26 Feb 2007

Controversial doctor meets controversial journal

Although we in the UK are familiar with the claims of Andrew Wakefield that the MMR vaccine is a cause of autism, we are less familiar with the claims from over the pond that mercury in vaccines is the cause of autism. Perhaps this lack of awareness is why Lancet Neurology has allowed Mark Geier, a highly controversial American doctor and anti-vaccines activist, to review a book on autism, but I doubt it.

Ben Goldacre has already done a fantastic job in explaining why Dr Geier may not be an ideal candidate to provide content for a respectable medical journal, and much more can be found on the Neurodiversity blog. From reading some of Dr Geier's work I know that I have doubts that it is sound, and the issues surrounding the ethical approval for his studies, his expert witness appearances and his patent applications certainly warrant close inspection.

It's not as though the Lancet journals are naive to this issue. The Lancet published Andrew Wakefield's original case series that brought about the MMR controversy and they had heard from Mark Geier before, when he wrote to criticise another researcher for their conflicts of interest (a case of pots and kettles). I know that the
Lancet journals delight in controversy, but I'd expect more sense than this from the editors.

24 Feb 2007

Publisher and journal nicknames

A previous handling editor of BMC Ear, Nose and Throat Disorders affectionately (?) referred to the journal as BMC Wax, Snot and Phlegm, and rumour has it that our independent journal Cough was almost called Cough and Phlegm. A blog going by the name wax, boogers, and phlegm actually exists.

The Public Library of Science (PLoS) is known by editors at the Lancet as SLoP, and I'm sure that the nicknames Evil Empire and Elseviley need no introduction. In the Pipeline lists the colloquial ways of referring to several journals in the field of organic chemistry, including the Journal of the American Chemical Society, known as "Jacks".

If anyone knows of more pejorative or affectionate names for publishers or journals, I'd be interested in hearing them.

A play with an anagram tool reveals that BioMed Central becomes melodic banter, metabolic nerd, atomic blender, dental microbe, clambered into, and mint or debacle.

15 Feb 2007

Declaration of Pomposity, and a Declaration of War?

Ahead of the EC Conference on Scientific Publishing in the European Research Area, a group of publishers have released what they dub the 'Brussels Declaration', which shamelessly echoes the Berlin Declaration on Open Access, the Budapest Open Access Initiative and the Bethseda Statement on Open Access Publishing. Richard Charkin, who works for Macmillan, has irreverently nicknamed it the Bognor Declaration, which will hopefully take some of the wind out of their sails.

They have stated that "we have decided to publish a declaration of principles which we believe to be self-evident". Oh, for pity's sake! Using language that apes the US Declaration of Independence makes them sound very pompous. Is it really 'self-evident' that "Copyright protects the investment of both authors and publishers"? Insisting on transfer of copyright to the publisher certainly helps maintain publisher profits, but how does that help the authors? The statement that "authors should be free to choose where they publish in a healthy, undistorted free market" is plainly a dig at PLoS (who have received philanthropic funding), but since when was journal publishing an 'undistorted free market'? The many mergers over the years have led towards the creation of monopolies.

The real target of this declaration is self-archiving. Stevan Harnad, the "archivangelist", optimistically commented on the IWR Blog that "There will be no war in Brussels. The meeting is about online access to European research findings. The European research community is meeting to decide how to maximise access, usage and impact for its research findings. The answer -- the very same answer -- has already been proposed by the European Commission [...] As a condition for receiving public research funding, all funded researchers should self-archive the resulting research publications online in an Open Access Repository, free for all would-be users".

In other news, Prime Minister Neville Chamberlain has declared that there will be "peace for our time". Um, perhaps not. The ninth "principle" in this declaration is that "Open deposit of accepted manuscripts [self-archiving] risks destabilising subscription revenues and undermining peer review [...] Free availability of significant proportions of a journal’s content may result in its cancellation and therefore destroy the peer review system upon which researchers and society depend". I sense that hostilities have started... Perhaps soon the publisher tanks will be parked on the University of Southampton's driveway?

Overall this declaration makes these publishers look self-satisfied and a bit silly. I'd have expected better from the BMJ Group, who are one of the signatories.

13 Feb 2007

We didn't pay him, honestly

The Filter, "Your regular dose of public-interest Internet news and commentary from the Berkman Center for Internet & Society at Harvard Law School", carries a piece from David Weinberger that so gushes about BioMed Central that I would have been embarrassed to write it myself. I'm not too embarrassed to link to it though.

11 Feb 2007

Bad Science debates open access

There's a fascinating article and subsequent debate about open access on Ben Goldacre's Bad Science website.

8 Feb 2007

CNS disease, or [ney-cher-sahy-uhns-uhnd-sel]

I've read some comments to the effect that PLoS ONE is a new competitor to Nature. You know who you are. The confusion appears to be wrought by the fact that PLoS ONE is a general science journal, but in reality it is poles apart from Nature, Science or Cell. If Nature is aiming to be at the tip of the publications pyramid, PLoS ONE is the broad base, much as the BMC series is also part of the broad base. And that's a Good Thing.

Harold Varmus has complained about ‘CNS disease’, the tendency to regard publication in these journals too highly. These three journals are mentioned in one breath so often that perhaps a new word could be coined: naturescienceandcell [ney-cher-sahy-uhns-uhnd-sel] -noun: 1. General science journals that cause researchers to temporarily lose their sanity.

Jan Velterop
estimates that 1 million scholarly articles are published each year, and I read somewhere this week that there were around 680,000 abstracts added to PubMed in 2005, so that estimate looks reasonable. A quick look at PubMed tells me that the hallowed trio of Nature, Science and Cell between them published in the ballpark of 3,000 research articles that year. As only around 0.5% of publications appear in these journals, the attention paid to them is a little bit unwarranted. I'd wager that at least some of the other 99.5% of articles have some merit.

In a similar vein, Doug Altman has pointed out that although randomized controlled trials in general medical journals get such attention paid to them, 93% of trials are not published in general medical journals and 90% of medical publications are not trials. The focus on these "big headline" RCTs that make up 0.7% of the medical literature appears to be due to reprints being bought by pharmaceutical companies -- the Vioxx article by Merck brought in $700,000 to the NEJM -- and due to what Ben Goldacre calls
Humanities Graduates In The Media hyping medical stories in the press.

It is worth remembering that although these journals have high impact factors, the impact factor doesn't determine the number of citations an article published in a journal will receive: the causation is the other way around. To their credit, Nature have been honest about the fact that their 2004 impact factor mainly (89% of it) derived from 25% of their articles, including the mouse genome paper that has been cited over 1,000 times. Not all articles published in Nature receive that kind of response, yet people still refer to Nature publications in awed tones. Some people might "read" Nature each week, but, seriously, does anyone actually read the research articles if they're not in the field?

Science depends
more on a slow and steady accumulation of knowledge than upon "breakthrough" papers. Geoff Watts has argued in the BMJ that we should "pension off the major breakthrough". I'd echo this, and I'd agree with Harold Varmus: we need a cure for CNS disease.

The full text is available for purchase

This article is about barriers to access to knowledge in Sub-Saharan Africa. The article costs $25 plus tax to read. Richard Smith pointed out the irony of this in a talk at our OA Colloquium.

6 Feb 2007

A loss for science?

"This is a great loss for science. It's a very sad day for science". These were the words spoken concerning the sentencing of someone convicted of molesting a then 9 year old child.

I'm afraid that I haven't followed the trial of W. French Anderson, but I find it unseemly that some scientists perceive that somehow his research achievements should mollify his crime. The sad day was not the sentencing, but rather a decade ago when that young girl first experienced something we should never wish upon anyone.

"The young woman said she was so distraught, she began to cut herself and contemplated suicide while she was in high school".

The Scientist chose to cover this story at all, let alone under the headline "Colleagues upset by Anderson sentence" is beyond me.

3 Feb 2007

Journal bundling

On the SPARC Open Access Forum, Sally Morris responded to criticism of journal bundling by arguing that "I know of no publishers (please correct me if I’m wrong) who only offer their journals as part of a ‘big deal’ bundle. Is anyone taking food manufacturers to task for not offering the same value in individual servings as in family packs?".

The family pack analogy is flawed. Imagine if you wanted to buy food and groceries (let's say bread and milk), but when you handed over your money to get what you wanted the shopkeeper insisted on you also paying for some nappies (when you didn't have a child) and some denture cream (when you still have all your teeth)... well, you'd go to another shop. No shop has a monopoly on bread and milk (at least not yet). The difference with journals is that if you want access to particular articles in one particular journal, you *can't* go to another journal to read them. That's why bundling is criticised as being anti-competitive.

Give the man a medal! Oh, they already did

Ben Goldacre is the doctor behind the Bad Science column and website, single-handedly fighting back the barbarian hordes of disingenuous nutritionists, media whores, and quackery in general. He does such a good job that if I believed in the honours system I'd campaign for him to be knighted. In lieu of that, a short note at the end of his latest column modestly tells the world that "Ben Goldacre won the Royal Statistical Society's inaugural award for statistical excellence in journalism last week". Nice one Ben. His winning article brilliantly points out the problems with media reporting of statistics, and you can read it here.

p.s. Ben will be speaking at BioMed Central's Open Access Colloquium next week on the topic of "Who benefits from OA publishing?".

1 Feb 2007

My favourite Firefox add-ons

You'll forgive me, I hope, if I digress for a moment. I've been a dedicated user of Firefox since it was announced in 2004, and I rarely look back even now that IE 7 has copied some of the best bits. After some cajoling, even the most luddite of our editors have made the shift.

One of the great things about Firefox is that anyone can write their own add-ons for Firefox. If you can think of something that you wish Firefox could do, the chances are that somebody will already have come up with the solution. At the risk of losing you, here are my favourite Firefox add-ons:

Search engines - almost any site you care to mention has one, and if it doesn't you can write one yourself (see my previous post). Matt Cockerill, our publisher, has written a few: two internal ones to search our manuscript and user databases, one to search our published articles, and one for Google Scholar.

Tab Mix Plus. Enhances your tabbed browsing. So useful that Firefox 2.0 included some of its best functions, but it is still great.

Context Search. Highlight text, right-click, chose any of your search plugins from a drop-down list, and a search is launched in a new tab for that text. Simple, but inspired.

SmartSearch. Much like Context Search, except that it uses Quick Searches instead of search plugins. The beauty of this is that Quick Searches are much quicker and easier to write that search plugins - simply get the URL of a search result, and replace the search term with %s.

Greasemonkey. I learned about Greasemonkey from Mark Wilkinson's iHOPerator article. This allow users to create and install scripts to adapt any website.

Digger, Go Up and Link Widgets. Want to go to the home page of the site, but can't see where to click? Here's your answer. These three add-ons allow easy navigation back up and around the directory structure of a website, at the click of a button.

Universal Print. Forget clicking Print for every tab you've got open - just use Universal Print to print all your open tabs at once!

Sage blog reader. "It's got a lot of what you need and not much of what you don't".

Adblock Plus. No more annoying adverts.

Flashblock. With this installed, Flash animations only appear if you click on them.

Cooliris Previews. This gives you the option to hover over a link, and see a pop-up window of what lies beyond. Move the mouse away, and the preview closes.

Download Statusbar. See and manage all your downloads at the bottom of the window - the annoying download window is no more!

Blogger Web Comments. Click a little speech bubble icon in the right-hand corner of the window, and up pops what the blogosphere thinks of the page you're looking at. You can even leave it open all the time showing the most recent comment or comments.

IE Tab. Opens a session of IE in a Firefox tab.

British English Dictionary. Useful for me most of the time, but our website content and Research Highlights are supposed to be in US English, which addles my poor little brain.

Littlefox theme. You can pack more onto the screen.

CuteMenus. It just makes your menus look better.