Chris Surridge's blog

Gambling on the press

Chris Surridge — Wed, 21 Nov 2007 02:37:09 -0800

After all the coverage lavished on Nigel the Nigersaurus last week we were a little worried that this week’s crop of papers in PLoS ONE would be unfairly overlooked. That would be a great shame as there are lots of good papers published this week. Two are particularly ‘media friendly’ but my colleague Rebecca and I disagreed on which would figure more prominently in the press, so we have a bet running on it.

Rebecca was convinced that The Golden Beauty: Brain Response to Classical and Renaissance Sculptures by Di Dio, Macaluso and Rizzolatti (PLoS ONE 2(11): e1201. doi:10.1371/journal.pone.0001201) was the more appealing to the press. It’s a neuro-art paper looking at the activation of brains by classical sculptures and how adjusting their anatomical proportions alters the beholder's opinion of which are beautiful.

I however thought that carnivorous plants would be more charismatic. A Viscoelastic Deadly Fluid in Carnivorous Pitcher Plants by Gaume and Forterre (PLoS ONE 2(11): e1185. doi:10.1371/journal.pone.0001185) investigates the secretions from the inside of the pitchers of Nepenthes rafflesiana and finds they have exactly the right properties to capture and render immobile any insects that come into contact with them. There are nice videos too.

So to settle this dispute - biophysics vs art if you will – we both took some time to help the respective authors write a killer press release and now we are sitting back watching Google News and Google Blog Search tally up the results. Currently I’m winning (11 news hits and 3 blog posts for pitcher plants; 2 news hits and 5 blog posts for Italian statues) so Rebecca is going to owe me 50 pence ('half a nicker' in old money).

Aside from celebrating my victory, the real point of this story is to point out the breadth of good and interesting science that is being published weekly by PLoS ONE and the other PLoS journals; freely available for everyone who hears about it on the news or in a blog to read at source.

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The Nigersaurus has landed.

Chris Surridge — Thu, 15 Nov 2007 08:23:06 -0800

PLoS ONE published a paper today. This might not sound very unusual but today is Thursday and PLoS ONE papers are usually published on a Wednesday (or to be precise late Tuesday in time for Wednesday). This paper however is a special case.

The paper in question is this one:
Sereno PC, Wilson JA, Witmer LM, Whitlock JA, Maga A, et al (2007) Structural Extremes in a Cretaceous Dinosaur. PLoS ONE 2(11): e1230. doi:10.1371/journal.pone.0001230

And shows a really nice fossil skull of a dinosaur that lived about 100 million years ago. The dinosaur had been known before but this new find shows the skull and particularly the teeth. It is the teeth that are particularly interesting; two straight rows making for a very wide flat mouth looking not unlike a pair of carpenters' pincers. With these the creature likely cropped the ferns around it, head down like some ‘Mesozoic Cow’.

Strictly speaking the publication date on this paper is November the 21st but we are using what is known as Early Online Release (EOR, pronounced ‘eeyore’ like the depressive donkey in Winnie-the-Pooh) to set it live today, 10:30 Eastern Standard time.

Why have we done this?

Simple. At 10:30 EST the fossil skull is being unveiled as the centrepiece of an exhibition at National Geographic Gallery in Washington DC. There is also a lot of information about the find at the website of Project Exploration, the Chicago-based science education organization.

This is superb example of the power of Open Access publishing. This fossil will be seen by hundreds and thousands of people in Washington and at the Sam Noble Oklahoma Museum of Natural History in Norman, Oklahoma which will be the exhibition's permanent home. Millions of people will read about the dinosaur in their newspapers throughout the World.

And because Paul Sereno and his colleagues chose to publish their work in a PLoS journal, every single one of those people will be able to read the detailed scientific description of their work first hand.

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Happy Birthday to Me

Chris Surridge — Thu, 20 Sep 2007 03:15:34 -0700

Today is my Birthday. I'm entering a prime of life, although I'm not going to tell you which one. I only mention this because PLoS ONE has given me an extra special gift. This day, my birthday as I may have mentioned, we accepted for publication our 1,000^th paper.

You will all have to wait a few more weeks to see my present but I can tell you that it is authored by one of the PLoS ONE Editorial Board and has the kind of highly rigorous mathematical analysis that particularly appeals to me.

Not sure how they arranged to accept the 1,000^th paper on my birthday (2:30 a.m. my time in fact) but for this, and everything, my unreserved thanks go out to the PLoS ONE team of Lindsay, Bonnie, Rebecca, Tessa (who made brownies) and Sharon; not forgetting Emma and Sarah who particularly care for clinical trials; the PLoS ONE Editorial Board for their tireless work; and everyone in PLoS.

Thanks guys, you're special.

Chris

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Nature knows no indecencies

Chris Surridge — Fri, 17 Aug 2007 04:33:49 -0700

There is a wonderful editorial in Nature this week which I have to share with you (it is closed access but there is an accessible copy here). Apparently Nature has been getting complaints about the fact that they continue to print verbatim their 1869 mission statement which talks about “scientific men”. Obviously this is causing female scientists to conclude that they can’t submit work to Nature and giving them a feeling of guilt if they read its content which is so clearly not meant for them.

The solution to the problem? Simple, add “[sic]” after the offending gender specific collective noun. “a Latin word meaning 'thus', after the phrase -- in effect expressing the sentiment 'alas, dear reader, this is what was said'" to quote the editorial. The mission statement printed in the journal now reads

"…Secondly, to aid scientific men[sic] themselves, by giving early information of all advances made….”

There is no question that sexism should have no place in science, and anyone doubting Nature’s credentials here could do a quick head count of their editorial staff, which contains at least as many women as men. So what has this actually achieved?

Suzanne Franks, over at Thus Spake Zuska, thinks this is a near pointless alteration, but it seems to me that Nature has uncovered a whole new function for [sic]. I had always thought it was a disclaimer when quoting text letting me indicate that I know there is an error in the text but that I am quoting verbatim. Basically [sic] says “I didn’t make a mistake, the error is in the original”. Now it seems we can use it to indicate that we disagree with the original wording and are sure that the author would too if they were around to ask.

This is going to be so useful. I can see it now. Jane Austen:

"It is a truth universally acknowledged, that a single man[sic] in possession of a good fortune, must be in want of a wife[sic]."

or Neil Armstrong

“That's one small step for man[sic]; one giant leap for mankind"

Best of all there is Mark Twain (as suggested by my colleague Rebecca):

"Nature knows no indecencies; man[sic] invents them”

Any more?

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Now we are ONE

Chris Surridge — Wed, 01 Aug 2007 03:57:48 -0700

A week can be a long time in politics; well, a year in scientific publishing can feel like an age. On 1st August last year, PLoS ONE opened its doors for submission and so we have decided to call today our official birthday. So what has the last year been like and how have things changed?

Well, back in August 2006 we were quite excited to have double figures of submissions in our first week. Last month we were averaging 60 submissions a week. Close to two thousand submissions in total.

A year ago we had a dedicated editorial board of 120 people. At the moment that number stands at 386. I cannot thank enough these people who are responsible for assessing all the papers that are submitted, managing their peer review and deciding whether or not they are ready for publication. If you are lucky, you may catch sight of one of them in the corridors of your institution sporting one of the new PLoS ONE first birthday t-shirts.

Most importantly of all though, in the last year, or, at least, in the months from December 2006, we have published 695 pieces of original research. All of that research is, of course, Open Access and all of that research can be annotated by users, discussed by users and for the last few weeks rated by users.

This potential for interaction is unprecedented in any other scientific publication and it is being used to an extremely high standard. If I had to choose a particularly good example of the post-publication culture of PLoS ONE, I would point to “On the Origin of the Functional Architecture of the Cortex” by Dario Ringach, although this paper has not been rated yet having been published back in February.

The initial success of PLoS ONE is something unprecedented in scientific publishing. It has been achieved because of the commitment and faith of hundreds of people: PLoS staff, editorial and advisory board members, reviewers, authors and particularly readers. And yet this is only a very small step towards an open, interactive and efficient literature that will accelerate scientific progress. Over the coming months, we will take further steps with additional functionality on the site, new publishing ventures launching and established ones taking more advantage of the opportunities afforded by the TOPAZ platform on which PLoS ONE is presented.

So, if it is a birthday, what about presents?

Well, PLoS ONE would like three things none of which are particularly expensive and which all of the readers of this blog can give us: three resolutions.

Whenever you write about a published paper, be it in a journal or on a blog, always provide a link to the freely available version of the paper if one exists.

Whenever you read a paper in PLoS ONE, always rate it before leaving.

And most importantly....

Whenever you write a scientific paper, always, always, always publish it Open Access.

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Rate Early, Rate Often

Chris Surridge — Tue, 10 Jul 2007 06:52:49 -0700

I’ve been waiting to write this Blog posting for a while and now I can. As from today PLoS ONE has a user rating system for its articles. All users can now rate articles in three subjective categories: Insight, Reliability and Style. We have made the tool, now we need you to come and use it.

User rating is a very common feature of websites these days, be it for movies, books, blog posts, pretty much anything. What user rating allows is a quick and easy survey of a communities opinion. Despite the obvious advantages to hard pressed scientists trying to get to grips with a vast literature this simple system hasn’t been much applied to scientific papers up to this point.

The major exception to this is probably Faculty of 1000, which has been providing ratings for papers for many years, but that is not based on the opinion of a whole community but only the thoughts of a select few.

So what will this new rating system look like? Well, if you go to any of the six hundred or so papers that PLoS ONE has so far published and look in the right had column you will see a little box containing five small stars. Those indicate the overall aggregate rating of the paper based on individual ‘votes’ from individual users.

You can also see there how many users have rated a paper and can expand the box to show the average rating in all three categories. You can also open up a separate page which shows you exactly who has rated a paper, what their ratings were and any comments they have made.

By far the most important thing in the ratings box though is the link marked “Rate This Article”. That will open up a box the window which allows you to give your own opinion as to how important, reliable and stylish the work described is on a 5 point scale: bland to profound, tenuous to unassailable, and crude to elegant. There is also the opportunity to leave a comment along with your rating.

Rating comments are intended to be shorter and pithier than annotation and discussion comments. These are where you can say ‘great paper, well done’ to the authors, or whatever else your opinion of a paper might be. Obviously, rules of civilised behaviour apply.

I could go on at length about how to use ratings but since it is all written up neatly and using proper grammar on our Guidelines for Rating page I won’t go on about it here. Instead I have a call to arms.

Any user rating system relies, like any system of voting, works better the more people engage with it. So here is my request to everyone reading this blog:

Never read a paper on PLoS ONE without leaving a rating

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New and Exciting in PLoS ONE

from A Blog Around The Clock on Wed, 2008-05-07 05:33

There are 56 new articles published in PLoS ONE this week and it was hard to make the picks as this seems to be a very, very good week with lots of cool papers. Here are some of the...

Free but not Open?

Chris Surridge — Tue, 03 Jul 2007 05:13:54 -0700

There is an interesting editorial out today in the Canadian Medical Association Journal (CMAJ). It applauds the establishment of the journal Open Medicine by former editors of CMAJ. It also gives a clear exposition of why it believes Open Access publishing is important. Finally it establishes itself to be the open access journal which in the World is leading in general medicine.

You might wonder why that last sentence is so convoluted. I’m not a great writer but still I ought to be able to do better than that. You might also be expecting me to tell you what the CMAJ says about Open Access publishing. Perhaps I might even give you some direct quotations.

Well I would love to but the fact is I’m a little scared. You see all the content of the CMAJ is copyright to the Canadian Medical Association or its licensors. And that copyright says that I can’t republish, redistribute, store in a retrieval system or transmit in any form or by any means, anything published there without explicit permission. I suppose I could trust to the vagaries of ‘Fair Use’ laws. But quite frankly I don’t want to take the risk.

This of course raises the question of whether CMAJ is right to call itself an open access journal.

A few years ago Open Access was a very clearly defined term but these days that clarity is becoming clouded. So let me take on the mantle of bellman and tell you again
the four unmistakable marks by which you may know, wheresoever you go, the warranted genuine Open Access publication.

1. Content is made freely and immediately accessible to all. This basically means that you can get it on the internet without paying anything in addition to what it costs you to access the internet.

2. Authors retain the rights of attribution. So the work is the authors. The author doesn’t sign over the copyright to the publisher or anyone else. Rather the author allows the publisher to publish the work under licence. A licence which also ensures that:

3. Content can be distributed and reused without restriction. So I or anyone else can take Open Access content and use it, in whole or in part, for any purpose including purposes that have not yet been dreamt of as long as I don’t infringe the Authors rights of attribution.

4. Papers are deposited in a public online archive such as PubMed Central. This ensures, as best as anyone can, that the above three conditions continue to apply to the Open Access content in perpetuity.

There is plenty of scope for argument about the details here, especially the exact conditions of the Open Access licence. Creative Commons have a number of possible licences from the least restrictive, full Attribution licence as used by us here at PLoS or the Attribution Share Alike license used by Open Medicine; to the most restrictive Attribution, Non-commercial, No Derivatives license that some argue is not an Open Access license at all and have nicknamed the ‘Free Advertising’ license. However, if a journal can’t meet all four of the above criteria, then it simply isn’t publishing Open Access however much they say they are.

Free Access to scientific research is great, and all publishers who make their content free to read should be praised for doing so. But this is not Open Access. It is like giving a child a Lego car and telling them that they can look at it, perhaps touch it, but certainly not take it apart and make an aeroplane from it. The full potential of the work cannot be realised.

It is depressing not to be able to take things on trust, but it would seem that these days, as with all gift horses, when someone tells you they are giving you Open Access you need to check the small print.

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Face to Face

Chris Surridge — Fri, 29 Jun 2007 09:47:09 -0700

A quick posting this to let everyone know that in our relentless attempt to be as web 2.0 as possible Liz Allen has just established a PLoS group on Facebook. I’m not completely sure what we are going to get up to over there but all of you with Facebook accounts come and join us and find out.

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Refs' Reports on PLoS ONE

Chris Surridge — Fri, 29 Jun 2007 09:30:24 -0700

This probably isn’t news to many of you but for some time now PLoS ONE has been posting referees' reports alongside the papers it publishes. Not all reports are posted and reports are often not presented in their entirety. Also some of them have the referees’ name attached and some don’t. This could be a little confusing so I thought it was time I explained what precisely we were doing and why.

It might seem obvious why we are posting referees’ reports given that PLoS ONE is trying to foster openness and discussion in the assessment of papers however the situation isn’t completely simple. Referees reports have a very specific function in helping an editor decide whether to publish a paper and advising authors how their paper should be revised. That means that much of a referees’ report is only intelligible in the context of the version of the paper that they were reviewing. PLoS ONE does not make that original submissions public. All the same we feel that the comments made about the work in general might be very helpful to readers.

From the very start of PLoS ONE we have been telling referees when papers they have helped to assess are being published so that they can come and comment on papers directly. However this hasn’t proved as successful as we had hoped and several referees have asked why we were wanted them to comment again when they had already told us what they thought of the paper.

So now as well as encouraging referees to come to the site and comment we also ask their permission to post the more general comments from their reviews. We hope that they will allow us to post their reviews with their name but as we allow anonymous pre-publication review we are content for them to maintain that anonymity if they so wish (for a referee’s view of the process see Heather Piwowar's blog entry and the letter we sent her).

So there you have it. All referees are asked for permission to post their reviews and if permission is granted the reviews are posted whether supportive or not. What is removed is only the very specific comments (like typos and such) which have been made completely obsolete in revising the manuscript for publication.

We hope that this will help readers to understand our editorial processes a little better; but chiefly we hope you find these reviews interesting and informative.

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PLoS ONE at 500

Chris Surridge — Tue, 05 Jun 2007 15:30:28 -0700

This needs shouting about. PLoS ONE just published its 500th paper! Yep that’s right since launch, a matter of five an a half months or twenty five weeks, PLoS ONE has published over 500 pieces of peer reviewed original research.

The 500th paper comes from Sarah Randolph and colleagues in Oxford, UK; Vilnius. Lithuania; Riga, Latvia; and Tallinn, Estonia and is called “Climate Change Cannot Explain the Upsurge of Tick-Borne Encephalitis in the Baltics”. Just to show off the big five-double-O again the full citation is:

Sumilo D, Asokliene L, Bormane A, Vasilenko V, Golovljova I, et al. (2007) Climate Change Cannot Explain the Upsurge of Tick-Borne Encephalitis in the Baltics. PLoS ONE 2(6): e500. doi:10.1371/journal.pone.0000500

What it shows is that politics has had major influence on the rise of tick-borne disease in Eastern Europe over recent decades making for a more complex picture than simply blaming climate change.

This is most certainly the cherry on the top of an incredible half year:

1,411 submissions

513 published paper

360 member editorial board and growing

19 day average acceptance to publication

> 600 post publication comments posted

Now to get to grips with the next 500!

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