10 Sep 2012

Lambert Academic Publishing (or How Not to Publish Your Thesis)

[Updated March 2014, see update below]

Lambert Academic Publishing (LAP) is an imprint of Verlag Dr Muller (VDM), a publisher infamous for selling cobbled-together "books" made up of Wikipedia articles mainly under their Alphascript Publishing imprint. LAP, on the other hand, specialize in "publishing" academic theses [update: they also use the names Scholars' Press and Editorial Académica Española (EAE)]. Below, I summarize what's known about LAP's operations (and my opinion of "publishing" a thesis with such an organization), but consider this first:

Lambert Academic Publishing on Facebook have an Acquisition Editor called "Kevin Woodmann". This is a little curious as Kevin is not a common German name, though apparently it was popular in East Germany in the 1990s. Here's his profile:

He's a handsome guy with salt-and-pepper hair; there's a touch of George Clooney to him.  There's a catch though - Kevin's photo is actually a stock photo of a "Confident middle aged man sitting and smiling against white background" by Yuri Archurs

Yasmine Watson, another Acquisition Editor, is actually a "Smiling business woman with colleagues at the back"; Sophia Campbell is a "Young business woman laughing over a thought"; Lisa Thompson is a "Happy casual business woman holding her coat over shoulder at her workplace".

And so on. Legitimate publishing businesses do not create false profiles on social media sites.

What else is known about VDM/LAP (and the many other names used by this company)?
- They find authors largely by bulk-emailing students who have recently published theses;
- They have no selectivity - anyone who submits their "book" will have it "published";
- They do not conduct peer review;
- They do not edit the "book", and they "publish" exactly what is submitted - and apparently they charge for any changes made by the author after submission;
- Authors will almost certainly never receive any royalties (a blogger notes that "I have yet to found the testimony of anybody who has received royalties");
- They do not market the "books";
- The "books" do not count in many research assessment processes.

For example, see this summary of the business practice of VDM/LAP from an Australian university:
"LAP Lambert does not conduct a peer review/editorial process. Manuscripts are published exactly as they are submitted to the publisher." 
"Where royalties average less than 50 Euro a month, the author is given book vouchers for other LAP Lambert stock. An author’s share is usually always under this because at the average rate of 80 Euro a book, it means they would have to sell 11 copies a month to exceed the 50 Euro threshold, which is difficult since the company does not undertake any marketing on behalf of the author." 
"This could adversely affect the opportunity to have your work accepted in a reputed peer-reviewed journal."
Also see this experience of "publishing" with LAP:
"I should point out that once you’ve submitted your publication-ready document to LAP’s online system, that’s it. If you’ve made a mistake and left off one-third of your reference list (as I almost did) they impose a hefty fee for having to intervene to make corrections." 
"My personal copy arrived last week. Looks just like my thesis (but with less expensive paper, a smaller font and packaged as a paperback!)" 
"When I checked my author's account at Lambert Academic Publishing at the end of the last financial year (after my beautifully paperbacked master's thesis had been on sale via Amazon for 12 months) not only had no royalties accrued to me, but zero copies of the book had been sold."
Is the publication of these "books" solely the responsibility of Lambert Academic Publishing and their ilk? (author mills, vanity presses, call them what you will) Are these authors all unwitting victims? I think the answer is no. Many new authors starting out on an academic career are desperate to get published, but "publishing" an unaltered thesis with a print-on-demand publisher without making clear that the "book" is a copy of the thesis is, in my opinion, an attempt to gain unearned academic credit for no additional work. I do not think that charging people $97 on Amazon to read a repackaged thesis is reasonable. I believe that many who buy these books will think that they are buying a published book and not an unedited thesis, and they will be misled and angry.

If you only want your thesis to be made available to more readers, there are many acceptable self-publishing and/or open access options. If you want to get academic credit beyond the qualification gained from publishing the thesis then there is no short cut: you need to publish with peer-reviewed journals or book publishers. See for example Resta et al. Publishing a Master’s Thesis: A Guide for Novice Authors. J Genet Couns. 2010 June; 19(3): 217–227  (free to access).

Find a reputable publisher and do not simply copy your thesis word-for-word - otherwise, don't be surprised to see your own academic reputation suffer.


Update, March 2014:

Lambert Academic Press continue to offer their "services" under a number of different names - Scholars' Press, Omniscriptum, GlobeEdit, the Spanish-language Editorial Académica Española (EAE) and Publicia, the Italian-language Edizioni Accademiche Italiane (EAI), the German-language Akademikerverlag, Südwestdeutscher Verlag für Hochschulschriften, and Saarbrücker Verlag für Rechtswissenschaften, the French-language Éditions Universitaires Européennes and Presses Académiques Francophones, Palmarium Academic Publishing, the Polish-language Wydawnictwo Bezkresy Wiedzy - and unwary authors continue to "publish" with them, but this blog post and others like it at least serve to warn some academics of the nature of their business. One of the latest is the delightfully titled "Please do not publish my thesis" by Eva Amsen, aka easternblot.

I was interviewed earlier this year by a journalist, Joseph Stromberg, based on this post.

"plenty of people consider the company’s strategy predatory—and in his research, Hodgkinson uncovered a curious pattern that lends credence to this" 
As well as interviewing me and Thorsten Ohm, the CEO of VDM, Joseph 'took one for the team' and "published" his own thesis with LAP, discovering in the process that LAP do a hard sell on their new authors to try to make them purchase copies, something I believe is a new angle on their business model.

"LAP Lambert’s real plan finally became clear: They make money not by selling arcane tomes to readers, but by selling the books back to their authors after they’ve already signed away the rights."
His fascinating piece, "I Sold My Undergraduate Thesis to a Print Content Farm", was published by Slate.

p.s. I noticed that Betascript, an imprint VDM uses to sell their collections of Wikipedia articles, uses the name "Lambert M. Surhone" for one of their fake editors. Someone at VDM obviously likes the name "Lambert".

9 Sep 2012

Will the real Wulfenia journal please stand up?

In mid-August, the AuthorAID mailing list came up with an intriguing case. An author asked "Can you help me? Is this journal is true or fake: "WULFENIA" http://www.wulfeniajournal.at/editorial.html".

The response on the list was clear: "I searched an article from their archive entitled 'Decision making-- Eastern and western style: A way to synthesize the best of each' by Felix Kaufmann. This is a real article but it was published in 1970 in Business Horizons, vol. 13, issue 6, pages 81-86. It looks like they pinch stuff from elsewhere to seem legitimate." The journal purported to be run by "Editor in Chief: Prof. Dr. Vienna S. Franz" at Landesmuseum Kärnten, Austria, but - though the institution was genuine - nobody by that name could be found. PLOS ONE Academic Editor Jack Gilbert also gave reason to be certain that this journal was fake: "Wulfenia - a fake journal using myself and others as 'editorial board members' that makes you pay for all 'articles'".

The author who queried the validity of wulfeniajournal.at let wulfeniajournal.com know, and this site posted a warning:

 "To all scientists about www.wulfeniajournal.at : 
Wulfenia journal has not a website, and it is published as hard copy. Wulfenia journal does not publish online and www.wulfeniajournal.at is a fake site. All http://sciencesarchive.com , www.sciencerecord.com and www.wulfeniajournal.at are for one person that he/she is a hustler. If you check 2009-2011 issues of this journals, You know that all published papers are for another journals which he/she used them for your trust and fraud. Wulfenia just publish as hard copy and just publish Biology science articles NOT ALL SCIENCE AND ENGINEERING. www.wulfeniajournal.com is made just for informing you about this fraud and does not accept any papers for reviewing."
I emailed the Landesmuseum Kärnten to let them know that "Your museum's name is being used by a fake journal", tweeted about it, and thought that would be the last of it. Yet one commenter on the AuthorAID list noted that: "Even the more legitimate journal is a bit suspicious".

He was right.

Roland K. Eberwein, Editor-in-Chief of Wulfenia Journal emailed me last week to say that "The site www.wulfeniajournal.com is a criminal site too!". Wulfenia, as it turns out, is an annual print journal in botany. As the real Wulfenia notes on its website:
"The websites http://www.wulfeniajournal.at and http://www.wulfeniajournal.com ARE NOT the official websites of the journal "Wulfenia: Mitteilungen des Kärntner Botanikzentrums" published by the Regional Museum of Carinthia. Both websites criminally usurp the identity of the official journal. They fraudulently use false informations, a false editorial board and false publication requirements to encourage authors to submit articles and to transfer page fees to a bank account in Yerevan (Armenia). The Regional Museum of Carinthia is not liable for any offence undergone by potential authors who would have submitted articles via the websites mentioned above. Download of articles from these websites which were published in the official journal Wulfenia is illegal."
He let me know that "You can find 'Wulfenia' at http://www.landesmuseum.ktn.gv.at/210226w_DE.htm?seite=15".

I asked about issues with indexing of the journal, and he replied that "I got an e-mail from Thomson Reuters. They told me that they are only indexing the printed journal."

The journal is treating this as a criminal case: "We have a meeting at the police to involve the Austrian Agency against Cyber Criminality. We want to close the website www.wulfeniajournal.at. It seems that this is possible. The site www.wulfeniajournal.com is not hosted in Austria - in this case, we have no chance".

http://www.wulfeniajournal.com is currently down, while the fake http://www.wulfeniajournal.at/index.html is still accessible.

Jeffrey Beall has also written about this and he notes that print journal Archives des Sciences has also been hijacked.

My advice - before sending money to any journal, be sure who you are dealing with. Watch for poor spelling, editors with no academic record, claims to be based in one country but requesting money to be sent to another. And other print journals without an online presence should get one before they get their identity stolen too.

31 Jan 2011

Who are WebmedCentral?

"It is our effort to instill more rapidity, accountability, and transparency into biomedical publishing". WebmedCentral

It is essential in biomedical publishing to be transparent and accountable. Indeed, this is something with which the publishers of WebmedCentral agree. However, on their website they only say that "We are a group of medical and management professionals with no affiliation to any major biomedical publishing group." As posted on their YouTube video by Larry Weisenthal,
"Transparency begins at home. This is one of the most opaque, allegedly scientific web sites I've ever seen. Can you imagine submitting a serious scientific paper to a black hole, where it's impossible to learn the names of the publisher, editors, contributing editors, etc.?"
We know what WebmedCentral is, but who are they?

Their address is Suite 250, 162-168 Regent Street, London W1B 5TD, UK, but this is a P.O. Box set up by completeformations.co.uk. The whois details reveal nothing because the domain was registered by Luxembourgian company PrivacyProtect.org. More searching reveals their IP address, hosted by Liquid Web Inc. in Lansing, Michigan. WebmedCentral are on Twitter, but have only tweeted twice and give no more details. Messages were posted to newsgroups on behalf of WebmedCentral in August 2010 by a Michael Carr and a John Williams, but no contact details are given and searching for people by those names does not turn up any leads.

WebmedCentral advertised for freelancers on Elance, where they revealed in June 2009 that "We are a group of doctors based in Newcastle upon tyne." A small lead, but we can do better. Companies in the UK are registered with Companies House, and WebmedCentral is no exception. Their operating name is WEBMED LIMITED, aka WEBMED PVT LTD. and they have the registered number 07436770. This company gives the same address as given on the website, confirming that it is the correct organisation. Companies need to file certificates of incorporation and to name directors. Indeed, Webmed Ltd. was incorporated on 10 November 2010.

In the interest of transparency and accountability, I can reveal the names of the directors of Webmed Limited. These directors also run WebmedCentral, as confirmed by the contents of test manuscripts visible via Google. They are three NHS hospital doctors and a management consultant based in the North of England:
Publications and comments like Kumar G, Mahawar KK. The number of authors in articles published in three general medical journals. National Medical Journal of India 2007 Mar-Apr; 20(2): 101-2, Peer Review Practices in Biomedical Literature: A Time for Change?, Who publishes in leading general surgical journals? The divide between the developed and developing worlds, this reply to an article, and a letter to the Lancet show that they've obviously put a lot of thought into how to reform peer review and publishing.

Drs Mahawar, Malviya, Kejariwal, Mr Jain, you should be proud of launching a site that aims to reform biomedical publishing. Why hide away?

What is WebmedCentral?

Loosely following the style of Jeffrey Beall's assessment in The Charleston Advisor of various OA startups, here is an assessment of WebmedCentral, a new post-publication review biomedical journal.

WebmedCentral is a post-publication review biomedical web portal launched in July 2010. It aims to "eliminate bias, increase transparency, empower authors, improve speed and accountability, and encourage free exchange of ideas." There is no pre-publication screening, although the instructions for authors imply some oversight for issues such as patient consent. Authors may submit revised versions. Articles can be read for free on the website, where they may be reviewed both by reviewers solicited by the authors and by readers. There is a list of "Scholarly Reviewers" on the site. Readers may also rate articles. Biomedical videos are also published. The journal has ISSN 2046-1690, but articles do not appear to have DOIs. It is not indexed in PubMed, but the articles are indexed on Google Scholar. The site aims to host other open access, open peer reviewed journals.

Content: Primary scientific research, case reports, and reviews make up the bulk of the articles, alongside opinion, hypotheses, and outright fringe science. None have been peer reviewed before publication.

Usability: The site has a category listing, browse by date, featured articles, popular articles, most reviewed articles, RSS feeds, basic and advanced search, latest reviews. The PDF is only available via a Javascript link.

Cost: Free to read and publish, unless the author pays the US$50 Premium Upload fee.

Licensing: Authors retain copyright. Personal non-commercial use, digital archiving and self-archiving are allowed, though no standard license is used and details are confusing

Address: Suite 250, 162-168 Regent Street, London W1B 5TD, United Kingdom
Phone: None given
Fax: None given
Email: contact@webmedcentral.com or http://www.webmedcentral.com/Contact_Us
URL: http://www.webmedcentral.com

Free to read and publish, the journal aims to receive income from advertising and sponsorship. They offer a "premium upload service" for $50 per article that allows authors to simply email their submission to the journal. Scholarly Reviewers who post three reviews can obtain a free "premium upload".

The simplest formulation is that "Authors keep copyright to the article but our readers will be freely able to read, copy, save, print and privately circulate the article." However, the details are less clear. At one point they say authors "are free to publish it elsewhere" but also say elsewhere that "we require ... an exclusive license". They also say that users have a "free, irrevocable, worldwide, perpetual right of access for personal non-commercial use, subject to proper attribution of authorship and ownership of rights" but then say users may "view or download a single copy of the material on this website solely for your personal, non-commercial use". But they allow self-archiving: "WebmedCentral allows the final version of all published research articles to be placed in any digital archive immediately on publication. Authors are free to archive articles themselves." The precise freedom all this gives to users to reproduce the text is unclear, but calling WebmedCentral "open access" would be misleading.

The approach of WebmedCentral is reminiscent of Google Knol, which is where PLoS Currents is hosted, or of a preprint server, except there is an active post-publication peer review system.

Open peer review and community peer review are not new ideas. A similar approach to that of WebmedCentral was tried by Philica in recent years without great success; the site rapidly filled with crank publications. Another was 'E-Biomed', which was stifled and instead became PubMed Central. Although anticipated a decade ago, biomedical publishing has been wary of preprints and other proposals to remove or reduce pre-publication peer review. BioMed Central's Genome Biology had a preprint server, but it closed in January 2006. A humanities institute is experimenting with community review on Shakespeare Quarterly, though they are using a hybrid model rather than abandoning invited pre-publication review. More generally, MediaCommons argue for community peer review in their book "Planned Obsolescence". They are far from naïve, noting that
'Too many digital publishing experiments, like Philica, have lagged due to an assumption that might be summed up as "if you build it, they will come."'
The journal requires appropriate ethical approval for human and animal studies and will remove studies if they find that they fail to meet ethical standards. Articles may also be removed in cases of scientific misconduct or plagiarism. They suggest that authors use statistical advice, and ask authors to adhere to reporting standards such as CONSORT. They ask authors of clinical trials to adhere to the Good Publication Practice guidelines, but do not specifically mention trial registration. They endorse the ICMJE criteria for authorship and the use of medical writers should be declared. Funding and competing interests should be declared, though there is no definition of a competing interest. They ask authors to suggest at least three reviewers and to not only pick "friendly reviewers", and say they may invite further reviewers. How these policies are enforced and who enforces them is not clear.

Technical issues:
Previous versions of an article should be linked to, but this fails. The journal allows digital archiving and digital preservation by LOCKSS members. Some test articles can be found as Word documents that are not visible via the search, which raises questions about site security. The presentations of figures is in a sidebar and sometimes without even a thumbnail, though the pop-up view is user friendly. The referencing could be improved, with clearer formatting and hyperlinks down to the references. Some of the formatting of the reviews is poor, with changes in font and font size, and several reviews are double posted.

Publication volume:
There are 366 published articles as of 30/01/2011. Submission rates appear to have peaked following publicity in August, and have since declined (see figure).

There is currently no indication on the articles that they have received no pre-publication review. As might be expected given the lack of pre-publication review, some of the articles are fringe science: aliens, homeopathy, prayer, and telepathy are all represented. There is an account of chiropractic care of a patient with fibromyalgia, an opinion article on the evidence for homeopathy in acute upper respiratory tract infections by Peter Fisher and colleagues, a study linking 'emotional quotient' and telepathy that has the obligatory mention of quantum theory, an article on the hunt for alien life that takes in the Higgs Boson, the Bermuda Triangle, and alien implants , a virtually content-free account of acupuncture in rats, and an intercessory prayer study. The latter is, thankfully, a deliberate satire.

When you get this kind of opportunity of publishing without a filter, sex always seem to come to the fore: step forward, a hypothesis on why women don't sleep with the first man they see when they ovulate, two case reports of priapism, an institutional review of Peyronie's disease, and a case report of penile fracture. As pointed out by two reviewers, it contained the unfortunate typo in the title of the corpus callosum (in the brain) rather than the corpus cavernosum, hence it was republished (demonstrating that the article version system is not working).

Many of the articles are unpublishable in any biomedical journal: a rant about academic exploitation; a review of the biological activities of a herb that the author seems to have forgotten to write; an account of a trauma registry that is confused and sketchy; a review of oral health and inequality for which the recommendations section appears to be lifted verbatim from Nunn et al. 2008, who are not cited. How many more of the articles will contain plagiarism would be interesting to see.

On the more positive side, there are a series of interesting articles by three authors: Leonid Perlovsky has published a series of mainly hypothetical papers, e.g. on language and cognition; William Maloney, a New York dentist, has published a series of overviews and historical accounts, e.g. the medical legacy of Babe Ruth; Uner Tan has published a series of articles of his observations and theories of quadrapedal locomotion in humans, e.g. these two cases.

Other interesting reads are a survey of the role of hairdressers and bartenders as informal emotional support following the 9/11 attacks and their responses to this role, a study by Robert Dellavelle on how journals don't require ethics approval for meeting abstracts, and a series of witty anecdotes by an Israeli psychiatrist of cases of "curing demons" in his patients.

Around a quarter of the articles are case reports. The insatiable demand of hospital doctors to publish case reports has clashed with a reluctance of medical journals to publish what are often "me too" publications offering little generalisable insights, and which are often poorly presented and incomplete. The recent trend of open access case report journals - BMJ Case Reports, Cases Journal, Journal of Medical Case Reports, Clinical medicine insights. Case reports, Case Reports in Ophthalmology etc. from Karger, Case reports in Medicine from Hindawi and the American Journal of Case Reports (free, not OA) - doesn't appear to be matching demand.

There are also 58 reviews, 31 opinion articles, and at least 15 of the "original articles" are not research articles; less than half of the articles on WebmedCentral are primary research.

Some of the reviewers are published researchers, but they usually have only a handful of publications and they would be unlikely to be selected as peer reviewers by a mainstream biomedical journal editor – this could be seen as a positive or a negative. There are pages listing reviewer details, but the reviews by a single reviewer are not listed.

Relatively few articles have received an insightful review or comment. Around 55% (201 articles) have received a review of some kind, and the most any article has received is six reviews (see right hand panel of the figure). 138 reviews were unsolicited and 211 were solicited by the authors. The quality of the reviews is usually low. Just over half of both solicited and unsolicited reviews contain critical analysis, i.e. at least some mention of improvements the authors could make to their article, meaning that probably less than 25% of all articles receive any degree of critical analysis. Many reviews are sycophantic, for example one case report is said to be "the best ever article publishe[sic] so far". Many merely state what the articles is about - one author-invited reviewer spends 358 words reiterating what the article says and telling us that it is a "must read" - or give the views of the reviewer on the subject rather than the article - another reviewer devotes a mere 23 words of a 430 word review to even mentioning the paper. Most reviews are very short: the average is only ~115 words for both author-suggested and unsolicited reviewers; the longest is just over 1500 words (see left hand panel of the figure for the length distribution). Comments with critical analysis are much longer (~175 words) than those without (~50 words). If I were to see reviews like most of those on WebmedCentral during standard peer review, I would never use that reviewer again.

Some of the reviews include comments such as "this is suitable for publication" or "I hope it is accepted", which indicate a lack of awareness of the publishing model.
One author has even reviewed his own paper. An article I consider unpublishable received the reviews, and I quote them in full, "good" and "No comment".

There are some examples where robust review has taken place. The concerns raised by the reviewers on this paper, including a lack of mention of ethics or consent, would lead most editors to reject such a paper – but WebmedCentral has no routine mechanism for doing this. Authors responded to reviews only on a handful of papers. A lively debate developed around a physician's self-case report, but this was a rare exception. I found one example of what appears to be functional peer review, with the authors revising their work and the reviewer stating that they are happy with the revisions.

In Bambi, Thumper's parents taught him that "If you can't say something nice... don't say nothing at all", but I think that the opposite applies in peer review. If you can't come up with critical comments about a paper, you're probably missing something: every paper has something wrong with it. The sycophantic nature of many of the reviews in WebmedCentral might be inherent to open (named) peer review, but in my experience and according to published studies, open peer review increases the length of reviews and makes them more polite, but has no effect on review quality. Another factor may be that many of the authors and reviewers of WebmedCentral are from India: R. A. Mashelkar argued in Science that "India must free itself from a traditional attitude that condemns irreverence", and Nikhil Kumar and Shirish Ranade argued in Current Science that "it is a preponderance of obsequious reverence and sycophancy that has placed the science in the country on a downhill slope." Are we seeing this unwillingness to criticise in action?

Overall assessment:
This is an interesting experiment in post-publication peer review, which both indicates the possibilities – instant publication, open community review – and the perils – unsound science, unbalanced opinion, and substandard writing being presented as part of the scientific literature.

Building a functioning publishing platform from scratch is no easy matter, and several hundred publications in seven months is an impressive figure. There has been a noticeable engagement from the community, with over 365 submissions and a total of nearly 350 reviews in seven months, 40% of them by reviewers not suggested by the authors. However, the submission rate is declining and the coverage and quality of reviews is not nearly high enough to functionally replace pre-publication review.

The onus is on the authors to obtain reviews: the journal states that it will obtain reviews, but this is not in evidence - just under half of the papers have no reviews, and 30% have only one review. More effort needs to be put into gaining reviews from qualified experts.

Reviews are essentially worthless if nobody pays any attention to them, be that an editor, the authors or the readers. Pre-publication peer review is not merely a filter, but it also acts to improve articles. On WebmedCentral there is no pressure for articles to be revised in accordance with any critical reviews, perhaps other than author embarrassment. As reviewers see a lack of response to their comments, they may lose enthusiasm.

Without a clear indication that reviewers have criticised an article and no indication that the articles are not peer reviewed, readers may view the work uncritically. If reviewers state for instance that the work is not sound, this should be clearly flagged up to readers near the top of the page, and articles should be sortable based on the answers given in the review from and the rating given by reviewers and readers. Another layer should be added, allowing articles to be promoted by agreement from their 'Scholarly Reviewers' to a "publication standard" level, giving authors an incentive to revise their work. "Featured articles" do exist, but the criteria used are not revealed. WebmedCentral are forming an "Advisory Board" of "eminent scientists"; perhaps this board will increase the rigour of the site.

Without the oversight of an editor choosing diverse reviewers and because most scientists are unaware of the site, it may become a closed community of the same authors positively reviewing each others' work – the precise opposite of the aim of the journal. Unless the process is reformed, WebmedCentral is likely to remain a "Cargo Cult science" journal, which in the main publishes articles that only superficially resemble the peer-reviewed literature, and that are reviewed in a manner that is only a pale imitation of pre-publication peer review.

Other commentary on WebmedCentral:
WebmedCentral and ginger pee on Pleion, a discussion on Ramy Aziz's FriendFeed, a blog review, a response to receiving an email from them, a brief welcome, a mention by Jenny Rohn in a Guardian comment thread, a comment by an author, an assessment in a sports science magazine, a mention in Lab Times, a critical appraisal of an article by PJ of Pyjamas in Bananas, a blog reaction in French, and a few Twitter comments.
But who runs this site?
"We are a group of medical and management professionals with no affiliation to any major biomedical publishing group" is all they say, but who runs the site shall be revealed in my next post: "Who are WebmedCentral?".

4 Oct 2010

Editing Wikipedia - for scientists

Wikipedia is now one of the most visited websites, and is probably the biggest source of fully free information. Wikipedia and Wikimedia in general fits well in the "open movement" alongside open source, open access, and open data. Many people, including scientists, find Wikipedia to be invaluable and read it on a daily basis, and some have even used it as a source, but you may find that the coverage is wrong or scanty. You can shrug and move on, or you can fix it yourself - and leave it better for the next reader.

If you're not contributing to Wikipedia already, as a scientist you're very well placed to do so as two of the main rules should be second nature - citing your sources and presenting the work of others neutrally. I could go into much more detail, but Darren Logan and his Cambridge colleagues have already written a brilliant guide in PLoS Computational Biology that is recommended reading for those who are as yet unfamiliar with the ins-and-outs of becoming a Wikipedian.

Joining PLoS ONE

I'm excited to say I've just started as an Associate Editor with PLoS ONE at the Public Library of Science, after freelancing with them since the beginning of the year.

It's interesting timing in the wake of a surge in submissions post-Impact Factor and the recent brickbats hurled at the journal by PZ Myers and David Gorski, but I'm looking forward to helping the journal go from strength to strength.

17 Sep 2010

Open access: the saviour for Chinese journals?

Discussing the announcement that the Chinese government is going to crack down on poor quality journals, a Nature editorial puts forward the welcome view that moving towards open access might be the best approach for Chinese publishers:

"The best opportunity to revive Chinese publishing, whether in Chinese or English, probably lies in an open-access platform — increasingly popular in Western journals. Many Chinese journals already charge authors a publication fee, so should be able to make a smooth transition to the open-access model, in which they are supported by fees rather than by subscription revenues."

5 Sep 2010

What is the scientific paper? 4: Access

This is a guest post by Joe Dunckley
Completing the series exploring the question "what is the scientific paper?", reposted from my old blog, and originally written following Science Online 2009. As I reminded people at the time, these were just my own half-thought through ideas, not the policy or manifesto of anyone or anything I'm affiliated with.
A friend of mine once told me how much she hated "the proliferation of these bioinformatics papers." All these simulations and models of what happens in real life. All of it utterly useless -- since when was the stuff that comes out of a computer worth anything? None of it even remotely reflects anything that happens in real life. And the methodology papers -- the endless methodology papers. They're making yet another neural network and modifying a bayesian something-or-other, when they haven't even found where they left the markov models yet! How can you have so many of these methodology papers? Clearly they can be no more than incremental advances. (Of course, BLAST is an exception -- it's old enough to have been around and heard of when we were undergrads, and is therefore a perfectly legitimate and mainstream molecular biology tool.)
Similarly, some people still voice their skepticism about the need for open access. Access isn't really a problem, is it? These open access advocates are just making facile arguments about the how the people who pay for scientific research should have some kind of say regarding its dissemination.[1] Come on, really, show me, who is in want of access? Everyone (everyone who matters) already has subscriptions, right? Access isn't a problem. And the open access "movement" isn't an ideology. It's just another business model.
And then, yesterday afternoon m'colleague shouted for advice handling an author of a scientific manuscript who was questioning the need to deposit her not inextensive collection of genomes in a database. I don't blame the author for wanting to get out of the chore—she had a lot of data, and depositing it will be a dull repetitive task. M'colleage was trying to write a letter and struggling to put into words the reason why we mandate deposition of sequence data, and why merely including them as supplementary MS Word files isn't good enough.
These attitudes, you will have noticed, have one particular thing in common: they all completely miss the fact that the biomedical sciences have moved on in the past quarter century. In almost every field (lets not wake the poor taxonomists) the science being done and the science being published today are not quite like that of 25 years ago. Even if the science of today were like that of 25 years ago the case for open data sharing would be strong enough; as it is, it's simply absurd to think that open sharing of data isn't worth doing.
Individual scientific papers -- the basic units of scientific research -- are rarely exciting; rarely even interesting. Where nerds get excited about science, it's where science offers a beautiful explanation for how the world works. And scientific papers don't do that. They offer some speculative interpretations of data on obscure problems in obscure systems. It is the literature as a whole -- hundreds of dull papers put together -- which tells a complete and exciting story. The sum is more than the parts -- the theory is more than the data.
In the field I know best -- cancer cell biology -- 99 in 100 papers published are tedious details, discovered with a science-by-numbers formula. The (anti-)proliferative effect of one abbreviation interacting with another abbreviation in three-letter-acronym-and-a-number cells, concluding with a suggestion that the authors' work might have implications for cancer treatment and a note that further work is necessary. Or even better, the complete lack of anything interesting at all happening when the first abbreviation interacts with the second. The abbreviations and their effects have been studied, in combination with others, in all of the most widely used three-letter-acronym-and-a-number cell-types, and somebody is scraping the barrel.
But the tedious details put together add up to an understanding of how the cell works and how it goes wrong. The details could be put together by a human, going through the thousands of papers on the topic, assembling the facts and finding the trends. Or, more plausibly, given the amount of tedious details out there, they could be assembled by a computer, with a database and a clever algorithm. Except that four in every five of those tedious details, discovered at great expense to taxpayers, will be inaccessible to that clever algorithm. They will be locked away in the basements of university libraries, hidden in human-readable prose that humans will never read. The results of billions of pounds of work searching for an understanding of cancer and a better chance at defeating it will be worthless, because they will never be amongst the parts that add up to the greater whole.
So I told m'colleague to explain to her author that unless she deposits her genome sequences, the last three years of her professional life will ultimately have been wasted. An average paper in a high-volume mid-tier journal that will be glanced at by a few colleagues when published. Another bullet point on a CV. They will never further science beyond that. They won't contribute any important discovery or real advance to the field. They will be forgotten. Nobody will seek them out when the time comes to make the leap forward.
That's just where biology is at these days: lots of tiny fragments of data, spread thin through the literature. The most interesting and important unanswered questions will require the synthesis of that work. The most interesting and important questions can't be answered without the heap of data that has already been produced, but which is locked away.
On machine readable data, Mike Ellis says, "at some point in the future, you'll want to do "something else" with your content. Right now you have no idea whatsoever what that something else might be." This is especially true in science: at some point in the future, tedious data obtained at great expensive, as part of the bigger picture, will finally be important and valuable. Right now, you can have no idea how important.
Publishers are allowed to get away with keeping science closed, holding it back, and wasting public money because there are still sufficient numbers of scientists who let them -- who have themselves failed to grasp that the world and science have changed.

2 Sep 2010

What is the scientific paper? 3: The metric

This is a guest post by Joe Dunckley
Continuing the series exploring the question "what is the scientific paper?", reposted from my old blog, and originally written following Science Online 2009. The topic of this post was originally discussed on FriendFeed, here.
On my recent post, what is wrong with the scientific paper?, Steve Hitchcock said that the most important problem with the paper is access, and that when we solve the problem with access, everything else will follow. I agree that access is hugely important, I recognise that we haven't won everyone over yet, and I know we do have to continue working away at the access problem, so I will devote a future post to reviewing that topic. But having thought about it a little longer, I am more convinced than ever that it is not access that is the big problem which is holding back the paper and journal, and open access is not the solution from which all others follow and fall into place.
There is one big problem, a single great big problem from which all others follow. The great ultimate cause is not, as I said last week, the journal. It is more basic than that. It is the impact factor. The journal is the problem with disseminating science, but the reason it has become the problem, the reason people let the problem continue is the impact factor. The impact factor is a greater problem than the access problem, because the former stands in the way of solving the latter. The impact factor is a great big competition killer; by far the greatest barrier to innovation and development in the dissemination of science.
Scientists can look at all of the problems with disseminating science, and they can look at us proposing all of these creative and extravagant solutions. They might agree entirely with our assessment of the state of the scientific paper and of the journal, and they can get as excited as us at the possibilities the flow from new technologies. But blogs and wikis are mere hobbies, to be abandoned when real work starts piling up; databases a dull chore, hoops to jump through when preparing a paper. So long as academics can get credit for little else besides publishing in a journal — a journal with an impact factor — any solution to publishing science outside of the journal will never be anything more than a gimmick, a hobby that takes precious time away from career development.
In a worse position than blogs and wikis, where cheap easy products are openly available, are the wonderful but complicated ideas that would benefit from financial backing to implement — the databases, and open lab notebooks, and the like — but which are currently artificially rendered unviable because no scientist could ever afford to waste time and money on a product that isn't a journal with an impact factor. No scientist can try something new; no business can offer anything new. Even such an obviously good idea and such a tame and simple advance as open access to the scientific paper has taken over a decade to get as far as it has in part because it takes so long for start-up publishers with a novel business model to develop a portfolio of new journals with attractive impact factors.
I am not a research scientist. I don't have to play the publish-or-perish game. So I have no personal grudge; no career destroyed or grant lost by rejection from a top-tier journal. It doesn't bother me how much agony, absurdity, and arbitrary hoop-jumping research scientists have to go through in their assessments and applications. But it bothers me greatly that, by putting such weight on the publication record — not actual quantity and quality of science done, but a specific proprietary measure of the average impact of the journals (and journals alone) that it's published in — public institutions across the world are distorting markets, propping up big established publishers, and destroying innovation in the dissemination of science. End the malignant metric and everything else will follow.

30 Aug 2010

What is the scientific paper? 2: What's wrong?

This is a guest post by Joe Dunckley
Once again, this is a re-post of something I wrote on my old blog a year ago after the Science Online conference, looking at the future of the scientific paper. As I reminded people at the time, these were just my own half-thought through ideas, not the policy or manifesto of anyone or anything I'm affiliated with.
So in response to the Science Online conference, we've been thinking about the question, "what is the scientific paper?" I already gave my answer to that a couple of weeks ago, but promised to have a go at answering the more interesting question, "what is wrong with the scientific paper?"
I've been thinking through how to sum up the answer all week, and I'm afraid the simple answer is, "the journal". The journal is what's wrong with the scientific paper. Or rather, the journal is what is holding back the development of efficient modern methods of disseminating science. So I thought I'd spend this second post making some observations on what the scientific journal traditionally is and does; what I think the modern journal shouldn't be doing; and a couple of case studies of alternative technologies that disseminate certain kinds of scientific communications better than a journal ever could.

What is the (traditional) scientific journal?
  • The journal is a collection of scientific papers limited to some kind of theme coherent enough to make it worth reading buying.
  • The journal is led by a charismatic editor-in-chief and editorial board who attract people to publish in the journal.
  • The journal is printed on pages. It can do text, still pictures, graphs, and small tables.
  • The journal publishes a sufficiently large number of papers to make it worth printing several issues each year, but a sufficiently small number of papers to make each issue manageable.
  • The purpose of the journal is to be read and cited by other scientists.
  • The purpose of the journal is to be purchased by university libraries.
  • The journal provides a peer-review, copy-editing, marketing and media relations service to their scientists.
  • Publishing in a journal provides a way for scientists to be cited and credited for their work, based on the reputation of that journal.
  • The journal decentralises scientific publishing, allowing individual pockets of innovation within the publishing world, but making change overall very slow.
What should the modern journal (not) be doing?
It is perhaps rather foolish for somebody who works for a publisher of journals -- who works developing technologies for a publisher of journals -- to say that the problem with publishing science is the journal. It would be even more foolish for me to say that publishers perhaps shouldn't be trying to fix the problem with technology. Here are a couple of interesting technological advances that the more forward thinking journals have come up with lately.
  • At Sci Online, Theo Bloom demonstrated iSee, a structural biology visualisation applet for your "supplementary information". In the same category is J. Cell Biol's DataViewer, which is presented to us as a device for visualising raw microscopy data. Did you know that the results that come out of modern microscopes are not just pretty static pictures, but vast datasets full of hidden information? The JCB DataViewer unlocks that hidden information, by providing it and an interface to it as "supplementary information" with a paper.
  • PLoS Currents: all the constraints and benefits of a traditional journal, but without the peer-review. Solves the problem of delays in publication. Publishes items that look just like the traditional paper.
Should publishers and journals be doing these things? When you look more closely at JCB's DataViewer, you find that, useful though it may be, most of its power and potential is currently wasted. The DataViewer is presented to us as a device for visualising the supplementary information of a paper; in fact, it is a potentially important database of microscopy datasets with a handy graphical interface attached. Restricted to a single journal, the database functionality lays unused.
PLoS Currents? This is supposed to be a solution to the problem of delays in publishing special types of science deemed to be important and timely enough to need rapid communication to peers in the field. What have PLoS done? What makes PLoS Currents unique? How does it speed up intra-field communication of those important results? It drops one single aspect of the paper: peer review. In all other respects, PLoS Currents does all it can to make its papers look like the scientific paper, and its "journal" look like the scientific journal. Scientists are still asked to spend hours writing up these important timely results, with an abstract, introduction, methods, results, conclusions and references, with select figures and graphs and tables. Nobody has the imagination to go beyond the paper-journal-publisher model. We would sooner give up peer review than publish science in anything that doesn't look like papers have looked for a century.
Or how about Journal of Visualised Experiments? JOVE is, for some inexplicable reason, held up as a brilliant example of innovation in publishing science -- of making the most of the new technology provided by the web. Those who point out that, well, it's not really a "journal", is it?, are chastised for their own lack of imagination. But surely it's those who can't conceive of a publishing format branded as anything other than the "Journal of ..." who are lacking the imagination.
Final example: while thinking about this post, PLoS Computational Biology kindly came up with the absurd idea of being a software repository. NO! Software repositories already make perfectly good software repositories, and there are plenty of them. Trying to turn a journal into a software repository is a suboptimal solution to a problem that disappeared long ago -- long before scientific publishers could have imagined that the problem even existed.
Breaking out of the journal
The web makes all sorts of new methods of publishing, communicating, disseminating science possible. It also comes with all sorts of well developed and widely used solutions to the problems of disseminating science. The big old publishers haven't even realised the web has happened, let alone thought about what to do with it. The hip young publishers know what's possible, and they want to be the ones to realise the possibilities. Good on the hip young publishers. But with each new possibility, scientists should be asking whether publishers, even the hip young ones, are really right for the job. Sometimes they are. Sometimes not.
GenBank, the database of gene sequences and genome projects, had to happen. Journals simply can't publish the raw results from a whole genome sequencing project. (Thought I don't suppose they gave up without trying.) And GenBank comes with dozens of benefits that papers, when spread across a decentralised system of journals, just can't have. Yes, I know that databases aren't the optimal solution for every variety of data, but they are suitable -- desirable; even required -- for more of them than you might think. The microscopy data in JCB dataviewer (or the structural data in iSee) would, I suspect, be of much greater value were it branded as a standalone public database with a fancy front-end, than as a fancy visualisation applet for some scattered and hidden supplementary files, restricted to a single journal.
Like it or not, science increasingly depends on data being published in public machine readable formats. Those who spend their days looking one-at-a-time at the elements of a single cell signalling pathway in every tumour cell line available to them are wasting our money if they bury their data in a fragmented and closed publication record. Nobody reads those papers, and the individual fragments of data don't tell us anything. Journal publishers think they can ensure that data is correctly published, but so far their only great successes are with the likes of GenBank and MIAME, where journals have ensured that data be deposited in public databases outside of the journal format.
ArXiV. Does this need any explanation? What does PLoS Currents offer that isn't already solved better by pre-print servers? Just a brand name that makes it look as though it's a journal. If you require rapid dissemination of important timely results and you want to go to the effort of writing a full traditional scientific paper, put it on a pre-print server while it's going through peer review in a real journal. Don't just abandon peer review while making it look like you've just published a real paper in a real journal.
Better yet, don't write a proper traditional paper. If you need rapid communication of important timely results, why waste time with all of the irrelevant trimmings of a scientific paper? The in-depth background and discussion and that list of a hundred references. Put these critical results on a blog with a few lines of explanation, and later submit the full paper for peer review in a real journal.
Credit where it's due
All the real scientists reading -- the ones looking for jobs and grants and promotion and tenure -- have spotted the one great big flaw in all these suggestions: credit. At least a paper in PLoS Currents can be listed in a CV. Nobody even reads blogs, let alone cites them. How can you get a grant on the back of a blog post? Am I suggesting you should be able to get a grant on the back of a blog post?
Maybe. I don't know. I don't think so. At the moment, publishing papers in journals is pretty much all a researcher can get any credit for. Asking researchers to go beyond the paper-in-journal format is going to create problems of assigning credit, and I don't know exactly what the solution to that problem might be. Simply, I haven't put much effort into considering solutions. I'm a consumer rather than creator of science, so that particular problem doesn't keep me awake at night. But there surely are solutions -- plenty of them.
Fact is, it's quite obvious to anyone in or observing science that the current method of ensuring that scientists are credited for their hard work is really quite broken. Trying to cram every new kind of "stuff" into that broken system is hardly helping.
Business models
Meanwhile, the publishers will be asking how we see the business models for these non-journal based methods of publishing working. Frankly, I'm not really interested. But then, JOVE is hardly the beacon of business success anyway. If publishers want science publishing to be a business, they need to find the new business models that work without strangling science. Otherwise, they're liable to find out that, on the web, some institutions and individual scientists can do a better job of disseminating science than the professionals can, and out of their own pocket.
The paper of the future
I don't necessarily think that anybody should stop writing papers -- perhaps not even the ones that nobody reads. The paper solves several problems better than any other proposed solution. A peer reviewed scientific paper, in a journal if you like, is as good a way as any to provide a permanent record of a unit of science done, and of a research group's interpretation of the significance of that unit of science. And it needn't change all that much. Making them shorter and a lot less waffley would be to my taste -- there's no need to put that much effort into words that won't be read. And give them semantic markup, animations, and comment threads, if you like. But don't pretend that those things are anything more than incremental advances. The real revolutions in the dissemination of science can only occur beyond the shackles of the traditional paper and journal. Every new Journal of Stuff is another step back.
Updates for 2010
Peter Murray Rust has been saying interesting things about domain-specific data repositories, which I am sure are worth paying more attention to than I have yet had time to.
When I originally posted this, I was challenged for not mentioning the problem of closed-access journals at all; that problem is addressed in the subsequent posts.

17 Aug 2010

What is the scientific paper? 1: Observations

This is a guest post by Joe Dunckley
Last year, after Science Online, I wrote a series of posts inspired by Ian Mulvany's question, what is the scientific paper? Those were originally posted on my old blog; now, with SoLo approaching once again, seems like a good time to revisit them, while migrating them over to Journalology.
Science Online charged us with answering the question, what is the scientific paper? Here is the answer. It comes from the perspective of somebody who has been middle author on just two, but who has spent a little bit of time working with them and with people who think a lot about them.
What does the scientific paper look like?

  • It's a few thousand words -- probably between 4 and 15 pages long (but can be <1 >100 pages).
  • It's mostly prose text, with a little bit of graphs, tables, and pictures.
  • It has a set matter-of-fact style and structure.
  • It's written in (American) English.1
What is in the scientific paper?
  • Who did the science.
  • Why the science was done.
  • How the science was done.
  • Data!
  • The authors' interpretation of what was achieved by doing the science.
  • Pointers to the other bits of science mentioned.
Where is the scientific paper?
  • It is in a journal, available in one or both of:
    • printed on 4-15 sheets of dead trees, between a pair of glossy (or not so glossy) covers in the basement of a library.
    • a journal website, possibly with technology deliberately designed to make it difficult and expensive to get to, probably only available in a clunky and poorly designed PDF file.
  • It might also be in-part or in-full in a searchable database, like PubMed.
  • If you're really lucky, it is available as HTML and XML.
What is the scientific paper for?
  • It aims to be a complete, objective, reliable, and permanent record of a unit of science done.
  • It's a way of telling your field what you've done.
  • It's a way of telling your field what you've found.
  • It's a way of giving data and resources to your field.
  • It's a (the?) way of proving to your (potential) employer/funder that you have done something worthwhile.
  • It's a way of making money for publishers
How is the scientific paper made?
  • The authors are given some money and lab space on the condition that they use it to do some science and write a paper about it.2
  • The authors do some science and write a paper about it.
  • They give it to a journal. The journal thinks about it.
  • Peer review! Months of scrutiny, discussion, and revisions.
  • Production! The words are turned into PDFs and printed pages.
What is the scientific paper not?
  • Part of a conversation.
  • Quick and efficient.
  • Diverse and flexible.
  • Possible to edit after acceptance by the journal (except in extreme circumstances, and via slow and unsatisfactory mechanisms).
  • Possible to edit by anybody except "the authors".
  • A way of making your data and resources reusable.
  • A way of telling the layperson what you've done and found.
Wait, that wasn't really what the question meant, you say? Well, indeed. But before we get to the real questions -- "what's wrong with the scientific paper?" and "what do you suppose we do about that?" -- it's good to define some terms and lay out the basics. Do you think I've got any of my observations wrong, or think I've overlooked some important property of the scientific paper? Do say -- it would be good to try to agree on what the paper is before going any further.
  1. Thanks to Hannah who added this point in the comments on the old blog
  2. Thanks to Cameron Neylon, ditto

Incentivising academic fraud

This is a guest post by Joe Dunckley
Catching up with the newsfeeds after a week working in Beijing (where citizens are saved from reading such subversive content as Journalology -- as they are all Blogspot blogs), I notice the Economist discussing academic fraud in China.

Being the Economist, it attempts to explain China's fraud epidemic focus on incentives:

China may be susceptible, suggests Dr Cong Cao, a specialist on the sociology of science in China at the State University of New York, because academics expect to advance according to the number, not the quality, of their published works. Thus reward can come without academic rigour. Nor do senior scientists, who are rarely punished for fraud, set a decent example to their juniors.
The trouble with this explanation is that these same incentives apply in many -- most -- other countries also. Science everywhere is plagued by the publish-or-perish game and the incentives it generates. Academic careers stand and fall on the basis of publication counts. Some countries at least try to judge quality of output in addition to quantity, but most methods are no more sophisticated than that used by China -- and every method has its incentives for fraud.

Nor does a lack of disincentives in China explain why they stand out. Fraud is rarely satisfactorily punished anywhere. If it is even discovered at all, the photoshopped figures and made-up numbers become an accident; the original data was lost sometime after that project was completed; the grad student who handled that particular experiment has moved on, and can no longer be contacted. A researcher getting fired for fraud is big news, not because fraud is rare, but because failing to weasel out of an allegation is rare.

It is my fear that China is perceived as having a higher rate of fraud compared to other countries not because it does, but because Chinese researchers aren't very good at it yet. Their fiddled figures are crude and easily spotted; their fictitious facts are amateur inventions that can not be believed. The worrying thing about these rough and unrefined fabrications is not that they themselves, easily found out and struck from the record, exist. The worrying fact is that they must be the tip of a great iceberg; 99% of the fakes are unseen, produced by forgers skilled enough to mask their work in convincing disguises and cover their tracks perfectly. As science in China matures, and the student to supervisor ratio falls and natural selection picks the cleverest conmen, the epidemic of clumsy and primitive fraud will end. That's when China joins the ranks of countries experiencing advanced and undetectable fraud epidemics.

Discussing fraud as a symptom of a Chinese problem -- of a failure of Chinese academic administration or a flaw in the Chinese culture and psyche -- is a nice distraction from the uncomfortable fact that fraud is a symptom of a global problem -- of failing academic administration everywhere. The Chinese copied the publish-or-perish game from the west. Soon they'll get good at it.

10 Aug 2010

New word - evoluating

"Evoluating". It's probably an attempt to use the French "évoluer" in English, I think it means "evolving".

6 Aug 2010

The Scientist has an attack of CNS disease

The Scientist this week tells us that
"Peer review isn’t perfect [who knew?]— meet 5 high-impact papers that should have ended up in bigger journals."
Wait, what? These high-impact papers got those citations despite ending up in "second tier" journals, so I doubt the authors have been crying into their beer about this "injustice". This is an example of CNS Disease, a term coined by Harold Varmus to characterise the obsession with Cell, Nature and Science. Not all high-impact papers must published in one of these journals, and not all papers published in these journals will be high impact. Biomedical publishing is not just a game in which editors sort articles by predicted future impact - at least, I hope it's not.

Authors chose their publication venue for all sorts of reasons, and it's hard to predict which new work will set the world on fire. Take BLAST - it was a "quick and dirty" algorithm that gave similar results to the Smith and Waterman algorithm only much faster, and the gain in speed came at a loss of accuracy. Only use by scientists in practice could decide whether this was a good approach. Focussing on the umpteen thousand citations to BLAST is missing the point: the important thing about BLAST is the millions or billions of hours of computer time saved by using it. As Joe, the other denizen of Journalology Towers, said recently:
"Lord protect us from the idea that an academic publication might have any value beyond its ability to accumulate citations."