experts who will qualify material? From what I’ve seen so far, being an academic expert in a particular field hardly protects one from edit wars–Julie and 172 are two primary examples of this. Meanwhile, the only qualification I have seen so far is that they have a B.A. Gimme a friggin’ break! (and before I get accused of academic elitism, I make it known that I dropped out of college and spend an inordinate amount of time at work correcting the BS from the BAs, MAs, and PhDs).

While anyone can still edit entries, the site is testing pages that require changes to be approved by an experienced Wikipedia editor before they show up, the so called Flagged protection and patrolled revisions. (see Wikimedia) This proposal is only for articles that are currently under normal mechanisms of protection (i.e. the Obama-article cannot be edited by a newcomer).

Although this seems logic, it is questionable whether “experienced” editors are per definition better qualified than newcomers. A recent interesting analysis of the Augmented Social Cognition group [31], (cited in the Guardian [32]) shows a slowdown in growth of Wikipedia activity, with the activity slightly declining in all classes of editors except for the highest-frequency class of editors (1000+ edits). Here is an increase in their monthly edits.

In addition the study shows growing resistance from the Wikipedia community to new content. The total percentage of reverted edits increased steadily over the years, but more interestingly, low-frequency or occasional editors experienced a visibly greater resistance compared to high-frequency editors . Together this points at a growing resistance from the Wikipedia community to new content, especially when the edits come from occasional editors.

This is more or less in line with an earlier finding [9] showing that Wikipedia members feel more comfortable expressing themselves on the net than off-line and scored lower on agreeableness and openness compared to non-Wikipedians, a finding that was interpreted as consistent with the possibility that contributing to Wikipedia serves mainly egocentric motives.

Image representing Medpedia as depicted in Cru...
Image via CrunchBase

Encouraging students, doctors and scientists (provisional)

One way of improving content, is to encourage experts to write. To achieve that the information on Wikipedia is of the highest quality and up-to-date, the NIH is encouraging its scientists and science writers to edit and even initiate Wikipedia articles in their fields [36]. It joined with the Wikimedia Foundation, to host  a training session on the tools and rules of wiki culture, at NIH headquarters in Bethesda.

A less noncommital approach is the demand to “Publish in Wikipedia or perish”, as described in Nature News [9]. Anyone submitting to a section of the journal RNA Biology will, in the future, be required to also submit a Wikipedia page that summarizes the work. The journal will then peer review the page before publishing it in Wikipedia.” The project is described in detail here [10] and the wiki can be viewed here

Wiki’s for experts.

One possible solution is that scientist and medica experts contribute to wiki’s other than the Wikipedia. One such wiki is the wiki-surgery [5]. PubDrugRxWiki , WikiProteins [11] and Gene Wiki [12] are other examples. In general, scientists are more inclined to contribute to these specialists wiki’s, that have oversight and formal contributions by fellow practitioners (this is also true for the RNA-wiki)

A medical Wikipedia

Yet another solution is a medical wikipedia, such as Ganfyd or Medpedia . Ganfyd is written by medical professionals. To qualify to edit or contribute to the main content of Medpedia approved editors must have an M.D., D.O., or Ph.D. in a biomedical field. Others, however, may contribute by writing in suggestions for changes to the site using the “Make a suggestion” link at the top of each page. Suggestions are reviewed by approved editors. Whether these medical wikipedias will succeed will depend on the input of experts and their popularity: to what extent will they be consulted by people with health questions?

I would like to end with a quote from Berci during twitterview (link in Wikipedia):

@Berci : @diariomedico And as Wikipedians say, Wikipedia is the best source to start with in your research, but should never be the last one. #DM1 9 months ago

REFERENCES

ResearchBlogging.orgScientific Articles

  1. Laurent, M., & Vickers, T. (2009). Seeking Health Information Online: Does Wikipedia Matter? Journal of the American Medical Informatics Association, 16 (4), 471-479 DOI: 10.1197/jamia.M3059
  2. Hughes, B., Joshi, I., Lemonde, H., & Wareham, J. (2009). Junior physician’s use of Web 2.0 for information seeking and medical education: A qualitative study International Journal of Medical Informatics, 78 (10), 645-655 DOI: 10.1016/j.ijmedinf.2009.04.008
  3. Lee, C., Teo, C., & Low, A. (2009). Fulminant dengue myocarditis masquerading as acute myocardial infarction International Journal of Cardiology, 136 (3) DOI: 10.1016/j.ijcard.2008.05.023
  4. Halavais, A., & Lackaff, D. (2008). An Analysis of Topical Coverage of Wikipedia Journal of Computer-Mediated Communication, 13 (2), 429-440 DOI: 10.1111/j.1083-6101.2008.00403.x
  5. Devgan, L., Powe, N., Blakey, B., & Makary, M. (2007). Wiki-Surgery? Internal validity of Wikipedia as a medical and surgical reference Journal of the American College of Surgeons, 205 (3) DOI: 10.1016/j.jamcollsurg.2007.06.190
  6. Clauson, K., Polen, H., Boulos, M., & Dzenowagis, J. (2008). Scope, Completeness, and Accuracy of Drug Information in Wikipedia Annals of Pharmacotherapy, 42 (12), 1814-1821 DOI: 10.1345/aph.1L474 (free full text)
  7. Mühlhauser I, & Oser F (2008). [Does WIKIPEDIA provide evidence-based health care information? A content analysis] Zeitschrift fur Evidenz, Fortbildung und Qualitat im Gesundheitswesen, 102 (7), 441-8 PMID: 19209572
  8. Amichai–Hamburger, Y., Lamdan, N., Madiel, R., & Hayat, T. (2008). Personality Characteristics of Wikipedia Members CyberPsychology & Behavior, 11 (6), 679-681 DOI: 10.1089/cpb.2007.0225
  9. Butler, D. (2008). Publish in Wikipedia or perish Nature DOI: 10.1038/news.2008.1312
  10. Daub, J., Gardner, P., Tate, J., Ramskold, D., Manske, M., Scott, W., Weinberg, Z., Griffiths-Jones, S., & Bateman, A. (2008). The RNA WikiProject: Community annotation of RNA families RNA, 14 (12), 2462-2464 DOI: 10.1261/rna.1200508
  11. Mons, B., Ashburner, M., Chichester, C., van Mulligen, E., Weeber, M., den Dunnen, J., van Ommen, G., Musen, M., Cockerill, M., Hermjakob, H., Mons, A., Packer, A., Pacheco, R., Lewis, S., Berkeley, A., Melton, W., Barris, N., Wales, J., Meijssen, G., Moeller, E., Roes, P., Borner, K., & Bairoch, A. (2008). Calling on a million minds for community annotation in WikiProteins Genome Biology, 9 (5) DOI: 10.1186/gb-2008-9-5-r89
  12. Huss, J., Orozco, C., Goodale, J., Wu, C., Batalov, S., Vickers, T., Valafar, F., & Su, A. (2008). A Gene Wiki for Community Annotation of Gene Function PLoS Biology, 6 (7) DOI: 10.1371/journal.pbio.0060175
    Other Publications, blogposts
    (numbers in text need to be adapted)

  13. Envision Solutions, LLC. Diving Deeper Into Online Health Search – Examining Why People Trust Internet Content & The Impact Of User-Generated Media (2007) http://www.envisionsolutionsnow.com/pdf/Studies/Online_Health_Search.pdf Accessed August 2009 (CC)
  14. New data available of the the Pew Internet & American Life Project are available here)
  15. http://www.thegooglecache.com/white-hat-seo/966-of-wikipedia-pages-rank-in-googles-top-10/
  16. http://www.seoptimise.com/blog/2008/05/why-wikipedias-google-rankings-are-a-joke.html
  17. http://wishfulthinkinginmedicaleducation.blogspot.com/2009/06/where-do-first-year-medical-students.html
  18. http://www.newscientist.com/article/mg20327185.500-should-you-trust-health-advice-from-the-web.html?page=1
  19. http://wishfulthinkinginmedicaleducation.blogspot.com/2009/07/where-do-junior-doctors-look-things-up.html
  20. http://www.shockmd.com/2009/07/06/how-and-why-junior-physicians-use-web-20/
  21. http://sandnsurf.medbrains.net/2009/07/how-and-why-junior-docs-use-web-20/
  22. Wikipedia used by 70% of junior physicians, dominates search results for health queries (casesblog.blogspot.com)
  23. http://scienceroll.com/2009/07/06/junior-physicians-and-web-2-0-call-for-action/
  24. http://scienceroll.com/2009/08/03/rorschach-test-scandal-on-wikipedia-poll/
  25. http://www.nytimes.com/2009/07/29/technology/internet/29inkblot.html (Rorschach)
  26. http://www.pcworld.com/article/170874/the_15_biggest_wikipedia_blunders.html
  27. http://www.futureofthebook.org/blog/archives/2006/07/reuters_notices_wikipedia_revi.html
  28. http://en.wikipedia.org/w/index.php?diff=prev&oldid=144007397
  29. http://business.timesonline.co.uk/tol/business/industry_sectors/media/article2264150.ece
  30. http://blogs.wsj.com/health/2007/08/30/abbott-labs-in-house-wikipedia-editor/
  31. http://www.brandweeknrx.com/2007/08/abbott-caught-a.html
  32. http://www.kevinmd.com/blog/2009/08/op-ed-wikipedia-isnt-really-the-patients-friend.html
  33. http://www.businessweek.com/technology/content/dec2005/tc20051214_441708.htm?campaign_id=topStories_ssi_5
  34. http://asc-parc.blogspot.com/2009/08/part-2-more-details-of-changing-editor.html
  35. http://www.guardian.co.uk/technology/2009/aug/12/wikipedia-deletionist-inclusionist
  36. http://www.washingtonpost.com/wp-dyn/content/article/2009/07/27/AR2009072701912.html
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MedLib’s Round, First Edition

13 02 2009

Welcome to the first edition of MedLib’s Round, a blog carnival of the “best blog posts in the field of medical librarianship”.

shht-librarian-costume1Starting a new blog carnival is often difficult. You have to recruit bloggers, who want to participate by submitting blogposts and/or hosting future editions. (see this older post on Scienceroll Thanks @hleman).

I didn’t sound out people to find if they were interested, but just gave it a try. — Therefore, I was very pleased that the idea was so enthusiastically received by many medical librarians ànd physicians from all over the world. Emergency physician Mike Cadogan (@sandnsurf) of Life in the First Lane already added the MedLib’s Round to his listing of Blogs Rankings and Rounds before it had even started.

Blog carnivals are meant to spread the word not only about established, but also about new bloggers. I’m therefore delighted that several librarians were inspired to (re)start blogging.

Shamsha Damani (@shamsha) accepted the invitation to become a guest writer on this blog to be able to submit a post (see below).

Alisha Miles (@alisha764) who start tweeting in Januari started her own blog Alisha 764 with the post “I am a Tree” saying: “I am no longer a mushroom, I am now a tree. Thank you to all of the other librarians’ posts & tweets that inspired me to start this blog.” Which clearly refers to the comment of @sandnsurf to the blogpost “What I learned in 2008 (about Web 2.0)“: “the most important thing is that you are actually a tree in this ecosystem, you are out there experimenting, thinking and trying to drive the revolution further…Most of my colleagues are still mushrooms…

The Pilgrimthinkera librarian explores health literacy, patient education and consumer health issues) even wrote a blogpost entitled “Thank you, Laika, for taking the initiative to start up a MedLib Blog Carnival. It was just the kick in the pants I needed to get back to blogging, with the added promise of some increased interest and posting from everyone.”

Thus apart from being a post-aggregator, a blog carnival can also inspire people with similar interests and connect them. From my own experience I know you can feel lonely as a blogger. So please  take a look at the above mentioned blogs/twitter accounts and help them to flourish into full grown trees, so we can all enjoy their fruits (and vice versa).

AND NOW FOR…..THE FIRST MEDLIB’S ROUND

The MedLib’s Round is about medical librarian stuff. This field is much broader than searching PubMed or interlibrary loaning; it is related to all stages in the publication and medical information cycles (searching, citing, managing, writing, publishing, social networking).

This carnival covers many facets of that cycle.

SEARCHING THE WEB

For medical librarians searching is an important facet of their job. There are different sources to search, including “the World Wide Web” and bibliographic databases like PubMed.

Hope Leman of AltSearchEngines has compiled a list of Top 10 Health Search Engines of 2008. She urges all those interested in medical search to give these tools a spin. Her Top 10 bares great resemblance to the Top 8 Bedside Health Search Engines 2008 of @sandnsurf (Mike Cadogan), indicating that the same engines are appreciated and used by physicians as well.
GoPubMed ranks 2 in both lists. According to Hope “GoPubMed is a useful complement to PubMed proper, particularly to determine who the leading authorities are on particular topics.
For further details on how to use GoPubMed see an earlier post of Mike and several posts of David Rothman (here and here).

On first position in both lists is the federated search engine Mednar. Hope submitted a second post merely devoted to this health search engine: Mednar Search…and Hope said, “It is good.” Well, if Hope, an expert in search engines, recommends Mednar it must be good. According to Hope Mednar is useful for (medical) librarians, as well as busy front-line clinicians and clinical researchers. Its main advantages are its ease of use, its elegant interface and “the access to an array of databases that are simply not mined by other health search engines, also called “The Invisible Web” (gray literature and similar hard-to find content)“. It is an useful complement to PubMed in that there is a shorter lag time before the very latest articles can be found.
Recently others have also reviewed Mednar, including (of course) @sandnsurf , as well as Creaky of EBM and Clinical Support Librarians@UCHC who concluded “I liked the results well-enough, but won’t give up using the precise technical limits and search filters available in PubMed, or the comprehensive, deep searches available by using the 15,000 journals indexed in Scopus”.

SEARCHING PUBMED (and Widgets)

3262152119_a1cc3c28a4-sl-award-guusGuus van den Brekel of DigiCMB , who just won the Alliance Virtual Library Golden Leaf Awards 2009 (Second Life), told me that PubMed is by far the most frequently used search database by the hospital staff and students of the University Medical Center Groningen, where he works. In 2007, EVERY 2 MINS somebody used the Pubmed link, and every 30 seconds somebody clicked the SFX-link resolver in PubMed. Guus believes that such a tool needs to be published to as many platforms as possible, and in any format the patrons would like them. So far a Toolbar, Widget, HTML-box, OpenSearch pretty much covers that wish. The Widgets can be found at PubMed Search & News Widget

PubMed has introduced (or rather continuously introduces) several changes, that have been amply discussed here. Major changes include the Advanced Search, the citation sensor and the way terms typed in the search bar are translated. Non-librarians often don’t know that PubMed automatically maps the words, but the way this is done has changed, i.e. multi-term words are split. In her post Mapping door PubMed, written in Dutch and English, de Bibliotheker shows that this altered mapping can have both unexpected positive and negative effects, and that it is always important to check the Details Tab.

Among the things that Nicole Dettmar (Eagle Dawg) of the Eagle Dawg Blog addresses at her post Eagle Dawg Blog: Hidden in the Bookshelf: PubMed & Discovery Initiative is the new Discovery Initiative of the NCBI, which is an effort to make the full potential of the NCBI Web services and underlying databases more available to users. Nicole gives various interesting links, which will tell you more about the upcoming changes.

MANAGING INFORMATION AND REFERENCES

Like many of her colleagues medical librarian Anne Welsh First Person Narrative noticed clinicians prefer to perform one word Google-style searches (hé, does that sound familiar!). However, realizing that her medical library “expert opinion” was based on nothing more than a series of anecdotes, Anne decided to have a  fish around for research on clinicians’ search strategies and information needs. Curious about the outcome? Then read the summary of the evidence in her well written research blogging post “Limiting the Dataset.

Indeed it is hard to keep up with the literature. Apart from specific (often Google-style searches), most clinicians also try to read a few interesting journals, for instance the BMJ and the Lancet. Instead of going to the library it is also possible to take an email alert or a RSS feed to the journals of your choice. You can generate custom RSS feeds in PubMed for you favorite search and/or Journal, but this is a kind of cumbersome procedure for most people not used to it (see for instance my earlier post in Dutch and this post of David Rothman – a must-read for people not acquainted with the use of RSS for this purpose).
Physician and medicine2.0 pioneer Ves Dimov of the Clinical Cases and Images – Blog has another solution to set up a RSS feed to journals, which I found astonishing simple and pretty awesome, because of the conveniently arrangement of the results. All you need is a free Google account to create Your Own “Medical Journal” with iGoogle Personalized Page. Want to know how it works, then please read his easy-to-follow post, which he has specially updated for this occasion. Ves has also included some ready made RSS feeds of the “Big Five” medical journals (NEJM, JAMA, BMJ, Lancet and Annals) plus 2-3 subspecialty journals as well as several podcasts in iGoogle.

Now, once you have the PDF’s of the papers you like you would like to store them in a handy way. Another physician, the Dutch psychiatrist Dr Shock MD PhD with a very eloguent blog of the same name, explores the use of Mendeley, a free social software for managing and sharing research papers and a Web 2.0 site for discovering research trends and connecting to like-minded academics (see Mendeley Manage Share and Discover Research Papers). Dr. Shock didn’t make up his mind yet whether he prefers Mendeley or Labmeeting (described in another post) as an online library. But offline he uses Sente, which he finds absolutely perfect. A chimera between Sente and one of the other tools would be his ideal management system.

PUBLISHING

Michelle Kraft of The Krafty Librarian was totally blown away by a presentation on Interactive Science Publishing at PSP 2009 Annual Conference (where she also gave a presentation herself). I didn’t know what interactive science publishing really meant, but Michelle can illustrate things so well, that you can readily imagine it all. This was needed as I could not access the examples she referred to without the risk of my computer becoming too slow or worse. But I understand from Michelle that it is a revolutionary new method of viewing online journals, although there are some answers to be addressed as well (see her post)

Imagine having the “PDF” of an article on congenital heart defects and be able to hear the heart sounds plus the video recording of the heart. The video would be more than just a snippet, it would be the entire video sectioned into “chapters” referenced within the various areas of the article. So while you are reading the article you can click on the link within the text referencing the image, sound, etc. and the image immediately jumps to that section the video. Imagine the data behind a large randomized controlled trial available in its entirety to all readers to be manipulated, reused, and viewed.

Another new publishing format is discussed by Shamsha Damani (@shamsha) on this blog (see: “How to make EBM easy to swallow“). Shamsha informs us that the BMJ will be publishing two summaries for each research article published. One called BMJ PICO, prepared by the authors, breaks down the article into the different EBM elements. The other called Short Cuts is written by BMJ itself. Here she hopes BMJ will shine, providing an easy to follow unbiased view of the article. Indeed, it would be very welcomed if more papers were in the ready-appraised-format, similar as found in the ACP-Journal Club. However, in the BMJ, it is the PICO-format written by the authors themselves which has the EBM structure, and is most preferred by the readers. According to some (including me) the Short Cuts are a bit woolly. Or as Shamsha says: “Personally I think it would have been better to have the BMJ reviewers write the PICO format, and do a bit more thorough critiquing”.

SOCIAL MEDIA & NLM, GOVERNMENTAL ORGANIZATIONS AND MEDICAL LIBRARIANS

In the same blogpost as mentioned above @Eagledawg mentions that the recent introduction of the #pubmed tag in Twitter (with the aim that you can later search for messages with this tag, see real time results here) led to various responses, which are not really appreciated as useful by the NLM because of the extreme short length of the tweets (140 characters including tag). It strikes Nicole that the NLM is not present on twitter (in contrast to the FDA and the CDC, also see a post of David Rothman). A good example of how the government could use using social media to respond to citizens is given by Andrew Wilson, a member of the recently introduced social-media team of the Department of Health and Human Service, who responded to the peanut-butter-and-salmonella recall issue on Twitter.

An interview with Andrew Wilson can be found here.
And, by the way The Library of Congres (see Dean Giustini’s blog) and the Cochrane Collaboration have also joined Twitter.

Health 2.0 people are well represented on Twitter. See for instance this list of Twitter Doctors, Medical Students and Medicine-related. made by @medicalstudent There is also a great slideshare presentation of @PhilBaumann on 140 health care uses for Twitter.

But how is Twitter used by medical librarians? David Rothman is not a huge fan of Twitter (he prefers friendfeed), but he does refer to a list of Great & growing resource for libraries/librarians on Twitter!
Dean Giustini
of UBC Academic Search – Google Scholar Blog wonders why there aren’t More Canadian (mapple Leaf) Librarians on Twitter? Well, I don’t know whether this is typical for Canadians, I don’t see many Dutch medical librarians either.
Dean plans to
write something for an upcoming issue of a health library journal about Twitter. Want to have an idea what Twitter is about, please read his short post on Twitter. Already on twitter but looking for twitterers in all the wrong places” than forget one bad idea and follow the half dozen good ideas Patricia gives in her excellent post on Twitter.

And what about the presence of the abovementioned contributors to this first Grand Round? Without exception they are all on Twitter and all but one use it on a regular basis. Now, assuming that most medical librarians aren’t on Twitter, doesn’t tell that something about this group? I wonder if Twitter presence is not the main reason for the swift start of this First MedLib’s Round.

That’s it for this edition.

741879088_29d01c359b_m-another-dead-librarian
I hope you enjoyed this first MedLib’s Round.
I surely enjoyed reading the many interesting and good quality posts that were submitted.

The next round will be hosted by Dragonfly, March 10.
Please submit your
favorite blog article to the next edition of medlib’s round before March 8 by using the carnival submission form (here) (!). Submission to the form makes it easier for the host to summarize the articles.

p.s. Perhaps you would like to host a future edition as well. If so, please inform me which edition (off May) you would like to host.

Jacqueline (“Laika”)


Photo credits (Flickr-CC)

Librarian’s Costume by Librarian Avenger

Namro Orman, SL

Another Dead Librarian by Doug!