Archive for October, 2013

The International Gang of Four (IGF)

October 30, 2013
 

 

Source: Norma Desmond’s Flickr Photostream

Here’s a wee story I’d like to share in real time.

In order to respect privacy, I’ve changed the names and omitted the nature of disease topic. In the grander scheme of things, what we’re doing is equally applicable to any condition anyway.

ONLINE COLLABORATION

My involvement in Patient Advocacy leads to a vast array of interesting avenues. On one of the Forum’s that McDawg frequents, off Forum, I’ve made contact with a few folks in particular who post extremely interesting and thought provoking comments and are clearly, very intelligent people. The majority of these comments are accompanied with links to abstracts in PubMed.

Now, I’m not suggesting at all that the content of posts from others are not of value. Far from it. Everyone has something to offer. Having navigated these waters for a number of years now, users of the Forum would be the first to agree however that some people do very much stand out from the crowd. I’m not one of them but my “connecting people” skills is appreciated there.

Last year in particular, the first person unbeknown to anyone at that time to be “recruited” to the IGF was “Margaret” in Australia and then “Laura” in New Zealand a few weeks later. Broadly speaking, we’ve all gathered a lot of useful information and share much common ground. Our backgrounds are all quite different but we all very much have a reason for being interested in a particular disease.

This year, off Forum, contact was established with “Thomas” in Canada. We all started off emailing each other separately and this gradually started to morph into something bigger – more collective.

Thomas proposed that it would be a good idea or formally structure what we were doing, and also proposed the name of the International Gang of Four and since all were in agreement, that’s how we formed the IGF.

This also ties in very nicely with a Review Manuscript I was already working on about the disease.

“Julie” from the USA has been the most recent addition a month or so ago. Now that we are up to five, we’re still trading at the IGF but the “F” now represents five, not four.

Rather than all working separately, I proposed that we should collaborate online using Google Docs. Some of us are more advanced than others in using it, but we’re making progress as a team.

We all still contribute to the Forum but in a way, as a group, we sort of outgrew it. Part of “the problem” is that off Forum, we share many Manuscripts using “Fair Use”, so are unable to continue with our detailed discussions in a public Forum.

What we are currently doing is uploading our own documents and presentations to Google Docs. At any given moment of time, any member of the IGF can access these, share, remix, whatever. We have a house rule that such access at the moment does not extend to those outwith the group.

This is somewhat ironic for an Open Access Advocate and indeed, someone interested in the concept of Open Notebook Science (ONS) and so on. Indeed, it was contributing to this thread on FriendFeed about writing a Manuscript on ONS and 2.0 social networking science stuff that prompted me to write this post.

So, should the IGF continue to collaborate in the way that we currently are or perhaps experiment with a wiki for example? I would say that we stick with doing what we are currently doing and think about this again at some point in the future.

Once we get to a point where we’ve actually produced something tangible, where do we go from there? Submit to a Journal for peer review? Most probably.

This is all very much a learning curve for McDawg at least in terms of scientific collaborations but not music collaborations. I’ve only done this once before (last year) with the end result getting published in Nature Precedings:-

Nature Precedings is a free online service launched in 2007 enabling researchers in the life sciences to rapidly share, discuss and cite preliminary (unpublished) findings. One year later, we look at some of the highlights.

Being a non scientist, a number of questions arise. How do scientists collaborate online? Do many actually do this? Should non scientists venture into such territories? What types of 2.0 tools do people/scientists use to collaborate online?

 
 
 

 
Advertisements

“Open Views” – 43 podcasts

October 7, 2013

“Open Views” – 43 podcasts

Originally posted on April 6, 2012 by Graham Steel

Back in August 2007, pretty much by accident, I stumbled across an ongoing series of podcasts – the series was named Open Views. There are 43 episodes recorded/uploaded between October 2006 and December 2007. When I found the series, the most recent upload was episode 37.

The first four episodes that I listened to were:-

30 – Open Views – David Lipman, National Institutes of Health

10 – Open Views – Mark Patterson, Virginia Barbour, Public Library of Science

12 – Open Views – Richard Poynder

and

16 – Open Views – John Wilbanks, Science Commons

At that juncture, I was only six months into my foray into all things Open Access so listening to the above was extremely helpful.

So, who was behind this and what is KRUU.fm ?

The person who put these episodes together was a guy called Sundar Raman.

And from http://kruufm.com/about

Who We Are

KRUU-LP 100.1 FM is a solar-powered, open source, independent, non commercial, listener-supported, grassroots community low power radio station, broadcasting 24 hours/day and 7 days/week since September 30th, 2006 from Fairfield, Iowa. 99.7% of the programs at KRUU are produced by some 100 volunteer hosts who create 80 shows a week. Only one program is not produced by KRUU hosts.

KRUU-FM – Giving Fairfield a Voice

The mission of KRUU is to give Fairfield a voice, and strengthen the community by encouraging creativity, dialogue and community involvement. KRUU is an open, inclusive, diverse forum for music, creative expression, information, and entertainment with a strong emphasis on locally created produced programming.

Very, very interesting….

Being the proactive person that I am, I submitted an entry to the SPARC Open Access Forum to alerts users about Open Views. I then contacted Sundar by email and received a lovely reply. Having told him a bit about my background, I sent him a copy of my Open Access Contact list which he was grateful for.

Quite by surprise, he asked if I would be interested in doing an interview !! McWOW… I gratefully accepted. I also assisted in connecting Sundar with Peter Suber and shortly thereafter, Sundar interviewed Peter Suber and I back to back.

And so it came to pass that episode 38 was:-

– Open Views – Peter Suber, OpenAccess

Whilst eagerly awaiting to hear my own interview, I helped to set up two others being:-

Episode 42 – Open Views – Matthew Todd, The Synaptic Leap

and

Episode 43 – Open Views – Matthew Cockerill, BioMedCentral

Episode 43 turned out to be the final one.

Sundar and I kept in touch and towards the end of the year, he emailed me a link to the unedited recording of my own interview. In January 2008, I uploaded a small section of the interview here and linked to it on my old blog here.

Finally, by July 2008, I got round to uploading and blogging the full edited version.

 

 

Anyways, enough about lil’ ole me….

Whilst it’s unfortunate that the series ended there, it still remains a fantastic online resource….

Open Views is an exploration of open-source and free-culture movements around the world, stretching beyond the limits of software. The show’s purpose is to provide a view into the rich world of collaborative development, open ideas, independent media, and new business models. This is a revolutionary time, with tools to aid the world, and collaboration possible from every corner of the globe. Open Views talks to the people at the front lines of this renaissance.

Click here for a short description of all of the episodes and here for a more in depth one

Listen to and download archived episodes of Open views by clicking on this link.

The Publishing “Sting”, the reaction, and the outcome

October 4, 2013

On 4th October, Science Magazine published an article titled Who’s Afraid of Peer Review?.

It was penned by John Bohannon, a biologist and science journalist based at Harvard University. Before going into detail, in a nutshell, Bohannon self handedly carried out a “sting” operation by submitting a bogus scientific paper to a ‘selected’ number (just over 300) of Open Access Journals and published his findings in his article. 157 of these journals published the paper in question. [1]

Bohannon’s article was placed under an embargo which lifted at precisely 2PM ET. Within seconds it sparked a huge amount of coverage on social media sites and not surprisingly, especially on Twitter. One of the first to comment was PLOS co-founder Michael Eisen who tweeted “I confess. I wrote the Arsenic DNA paper to expose flaws in peer-review at Science http://www.michaeleisen.org/blog/?p=1439  @sciencemagazine

A pull-quote from his blog post, “There are deep problems with science publishing. But the way to fix this is not to curtain open access publishing. It is to fix peer review.”

Shortly after, Ivan Oransky of Retraction Watch tweeted, “.@sciencemagazine reporter spoofs hundreds of open access journals with fake papershttp://bit.ly/1bAt5Hu

A pull-quote from that blog post, Bohannon’s analysis, which goes into far more depth, demonstrates an appalling lack of peer review and quality control at the journals he spoofed. But it’s important to note, given the heated and endless debates between open access advocates and traditional publishers, that there was no control group”.

Further posts continued to emerge so it became clear that certain people had clearly seen Bohannon’s article prior to the embargo being lifted.

Going back to the article itself:-

“The bait

The goal was to create a credible but mundane scientific paper, one with such grave errors that a competent peer reviewer should easily identify it as flawed and unpublishable. Submitting identical papers to hundreds of journals would be asking for trouble. But the papers had to be similar enough that the outcomes between journals could be comparable. So I created a scientific version of Mad Libs”.

To learn the location of online journals that accepted or rejected Bohannan’s paper, see this interactive global map.

“The sting

Between January and August of 2013, I submitted papers at a rate of about 10 per week: one paper to a single journal for each publisher. I chose journals that most closely matched the paper’s subject. First choice would be a journal of pharmaceutical science or cancer biology, followed by general medicine, biology, or chemistry. In the beginning, I used several Yahoo e-mail addresses for the submission process, before eventually creating my own e-mail service domain, afra-mail.com, to automate submission”.

And in part:-

“The results

By the time Science went to press, 157 of the journals had accepted the paper and 98 had rejected it. Of the remaining 49 journals, 29 seem to be derelict: websites abandoned by their creators. Editors from the other 20 had e-mailed the fictitious corresponding authors stating that the paper was still under review; those, too, are excluded from this analysis. Acceptance took 40 days on average, compared to 24 days to elicit a rejection”.

Dr Martin Eve’s post “What’s “open” got to do with it?” is very much worth of a read, as are other posts which have since emerged:-

Peter Suber – New “sting” of weak open-access journals

Mike Taylor – John Bohannon’s peer-review sting against Science

Scholarly Kitchen – Open Access “Sting” Reveals Deception, Missed Opportunities

Bjoern Brembs – Science Magazine Rejects Data, Publishes Anecdote

The Guardian – Hundreds of open access journals accept fake science paper

The Faculty Lounge – The Troubled Peer Review System, the Open Access Wars, & the Blurry Line Between Human Subjects Research & Investigative Journalism

The Economist – Science’s Sokal moment

Curt Rice – Open access publishing hoax: what Science magazine got wrong

The Verge – Sham science: fake research paper accepted by over 100 journals

NPR – Some Online Journals Will Publish Fake Science, For A Fee

Zen Faulkes – Open access or vanity press, the Science “sting” edition

Ernesto Preigo – Who’s Afraid of Open Access?

OASPA – OASPA’s response to the recent article in Science entitled “Who’s Afraid of Peer Review?”

A key message is contained in the OASPA post:-

“In our view the most important lesson from this recent article in Science is that the publishing community needs stronger mechanisms to help identify reliable and rigorous journals and publishers, regardless of access or business model.  OASPA will continue to scrutinize membership applications according to our membership criteria, and listen to feedback from the community, so that membership within OASPA can continue to be an important signal of quality within the open access ecosystem”.

Moreover, it was also pleasing to see this (in part) statement from the DOAJ:- “DOAJ fully supports the statement issued by OASPA earlier today which highlights what can and cannot be concluded from the article. It is important to remember that the conclusions drawn by the article only cover a small percentage of open access journals and cannot be applied to the wider open access community”.

To conclude, despite its (Bohannon’s analysis) many flaws and weaknesses, lessons can be learned from all of this and the responses from OASPA/DOAJ are indicative of that.  The more transparency the better in terms of publishing and I fully support the statements from OASPA and the DOAJ.

[1] Note – There are currently 9948 listed in the DOAJ and in terms of the overall number of scientific journals, there are in excess of 25,000. As pointed out by many, crucially, there was no “control group” in this operation.

So doing the math, there are > 25k scientific journals. Science’s target, speared by Bohannon, was just over 300, mainly based in India – which equates to 0.628 % of all journals on the planet who published it.

Talk about scoring an own goal !!!