Category Archives: PLoS

PLoS Blogs – the science blogging network!

Earlier today, Public Library of Science (PLoS) launched a wonderful (if I may say so myself) new science blogging networks – PLoS Blogs!

The network was built by Brian Mossop, the Community Manager at PLoS Hubs and blogger at Decision Tree (Twitter). Any questions? Just e-mail him at:

Brian was ably assisted by a team of PLoS staffers, including Sara Wood, Pete Binfield, Liz Allen and Richard Cave, among others (yup, I left a few fingerprints around the site as well).

You should read the About section at the network, introductory post by Liz Allen, and a post describing the history of the project and the concept by Brian Mossop.

The network has two parts. The PLoS Blogs are editorial blogs you are already familiar with from before: the official PLoS Blog, everyONE (PLoS ONE community blog) and Speaking of Medicine (PLoS Medicine community blog).

The other part, the new part, is The PLoS Blogosphere, a collection of independent science bloggers who have moved (or started new) blogs on the network today.

While media organizations have stable-fulls of professional writers and may tend to want to enlist scientists to write their blogs in a different tone from the rest of their fare, or as scientific societies may like to enlist professional writers to do the blogging for them, PLoS wanted to do something different: have scientist-bloggers and science-journalist-bloggers writing side by side.

PLoS possesses a huge database of excellent scientific research in their seven journals. But scientific papers tend to be written for other researchers in the same field and can be difficult to read – they need translation. On the other end, PLoS has an excellent social media presence and great ongoing relationship with bloggers elsewhere. What this network does is provide the stuff in-between – a translation of research and other science news targeted at educated lay audience interested in science.

The starting line-up at the network is:

Speakeasy Science: Deborah Blum

The Language of Bad Physics: Sarah Kavassalis

Body Politic: Melinda Wenner Moyer

Wonderland: Emily Anthes

Take As Directed: David Kroll

Neuroanthropology: Daniel Lende and Greg Downey

Obesity Panacea: Peter Janiszewski and Travis Saunders

Gobbledygook: Martin Fenner

GenomeBoy: Misha Angrist

NeuroTribes: Steve Silberman

The Gleaming Retort: John Rennie

Check them out, and go say Hello in the comments on their first posts on the network.

Grab the RSS feed (I have already placed it on the homepage of

You can follow the network also on Twitter – @plosblogs or the hashtag #plogs.

Check out the blog posts reacting to the launch as well: Phil Yam at Scientific American, Daniel Lende, Jason Goldman, Greg Laden, John Dupuis, Deborah Blum, ihatewasabi, Sara Kavassalis, Hank Campbell, John Stafford, Grant Jacobs, Casey Rentz, Sammy Smith and Carl Zimmer.

The August 2010 PLoS ONE Blog Pick of the Month…

…has been revealed here.

Miscellaneous PLoS news

– if an image is Worth a Thousand Words: how cells adhere to spider silk.

– incredible Media Coverage of the Marine Biodiversity and Biogeography Collection.

– a monthly (instead of weekly) post compiling the PLoS ONE News and Blog Round-Up

– new PLoS Editorial Manager (EM) for submitting manuscripts is now live, so here are the FAQs.

July 2010 PLoS ONE Blog Pick of the Month….

….was just announced on the everyONE blog.

Seven Questions….with Yours Truly

Last week, my SciBling Jason Goldman interviewed me for his blog. The questions were not so much about blogging, journalism, Open Access and PLoS (except a little bit at the end) but more about science – how I got into it, what are my grad school experiences, what I think about doing research on animals, and such stuff. Jason posted the interview here, on his blog, on Friday, and he also let me repost it here on my blog as well, under the fold:

Continue reading

PLoS ONE Blog Pick of the Month for June 2010…

…was just announced on everyONE blog. Go and see who won!
And while there, check out the latest edition of the (bi)weekly Blog/Media coverage.

Lizards, carcasses and bacteria

Do Komodo dragons kill their prey by making them sick with the bacteria from their dirty mouths? Or do they kill with strength, speed and venom while bacteria are just incidental? Or is it bacteria who hitch a ride on the lizards on their journeys from one juicy carcass to the next?

PLoS ONE Blog Pick of the Month for May 2010

The winner, as always, has been announced on the everyONE blog so jump on over there….

April 2010 PLoS ONE BLog Pick Of The Month….

… was just announced!

Stuff I showed on my panel at AAAS

Since I don’t do PowerPoint but use the Web for presentations instead, and since the recordings from AAAS are not free (yes, you can buy them, I won’t), and since some people have asked me to show what I showed at my panel there, here is the list of websites I showed there. I opened them up all in reverse chronological order beforehand, so during the presentation itself all I needed to do was close each window as I was done with it to reveal the next window underneath.
I started with to explain the new interactive, collaborative methods in science journalism we discussed there.
Then I showed this series of tweets:
as an example of how that system can work:
I then showed how I filter my Twitter stream to eliminate much of it and only get to see what people I trust deem important:
I pointed out that some people got jobs on Twitter:
I showed how some people – including myself – got jobs on their blogs:
Then I showed an example of a PLoS ONE paper, as a center of an ecosystem, and the comments and links as an outer shell of that ecosystem:;jsessionid=2009BD9E7195AADA6D62474B19ABA3FE
I particularly showed the links to the blog posts aggregated on to show the reputability of science blogging in the current science publishing ecosystem.
Then I discussed
and as example showed how I collect important links about Dunbar Number from Twitter to FriendFeed for a future blog-post:
A blog-post or a series of them can lead to an MSM article, and perhaps a series of articles can lead to a book contract. But even without that, one can potentially have a blog post published in a book, e.g., in the Open Laboratory:
Finally, if one gets a book published, there is nobody organizing the marketing and the book tours any more, so I showed how Rebecca Skloot organized it herself, by tapping into her online community:

Two new PLoS Collections

PLoS recently started two new thematic collections of articles: RECOMB Regulatory Genomics and Systems Biology 2009 and the Rabies Collection. Check them out.

Good article about the history and current state of Open Access

US seeks to make science free for all by Declan Butler:

The push to open up scientific knowledge to all looks set to go into overdrive. Over the past decade, the accessibility offered by the Internet has transformed science publishing. Several efforts have already tried to harness the web’s power to make research papers available for free. Now two parallel efforts from the US government could see almost all federally funded research made available in free, publicly accessible repositories…..

Read the whole thing….

Various PLoS news

For those of you not subscribed to the PLoS Blog or everyONE blog, here are some of the latest news:
Introducing the PLoS Medicine iPhone application
A new search server is powering the PLoS journal websites
Author Spotlight: Interview with Joseph Sertich and Mark Loewen
PLoS ONE reviewed by leading library journal
Weekly PLoS ONE News and Blog Round-Up
Paleontology Research Articles in PLoS ONE
PLoS ONE Publishes 10,000th Manuscript!
You can get updates from PLoS on Twitter, FriendFeed and Facebook.

PLoS ONE Blog Pick of the Month for March 2010….

…..was just announced on the everyONE blog so go ahead and click right here and go see who won this month’s prize.

News from PLoS ONE

Over the past week, if you are not a regular visitor to the everyONE blog you may have missed those, we have posted an Update to PLoS Article-Level Metrics Data, the regular Weekly PLoS ONE News and Blog Round-Up and the ‘featured image’ post – Worth a Thousand Words. Check them out.

Why it is important for media articles to link to scientific papers

You may be aware that, as of recently, one of my tasks at work is to monitor media coverage of PLoS ONE articles. This is necessary for our own archives and monthly/annual reports, but also so I could highlight some of the best media coverage on the everyONE blog for everyone to see. As PLoS ONE publishes a large number of articles every week, we presume that many of you would appreciate getting your attention drawn to that subset of articles that the media found most interesting.
So, for example, as I missed last week due to my trip to AAAS, I posted a two-week summary of media coverage this Monday. And that took far more time and effort (and some silent cursing) than one would expect. Why?
I don’t think I am a slouch at googling stuff. Some people joke that the entire Internet passes through my brain before it goes to the final audience. After all, I have been monitoring the Web for mentions of ‘PLoS’ and ‘Public Library of Science’ on blogs, Twitter, FriendFeed, Facebook and elsewhere for a few years now. If I don’t catch a mention within minutes of it being posted, you can bet one of my many online friends/followers/subscribers is bound to quickly let me know by e-mail or Direct Messaging somewhere. If someone says something nice about PLoS, I am quick to post a ThankYou note. If someone asks a question, I try to answer or to connect the person with the appropriate member of the PLoS staff. If someone is publicly musing about submitting a manuscript to one of our journals, I am right there to give encouragement. If someone makes a factual error, I gently correct it. It is very, very rare that I need to raise the Immense Online Armies because someone is wrong on the Internet 😉
So, why is it difficult then to compile a collection of weekly media coverage? Let me walk you through the process….
First, as you probably already know, PLoS makes no distinction between Old and New media. We have bloggers on our press list who apply/sign-up in the same way and abide by the same rules as traditional journalists (and, unlike mainstream media, bloggers NEVER break embargos, not once in the past three years since we started adding bloggers to our press list). For the kind of coverage we prefer to see, we point bloggers to the criteria. In return, bloggers can send trackbacks to our articles, their work is showcased side-by-side with the traditional outlets in our weekly posts, they can be discovered via Google Blogsearch, Postgenomic and links directly from each article, and one blogger per month wins a t-shirt and special recognition.
So, I start with blog posts first. The first thing I do is take a look at Those are the best of the best posts – not merely mentioning our articles, but adding analysis, commentary, critique, context and additional information. How do I find them? I just search the site for the phrase ‘journal.pone‘. That search brings up every single post that mentions a PLoS ONE article because that phrase is a part of every possible form of the URL of the article (including the shortest one, which includes just the DOI). If a post links to our article (and that is the only way to get aggregated on I will find it this way. Needless to say, this process takes just a few minutes per week.
Knowing that there are some good blogs out there that are not registered at (which is strange and unfathomable why – is a ‘stamp-of-approval’ place for science blogs recognized by the outside world of journals and media, as well as a nice way to get extra recognition and traffic, and even awards), I then repeat the same search – for ‘journal.pone‘ – on Google Blogsearch. This may bring up a few more posts that I did not catch yet. Occasionally, some of these are good. Another couple of minutes. Blogs are now done. Move on to traditional media….
And this is where the Hell starts. Try searching Google News for ‘journal.pone‘…?! All I get are a couple of prominent blogs that I have already counted, e.g., those blogs that are listed by Google News ( blogs, Ars Technica, Wired blogs, etc.). Where are the others?
The problem is, nobody in the mainstream media links to papers.
So I have to search for PLoS and for Public Library Of Science and then figure out which ones are covering specifically PLoS ONE articles (sometimes they don’t specify, sometimes they name the wrong journal – last week an article on PLoS Current-Influenza was reported to be in PLoS ONE by a number of outlets copying the error from each other). Then I have to search for keywords for individual articles I suspect may have received some coverage. Last week, for example, I searched for “swallows+antioxidants” and “St. Birgitta”, among many others. This lasts for hours! And at the end I am still not 100% sure I caught everything. How frustrating!
Not just is there a big difference in time and effort spent between finding blog posts and finding media articles, but there is an even bigger disparity when one considers what results come out of these searches. I have been doing this for a month now. I expected that there would be poor blog posts and poor media articles, that there would be good blog posts and good media articles, and that there would occasionally be some excellent blog posts and excellent media articles. So far, that is true…. except I have yet to discover an excellent media article. As a rule, the very best coverage of every paper in the past month was done by a blogger or two or three. Then there are some other, good pieces of coverage in both the New and Old media, and then there are some really bad pieces in both realms as well (not all blog posts I count here are really bad – they may just be too detailed, technical and dry for lay audience because the blogger is intentionally targeting scientific peers as audience, which is fair thing to acknowledge).
So, every week, it takes me a few minutes to find the very best coverage (which is on blogs, usually those aggregated on And then I spend hours looking for remnants, in the traditional media, which turn out to be so-so, some OK, some not so good, some horrible. If I wasn’t paid to do this, I would not do it – it cannot be good for my long-term mental health.
The resistance to post links is an atavism, a remnant of an old age before the Web. I know (because I asked many times) many good science journalists keep trying to add links, but the editors say No. The traditional media has still not caught on to the Ethic of the Link, which is an essential aspect of ethics of online communication.
I can think, off the top of my head, of three good reasons why everyone who publishes online should include a link to the scientific paper described in the article (just post the DOI link that comes with the press release if you are on the press list – if it does not resolve immediately, it is not your fault, you can always blame the journals for being slow on it – though this should never happen with PLoS articles):
Reason One: I will not go crazy every week. I am assuming that every scientific publisher has people on the staff whose task is to monitor media coverage and each one of these people is cussing and cursing YOU, the Media, every day. Try to make friends with people who provide you with source material on a regular basis.
Reason Two: Media coverage is one of the many elements of article-level metrics. Furthermore, links from the media affect the number of views and downloads of the article, and those are also elements of article-level metrics. Number of views/downloads then, in the future, affects the number of citations the work gets which is also and element of article-level metrics. Thus omitting the link skewes the ability of readers and observers to evaluate the papers properly.
The current ecosystem of science communication has a scientific paper at its core, additions to the paper (e.g., notes, comments and ratings, as well as Supplemental materials, videos posted on, etc) as a shell, and incoming and outgoing links – trackbacks, cited papers, citing papers, links to other papers in the same Collection, links to other papers with the same keywords, and yes, incoming links from the media – as connections building a network: the entire inter-connected ecosystem of scientific knowledge.
By not linking to scientific papers, traditional media is keeping itself outside of the entire ecosystem of empirical knowledge. By doing this, the traditional media is fast making itself irrelevant.
Reason Three: if an article in the media discusses a scientific study, that scientific paper is the source material for the article. If the link is missing, this is an automatic red flag for the readers. What is the journalist hiding? Why is the article making it difficult for readers to fact-check the journalist? Something does not smell good if the link is not provided (or worse, it is impossible to figure out even who are the authors and in which journal did they publish – yes, that is more common than you think).
The instant and automatic response of the readers is mistrust. Every time you fail to link to the paper, you further erode whatever trust and reputation you still may have with the audience. You soon cease to be a legitimate source of information. Sure, most readers will not go hunting for the paper to read it in order to fact-check you. But two or three will, and they will let everyone else know if your article is trustworthy or not, either in the comments under the article on your own site, or on their blogs which will be quickly picked up by Google (remember: Google loves blogs).
So please, media types, hurry up and catch up with the world. The 21st century is already a decade in – you really need to do some very fast learning. Right now. Or you’ll go extinct in a nanosecond. And despite my reputation, I never said that I’d consider that result to be a Good Thing. We are in this together, you just need to do your part. To begin with, start linking.

New user functionality at PLoS – referenced PDFs via Pubget

Often when a scientific paper gets cited, one wants to see how exactly it was cited. Thus one needs to download the citing article. There are numerous ways to do so, but starting today, you can get this done with just a click or two on all PLoS articles. How?
Go to the Metrics tab of the article, scroll down until you see CrossRef citations, click to expand the list of papers that cite the paper you are on. You will see, next to some papers, a tiny PDF icon. Clicking on that icon will open the PDF of the paper you are looking for.
How is that possible? PLoS partnered with PubGet to make this work. Unfortunately, not every article has the PDF icon because not every paper is freely accessible. It works with Open Access articles, but if the paper is not, then it may still work if you are affiliated with one of the 170 institutions in the PubGet network. If your institution is not a part of their network, you should work on getting it included there: just tell your library – Pubget is free.
But it is hard to explain how cool and quick and easy this is in mere words. It is much better to use the magic of screencast video, so here is a brief tutorial:

PLoS ONE Blog Pick of the Month for February 2010….

…goes to….you’ll need to click here to see.

AAAS 2010 meeting

In San Diego this week. Check it out. I’ll be there – see my session. If you will be there, let me know. Let’s have coffee or lunch, etc. My session is on 21st in the morning, and there is a lot of social stuff I agreed to on the 19th in the afternoon and evening, and of course I want to see a lot of other sessions, but I am generally flexible. Just ping me over e-mail or Twitter or phone (if you have my number) or post a comment here.

T.rex, Space, lively colors, mugs, and future scientists – the PLoS Store Spring Collection

PLoSbrainimage.jpgPLoS shirts are always hot items in labs and at conferences. People just love them. They ask for them, get them as prizes, or buy them, and proudly post pictures of themselves wearing them….

With the spring coming, we decided to make the range of items available in the PLoS store much more diverse. You can now find tiny Future PLoS Author shirts for kids. And elegantly done embroidered tees, hats and hoodies.

We introduced items with a lot more fun colors. And added T.rex to a number of dino tees, mugs and mousepads. There is LOTS to choose from, so take a look around the PLoS store.

PLoSspaceimage.jpgPLoSmug.JPGPLoSdinoimage.JPGHmmmm, I want some of these things myself!!!!

PLoS ONE blogging

With Bex Walton moving on to another job, it is now my duty to take over posting about media coverage over on everyONE blog, as well as to pick a cool image of the week. So I started this week with Weekly PLoS ONE News and Blog Round-Up and Worth a Thousand Words. Take a look. Am I doing it right?

January 2010 PLoS ONE Blog Pick Of The Month….

…has just been announced. To see who won, you will have to click on this link right here 😉

PLoS ONE Blog Pick Of The Month…

…for December 2009 is….you’ll find out if you click here. posts now a part of Article-Level-Metrics at PLoS

Two years ago, at the 2008 Science Blogging Conference, Dave Munger introduced to the world a new concept and a new wesbite to support that concept – What is that all about?
Well, as the media is cuttting science out of the newsroom and the science reporting is falling onto institutional press information officers and science bloggers, more and more people are looking for scientific information on science blogs, especially as the expertise of the blogger is likely to provide a more accurate assessment of a freshly published study than the mainstream media can usually do.
But many new readers of science blogs were put off by the fact that a blog is a personal platform. In other words, not every post was about pure science news. There may be a beautiful nature picture, a personal story, a YouTube video, a comic strip, an aggressive defence of science from the latest attack by the politically motivated anti-science groups, etc. They were asking “where is science on science blogs?”. Well, it’s there if one looks around for more than a few seconds. But not everyone has patience to look around. So Dave came up with the idea….
And the idea was to a) come up with a method for approving science bloggers, b) give such bloggers tools to tag their posts that are specifically covering peer-reviewed literature, and c) use the tags to aggregate links to all such posts in one place. Thus, the was born.
In the two years since its inception, has grown and improved and gained quite a lot of respect. A few languages other than English were added. Weekly ‘editors’ picks’ in various disciplines started getting posted. Seed Media Group became a partner. I use it as the only source of posts when considering the entries for my PLoS ONE Blog Pick Of The Month (only 13 days to go in December, folks, keep blogging!).
Yesterday, a new milestone was reached. Coverage of a PLoS article (in any of the seven PLoS journals) by a blog post that gets aggregated on was added to the article-level-metrics found on each PLoS article (under the “Metrics” tab) so it can be discovered by a single click from the article itself. Here is a short video demonstrating how it works:

Sure, PLoS articles can receive (and showcase) trackbacks from blogs which we encourage you to do, but some blogging platforms cannot send trackbacks, some trackbacking posts are just lists of links without additional explanations, or may even come from spam blogs. The advantage of linking only to blog posts aggregated at is that there is a vetting mechanism for blog authors, minimal criteria for inclusion of a post, and ability to flag and potentially remove inappropriate posts from it. Thus, only those blog posts that add value to the article are included. A one-stop shopping place for the best blog coverage of the article.
You can read in more detail about the news at news blog and on everyONE blog.

PLoS ONE Blog Pick of the Month for November 2009….

…has been announced on the everyONE blog.

Introducing the (rigorously peer-reviewed, of course) PLoS store!

OA PLoS shirt.jpgIf you ever saw me at a conference, you probably asked me for one of the famous PLoS t-shirts. Or you did not even have to ask – I just gave you one.
Or perhaps you won one of our contests in the past – a synchroblogging anniversary competition, or a Blog Pick Of The Month – in which case you also got one of the shirts.
If you attended one of the previous ScienceOnline meetings, you got a PLoS ONE shirt.
Over the past two years or so, I went through an enormous box of PLoS swag, not just shirts, but also stickers, mouse-pads, pens, decals, etc. Other PLoS employees do the same, whenever they travel.
hamsters PLoS shirt.jpgAnd we’ll keep doing this, of course. But now, we will have a much broader range of products to offer AND, most importantly, you don’t have to wait to meet us – you can now order one for yourself.
Yes, yesterday we launched the amazing PLoS Store. We peer-reviewed all the potential suppliers and chose Zazzle. We even peer-reviewed the shirts ourselves: San Francisco staffers got some shirts, wore them, washed them, and reported that they held up nicely.
Go take a look and get your holiday shopping started!

PLoS ONE Blog Pick of the Month….

…for October can be found here.

Genomics of Emerging Infectious Disease PLoS Collection

If you follow me on Twitter or peruse the links in my daily Tweetlinks summaries, you may have noticed I posted several links to a new Collection at PLoS. This one is not a PLoS ONE Collection, but a PLoS-wide one, spanning six of the seven journals in the house.
The Collection Genomics of Emerging Infectious Disease, was compiled by Jonathan A. Eisen (who you probably know from his excellent blog), the Academic Editor-in-Chief at PLoS Biology.
Jonathan, together with PLoS Biology Senior Editor Catriona J. MacCallum, wrote the introductory editorial explaining what the Collection is about and I particularly like the comparison to the world of birding:

When an American robin (Turdus migratorius) showed up in London a few years ago, birders were rapidly all atwitter and many came flocking to town [22]. Why had this one bird created such a stir? For one main reason–it was out of place. This species is normally found in North America and only very rarely shows up on the other side of the “pond.” Amazingly, this rapid, collective response is not that unusual in the world of birding. When a bird is out of place, people notice quickly.
This story of the errant robin gets to the heart of the subject of this collection because being out of place in a metaphorical way is what defines an emerging infectious disease. Sometimes we have never seen anything quite like the organism or the disease before (e.g., SARS, Legionella). Or perhaps, as with many opportunistic pathogens, we have seen the organism before but it was not previously known to cause disease. In other cases, such as with as pandemic H1N1 2009 or E. coli O157:H7, we have seen the organism cause disease before but a new form is causing far more trouble. And of course organisms can be literally out of place, by showing up in a location not expected (e.g., consider the anthrax letters [2]).
Historically, despite the metaphorical similarities with the robin case, the response to emerging infectious disease is almost always much slower. Clearly, there are many reasons for these differences, which we believe are instructive to consider. At least four factors are required for birders’ rapid responses to the arrival of a vagrant bird: (1) knowledge of the natural “fauna” in a particular place, (2) recognition that a specific bird may be out of place, (3) positive identification of the possibly out-of-place bird, and (4) examination of the “normal” place for relatives of the identified bird.
How are these requirements achieved? Mostly through the existence of high-quality field guides that allow one to place an organism such as a bird into the context of what is known about its relatives. This placement in turn is possible because of two key components of field guides. First, such guides contain information about the biological diversity of a group of organisms. This usually includes features such as a taxonomically organized list of species with details for each species on biogeography (distribution patterns across space and time, niche preferences, relative abundance), biological properties (e.g., behavior, size, shape, etc.), and genetic variation within the species (e.g., presence of subspecies). Second, a good field guide provides information on how to identify particular types (e.g., species) of those organisms. With such information, and with a network of interested observers, an out-of-place bird can be detected with relative ease.
In much the same way, a field guide to microbes would be valuable in the study of emerging infectious diseases. The articles in this collection describe what can be considered the beginnings of species-specific field guides for the microbial agents of emerging diseases. If we want to truly gain the benefits that can come from good field guides it will be necessary to expand current efforts to include more organisms, more systematic biogeographical sampling, and more epidemiological and clinical data. But the current efforts are a great start.

On the PLoS blog, Catriona J. MacCallum explains:

The collection is a collaborative effort that combines financial support from with the editorial independence and rigor of PLoS and the expert opinion of leading researchers from several different disciplines. You can read more about’s involvement in a blog post from Frank Rijsberman. In one of the articles (from PLoS Biology), Gupta et al. discuss’s vision as a funding agency for how the international community might unite to best take advantage of the new technology for combating infectious disease. The challenges are large and each article ends with a section summarizing what these are and how they might be overcome.

You can also download and listen to the podcast about the Collection, in which Dr.Kirsten Sanford interviews Jonathan Eisen and two of the authors of Collection artices Siv Andersson, and Raj Gupta (both Dr.Eisen and Dr.Sanford will also attend ScienceOnline2010, for those of you interested in the event).
The press release (also here) also contains all the relevant links:

Emerging infectious diseases are caused by a wide range of organisms, but they are perhaps best typified by zoonotic viral diseases, which cross from animal to human hosts and can have a devastating impact on human health. These zoonotic diseases include monkeypox, Hendra virus, Nipah virus, and severe acute respiratory syndrome coronavirus (SARS-CoV), in addition to influenza A and the lentiviruses (HIV) that cause AIDS. As Albert Osterhaus and colleagues from the Erasmus Medical Center, Rotterdam, The Netherlands, point out in their article in the collection, the apparent increased transmission of pathogens from animals to humans over recent decades can be attributed to the unintended consequences of globalization as well as environmental factors and changes in agricultural practices.
Articles in the collection also shine a spotlight on specific pathogens, some familiar and widespread, such as the influenza A virus, some “reemerging,” such as the Mycobacterium tuberculosis complex that causes tuberculosis, and some identified only relatively recently, such as the bacterium Helicobacter pylori, which is associated with peptic ulcers and gastric cancer. Others discuss the broader implications of genomics research in this area, such as what it means for researchers in developing countries or for our biosecurity. As Jacques Ravel and colleagues from the US University of Maryland School of Medicine note, genomics can and should be used proactively to build our preparedness for and responsiveness to biological threats.

On the official Google blog Frank Rijsberman writes:

The first outbreak of the new “swine flu” strain, now known as H1N1, earlier this year in Mexico caught the world by surprise. Public health officials around the world tried to stop the virus at the borders but were largely helpless. Shortly after, on the other side of the world from Mexico, I saw the health check posts in Cambodia at the airport and at a borderpost with Vietnam, right when the country found its first H1N1 cases which were flown in by US exchange students. The weapons used by the health officials to combat the spread of the virus were primarily paper survey forms and thermometers; the virus won, very quickly. Genomics is rapidly changing both the way diseases are diagnosed and the way medications and vaccines are developed – but will it give us the tools to prevent the next pandemic?

So take a look at the Genomics of Emerging Infectious Disease Collection today and read all the exciting articles in it.

Blog Pick of the Month – only a week left

The October winner will be announced on the 1st of November. Make sure your posts are aggregated on

It’s so easy to re-use Open Access stuff (video)

It’s barely been a day since PLoS ONE published the article Discovery of the Largest Orbweaving Spider Species: The Evolution of Gigantism in Nephila when a video appeared on YouTube mashing up images and text from the press release:

Of course, as this is Open Access, nobody needs to worry about copyright and stuff….though a direct link to the paper would have been nice (or, considering the infamous YouTube commenters, perhaps better not!).
See the related blog post as well.

Open Access Week

This week – 19th-23rd October 2009 – is the Open Access week around the world – fitting nicely with the 5th birthday of PLoS Medicine. And when I say ‘around the world’ I really mean it. Just check out all the global events happening this week.
The OA Week is co-organized by Open Access Directory, PLoS, SPARC, Students for Free Culture, eIFL (Electronic Information for Libraries) and OASIS.
Many countries are participating this year, including some with numerous events all around the country. See, for example, all the events in Germany (there are 67 events in that country alone!), Netherlands, China and Japan.
You can get all the information and follow the events on the Open Access Week blog. There is also a nice round-up on the SPARC site.
As the week unfolds, I will blog more about it here. In the meantime, you can follow the news of the OA week on Facebook or by following PLoS on Twitter.You may also want to sign up to participate in the OASPA webinar (locationless – sign up to participate online).
I love this video in which Jennifer McLennan and Heather Joseph of SPARC explain what the OA week is all about:

And in this video, Walter H. Curioso, M.D., M.P.H., talks a bit about his views of Open Access and how it can help in developing countries.

The PLoS ONE Blog Pick of the Month for September 2009 is…

….to be found on the everyONE blog.

Article-Level Metrics at PLoS – Download Data (updated with links)

If you are a regular reader of this blog, you are certainly aware that PLoS has started making article-level metrics available for all articles.
Today, we added one of the most important sets of such metrics – the number of times the article was downloaded. Each article now has a new tab on the top, titled “Metrics”. If you click on it, you will be able to see the numbers of HTML, XML and PDF downloads, a graph of downloads over time and a link to overall statistics for the field, the journal, and PLoS as a whole.
Mark Patterson explains (also here and here), what it all means:

We believe that article-level metrics represent an important development for scholarly publishing. While some publishers are providing limited data, we are not aware of any publisher that has gone as far as PLoS in providing such a broad range of indicators and metrics, and in making the data openly available. We invite you to visit our journal sites and seek out the Metrics tab for each article.
It’s also important to emphasize that online usage should not be seen as an absolute indicator of quality for any given article, and such data must be interpreted with caution. To provide additional context and to aid interpretation, we have provided a series of summary tables indicating the average usage of categories of article (grouped by age, journal and topic area). Users will also notice that a number of articles do not have any usage data, because of problems with the log files. We are working hard to add data for these articles, and we also encourage readers to let us know if they find any anomalies or have any questions about the data.

You can also download the entire dataset for all seven PLoS Journals. If you click on this you can download a ZIP folder that contains an Excel file that lists all the metrics for all the articles. Please play with the data – let us know what you find, or blog about your impressions.
You can find more information (with lots of detail about the methodology, caveats, etc) about all article-level metrics on the pages of individual journals (here is the example for PLoS ONE) or specifically about download data here.
There is also a FAQ page and an entire new website devoted to explaining the new metrics. Take some time and explore. And experiment with the data and let the world know what you found.
As you may be aware, download statistics strongly correlate with subsequent citations. And just like researchers have perfected ways to game the citation numbers, of course the downloads can be gamed as well. Which is why we provide all the raw data and methods we used to get them. So you can figure out everything for yourself. It is all transparent.
The first reactions are in. Christina Pikas wrote on her blog:

So I’m very excited to hear that PLOS is offering article download information. So no begging of your acquisitions folks, no looking at the “top downloads” listing to see if your article is there. You can get it right at the article if you happen to get your article accepted into a PLOS journal. Oh, and even cooler, you can download the whole shebang in a spreadsheet! (Quick, find me a research question using this data!) You can also get how many times things are cited from a couple different sources.
If you’re a scientist, this is also one way to filter for articles that are worthy of more attention when there are so many new articles coming out. (things will have more downloads if they have press releases, etc., but still). Read more about the PLOS article level metrics here.

One of PLoS authors, Jamie Sundsbak, says:

I have written before on how impact factors of journals and their publications are being rethought. I believe that by providing the data on how scientific publications are disseminated into the world, we will truly be able to judge an article on its individual scientific worth, not just on the authors’ reputatons or where it is published.

And this from Karen Grepin:

As academic research is increasingly disseminated through new media channels, I think this is a very important improvement in measuring the impact of work. Old metrics, such as just the number of citations, may miss the importance of many academic publications. Here’s to hoping that more journals begin to report such data.

Duncan Hull took a look at the some of the articles and said:

So all the usual caveats apply when using this bibliometric data. It is more revealing than the useful (but simplistic) “highly accesssed” papers at BioMedCentral, which gives little or no indication what “highly” actually means without the raw data to back it up. It will be interesting to see if other publishers now follow the lead of PLoS and also publish their usage data. For authors publishing with PLoS, this data has an added personal dimension too, it is interesting to see how many views your paper has.
As paying customers of commercial publishers, should scientists and their funders be demanding more of this kind of information in the future? I reckon they should.

And Andrew Farke wrote a longer post:

So what’s to like here? Well, an author gets an immediate sense if someone is paying attention to a publication. Page views and PDF downloads are a valuable tool for gauging community interest. In concert with citation data, it’s probably a far better gauge of a paper’s worth than the impact fact[or] that the publication happens to show up in. The data are also freely available, transparent, and frequently updated. The latter is particularly important because it may be years before a paper’s full impact is known. An open-access metric for an open-access world.
I suspect that other journals will follow suit – it may not happen tomorrow, but it will happen. We may be seeing the death of the traditional, sometimes tyrannical, “impact factor.” Let’s hope we don’t replace it with a new despot!

And on the Small Gray Matters blog:

You can now see the number of citations, blog mentions, article views and PDF downloads for every PLoS article, so if you’ve published in one of the PLoS journals, you’re free to go find out just how many times your article’s been viewed compared to everyone else’s. And then you of course you’re free to make up all sorts of convenient excuses for the fact that your stats suck and your paper’s only been viewed seventeen times in the last three years.
What’s even cooler is the PLoS editors have collated all of that information and released it as one monstrous Excel spreadsheet. So you can now run off and do a quick regression analysis to determine whether or not having longer paper titles leads to more citations, if you’re so inclined.

Other mentions:
Library Stuff
Greg Laden
UBC Library eResources: Service Bulletins
Pimm – Partial immortalization
The Tree of Life
And check out A.J.Cann on his blog and on YouTube

The Public Library of Science (PLoS), announced the release of an expanded set of article-level metrics on its scientific and medical journal articles (some 14,000 articles across 7 journals). The article-level metrics program was launched in March 2009, and with this addition of online usage data, PLoS is providing an unprecedented set of information on every published article. Such information will be of value to researchers, readers, funders, administrators and anyone interested in the evaluation of scientific research. The PLoS article metrics include the new online usage data (HTML page views, PDF downloads and XML downloads), as well as citation counts, comments, ratings, social bookmarks and blog coverage. Usage data will be updated daily and currently include more than four years of statistics from all seven peer-reviewed PLoS journals. With this growing and detailed set of metrics on every article, PLoS aims to demonstrate that individual articles can be judged on their own merits rather than on the basis of the journal in which they are published. Because very few data have previously been made public by scholarly publishers, visitors to the journal sites will need help to understand these data. For example, it is clear from the PLoS data that online usage is dependent on the age of the article, as well its subject area. In order to place the new usage data in context, PLoS is therefore providing summary tables to allow users to see how an article compares with various average measures. For anyone wishing to examine the data in detail the complete raw data set is also available as a download. PLoS is still in the early stages of the article-level metrics program, but this is the first attempt by a major publisher to place such a broad range of data on each article. PLoS therefore hopes that the provision of these data will encourage other publishers to make such data available, which will lead ultimately to broader improvements in scholarly communication and research assessment.

drdrA over on Blue Lab Coats has this to say:

One of these tabs is the ‘metrics’ tab. If you click on it it takes you to a page that shows the metrics – things like article views, and downloads, for that particular article. Here is an example from that article that I posted on the other day. That article was just published, but you can also see metrics on older articles that were collected prior to the appearance of this feature-… like for this article for example. I love this feature because it reflects reality to the level of readership of a given article better and more immediately than the traditional pre-electronic media age measures such as citation rate or total citation number could. And, I’ve gotten quite used to looking at readership data in terms of hits and page views- running this blog and whatnot… so I’ve kind of got a feeling for this kind of data anyway.
And see that ‘Related Content’ tab up at the top there too. From that page you are set up to quickly search for related articles, bookmark things in CiteULike (which I need to become more savvy with), AND LOOK FOR RELATED BLOG POSTS!!! How awesome is that!!?? Now you are immediately connected to related scientific literature, and to the immediate response to a given article in the blogosphere, with all the commentary that brings with it.

Cameron Neylon (guest post on the PLoS blog):

Actual public interest in your paper? Real educational value being gained from it? These are things that you want to know about. It would be even better if we could separate these out, and I find the prospects of using download versus citation metrics in the future quite exciting. But in the meantime, it gives us a new measure that we can compare with what we already have available.
And, at the end of the day, that is how I think we should see these new metrics–it is more information. It isn’t yet clear how best to use these measures, but it is up to us as scientists, who, after all, make our living out of measurement and analysis, to figure out how best to use them. The approach PLoS is taking of simply presenting the data, and as much of it as is possible, is to me exactly the right approach. It is not the responsibility of journals to tell us how to measure and report things–it is up to us.
In the end, there is only one way of determining whether a particular paper is important and relevant to you personally, and that is to read it, digest the information, critically analyze it, and come to your own conclusions. You can’t avoid this and you shouldn’t. Where download and other article-level metrics can help is in making that decision about how much time you want to invest in a given paper. We need better ways of making that decision, and more data can only help.

A new Longneck discovered

Longneck.jpgToday PLoS ONE published a paper describing a very cool new fossil of a sauropod from Niger – an exquisitely preserved, almost complete skeleton. Of course, you can read it for free at:
A New Basal Sauropod Dinosaur from the Middle Jurassic of Niger and the Early Evolution of Sauropoda:

The early evolution of sauropod dinosaurs is poorly understood because of a highly incomplete fossil record. New discoveries of Early and Middle Jurassic sauropods have a great potential to lead to a better understanding of early sauropod evolution and to reevaluate the patterns of sauropod diversification.
Principal Findings
A new sauropod from the Middle Jurassic of Niger, Spinophorosaurus nigerensis n. gen. et sp., is the most complete basal sauropod currently known. The taxon shares many anatomical characters with Middle Jurassic East Asian sauropods, while it is strongly dissimilar to Lower and Middle Jurassic South American and Indian forms. A possible explanation for this pattern is a separation of Laurasian and South Gondwanan Middle Jurassic sauropod faunas by geographic barriers. Integration of phylogenetic analyses and paleogeographic data reveals congruence between early sauropod evolution and hypotheses about Jurassic paleoclimate and phytogeography.
Spinophorosaurus demonstrates that many putatively derived characters of Middle Jurassic East Asian sauropods are plesiomorphic for eusauropods, while South Gondwanan eusauropods may represent a specialized line. The anatomy of Spinophorosaurus indicates that key innovations in Jurassic sauropod evolution might have taken place in North Africa, an area close to the equator with summer-wet climate at that time. Jurassic climatic zones and phytogeography possibly controlled early sauropod diversification.

What are dino-bloggers saying so far:

….But this … this blew me away
….That animal is just flat badass.
…..It has a goddamn thagomizer!!!

Interview with Dr.Derya Unutmaz, Section Editor for Immunology at PLoS ONE…

….is now posted on everyONE blog.

w00t! PLoS ONE wins the ’09 ALPSP Award for Publishing Innovation!

Here are all the finalists. And here is the proof:

PLoS Medicine’s 5th anniversary competition

On Speaking of Medicine:

PLoS Medicine turns 5 years old on October 19th, 2009. To highlight the crucial importance of open access in medical publishing we’re holding a competition to find the best medical paper published under an open-access license anywhere (not just in PLoS) since our launch.
Vote for your choice from the 6 competing papers, detailed below — nominated and then shortlisted by our editorial board. Winners will be announced during Open-Access week (19-23rd October 2009). If you’re interested in how we came up with this shortlist of top-quality open-access medicine papers, please read on below the poll.

Go vote!

PLoS ONE Blog Pick Of The Month for August

And the winner is….

PLoS & Mendeley live on the Web! Science Hour with Leo Laporte & Dr. Kiki (video)

Leo Laporte and Kirsten Sanford (aka Dr.Kiki) interviewed (on Jason Hoyt from Mendeley and Peter Binfield from PLoS ONE about Open Access, Science 2.0 and new ways of doing and publishing science on the Web. Well worth your time watching!

PLoS ad (video)

Wow – I had no idea this existed:

Until Graham Steel visited the Cambridge office and posted about his experience. Instead of trusting Google Maps (which always gets me lost in Durham, NC) I relied on the experience of a Cambridge cab driver when I visited last year.

Introducing PLoS Currents: Influenza

Yesterday PLoS and Google unveiled PLoS Currents: Influenza, a Google Knol hosted collection of rapid communications about the swine flu.
In his blog post A new website for the rapid sharing of influenza research (also posted on the official Google blog), Dr.Harold Varmus explains:

The key goal of PLoS Currents is to accelerate scientific discovery by allowing researchers to share their latest findings and ideas immediately with the world’s scientific and medical communities. Google Knol’s features for community interaction, comment and discussion will enable commentary and conversations to develop around these findings. Given that the contributions to PLoS Currents are not peer-reviewed in detail, however, the results and conclusions must be regarded as preliminary. In time, it is therefore likely that PLoS Currents contributors will submit their work for publication in a formal journal, and the PLoS Journals will welcome these submissions.

The response from the community has been overwhelmingly positive so far. For example, Frederic Lardinois writes, on ReadWriteWeb – Finally a Good Use for Google Knol: Sharing Information About Flu Research:

Overall, we think this is a great project. Knol is a good, easy-to-use platform for these kinds of publications, and given that the articles are also archived on other servers, this project also doesn’t rely on Google to keep Knol’s servers running indefinitely.
PLoS, being a non-profit, is also the right organization to give this project a try. Commercial publishers are still wary of the Internet, and while the open access movement has been gathering some support over the last few years, a lot of research in most scientific fields will still be hidden behind paywalls for a long time.

On Tech Babble: PLOS Currents : Influenza:

PLOS Currents : Influenza is built utilizing Google Knol and a new service from the National Center for Biotechnology Information (NCBI) called Rapid Research Notes. This service allows the user an easy way to follow current research and search for relevant scientific information.
As we approach influenza season, expect greater levels of concern and interest in H1N1.

Steven Salzberg, one of the moderators of PLoS Currents: Influenza, wrote on his blog – Opening up influenza research with a new kind of journal:

What’s the difference between this and a regular journal? Well, first of all, submissions won’t be thoroughly reviewed, which means they don’t “count” as journal papers, but it also means you can publish them later in a peer-reviewed journal. The Public Library of Science has already bought into this model – they’re sponsoring PLoS Currents, after all – and we expect other journals to do so also. So why publish, you might ask? That’s easy: in a highly competitive field such as influenza research, different scientists are often racing to answer the same question. By publishing super-rapidly in PLoS Currents, you will get a citable, time-stamped reference that establishes your discovery, and most importantly, establishes when you made it.
The big win here, we hope, is that scientists will be empowered to announce their results to the world without worrying about being “scooped” – a common fear that leads to many results being kept secret for months while papers are prepared and revised. This in turn will speed up scientific progress overall, which is the real goal behind PLoS Currents.

Eddie Holmes, Chief Moderator of PLoS Currents: Influenza, wrote in a guest-post on the PLoS Blog – Welcome to PLoS Currents: Influenza:

The central idea of PLoS Currents: Influenza is to rapidly disseminate data and ideas in the realm of influenza research, stimulated by the ongoing epidemic of swine-origin influenza virus (H1N1pdm). Given this backdrop, it is no surprise that some of first contributions consider important aspects of the H1N1pdm epidemic.
Although PLoS Currents: Influenza was inspired by H1N1pdm, it will cover all types of research on all types of influenza virus. Indeed, the emergence of H1N1pdm brings into focus the need for basic research into many fundamental aspects of influenza biology.
These initial contributions have given PLoS Currents: Influenza an excellent start. The next few months should prove to be very exciting. I therefore encourage all of you working in the area of influenza to send a contribution to PLoS Currents: Influenza, however preliminary, so that your data and ideas are rapidly distributed to a wide audience.

Iddo Friedberg, on ByteSizeBio: PLoS Currents: Influenza. Because knowledge should travel faster than epidemics:

So here we have all chief elements of scientific communication: credibility (by the moderators), timeliness (immediate online publishing) and attribution (by public archiving). PC:I is heavily skewed towards timeliness. The rationale being that in Influenza research and monitoring, time is of essence. After all, a report going through the usual peer review mill can take months: which is exactly the time required for a full-blown pandemic.
Not that other scientific fields are not in need of timeliness. Physicists and mathematicians have known that for almost two decades now. Nature Precedings are also providing an outlet for rapid communication in life sciences. But the combination of speed, accessibility and credibility offered by PC:I is indeed something new and welcome.

Vincent Racaniello on Watching The Watchers: Rapid Sharing of Influenza Research:

Contributions that will be welcome at PLoS Currents: Influenza include research into influenza virology, genetics, immunity, structural biology, genomics, epidemiology, modeling, evolution, policy and control. The manuscripts will not be subject to peer-review, but unsuitable submissions will be screened out by a board of expert moderators. This policy will enable rapid publication of research.
The path to publishing original scientific research is often long and tortuous. A manuscript describing the findings is prepared and submitted to a scientific journal (such as Nature, Cell, Journal of Virology). The manuscript is assigned to two or three expert reviewers, generally scientists involved in the same area of research. If their reviews are favorable, the paper is published. Usually additional experiments are called for, which may require additional time to complete. Many months to a year may pass before the paper is published, although some manuscripts (e.g. those on 2009 pandemic influenza) may be expedited. The point is that PLoS Currents: Influenza will allow everyone – including non-scientists – to read about research soon after the authors have prepared the paper.
PLoS Currents: Influenza is a terrific idea, and I welcome this venture with great enthusiasm. I hope that PLoS Currents will grow to include other areas of science.

David Bruggeman on Pasco Phronesis blog – PLoS Currents – An ArXiv for the Rest of Us?:

Presently in beta, Currents is accepting “new scientific data, analyses, and ideas” and encouraging the discussion and analysis of this information. The material is not peer reviewed as it would be for a regular PLoS publication, but is screened by moderators who are experts in the field at issue. The idea is that the work posted and discussed in Currents would lead to papers in peer reviewed journals at a later date.
So policy research could find its way into a science journal – excellent.
While the material is hosted by Google, as the PLoS explains on its blog, it is also archived at the National Center for Biotechnology Information. Hopefully the Currents topics will not be simply reactive, but consider a number of different topics that aren’t breathing down our collective neck.
As the ScienceInsider article suggests, this is not the first time a preprint collection has been suggested for biomedical topics. Apparently when PLoS co-founder (and current PCAST co-chair) Harold Varmus tried this when he was leading the National Institutes of Health, some scientific societies raised a ruckus and the effort was discontinued. Hopefully history won’t repeat itself.

Glyn Moody, on his blog ‘Open….’, writes – PLoS Reinvents Publishing and Saves the World:

As someone who has been writing about open access for some years, I find myself returning again and again to the Public Library of Science. That’s because, not content with pioneering open access, PLoS has time and again re-invented the broader world of scientific publishing. Now, it’s done it again.
The current system of publishing papers is simply too slow to deal with pandemics, where speed is of the essence if we’re to have a chance of nipping them in the bud. It’s good to see PLoS stepping in to help address this major problem.
This is really exciting from many viewpoints. It’s pushing the ideas behind open access even further; it’s reshaping publishing; and it may even save humanity.

So, what do you think?

The Future of Online (Academic) Publishing

Talk given by Peter Binfield at the ISMTE meeting (slides and audio):

Not-so-self-correcting science: the hard way, the easy way, and the easiest way

Two recent events put in stark relief the differences between the old way of doing things and the new way of doing things. What am I talking about? The changing world of science publishing, of course.
Let me introduce the two examples first, and make some of my comments at the end.
Example 1. Publishing a Comment about a journal article
My SciBling Steinn brought to our collective attention a horrific case of a scientist who spent a year fighting against the editors of a journal, trying to have a Comment published about a paper that was, in his view, erroneous (for the sake of the argument it does not matter if the author of the original paper or the author of the Comment was right – this is about the way system works, er, does not work). You can read the entire saga as a PDF – it will make you want to laugh and cry and in the end scream with frustration and anger. Do not skip the Addendum at the end.
Thanks to Shirley Wu for putting that very long PDF into a much more manageable and readable form so you can easily read the whole thing right here:
See? That is the traditional way for science to be ‘self-correcting’….Sure, a particularly egregious example, but it is the system that allows such an example to be a part of that continuum somewhere on its edge – this is not a unique case, just a little bit more extreme than usual.
Janet wrote a brilliant post (hmmm, it’s Janet… was there ever a time I linked to her without noting it was a “brilliant post”? Is it even possible to do?) dissecting the episode and hitting all the right points, including, among others, these two:

Publishing a paper is not supposed to bring that exchange to an end, but rather to bring it to a larger slice of the scientific community with something relevant to add to the exchange. In other words, if you read a published paper in your field and are convinced that there are significant problems with it, you are supposed to communicate those problems to the rest of the scientific community — including the authors of the paper you think has problems. Committed scientists are supposed to want to know if they’ve messed up their calculations or drawn their conclusions on the basis of bad assumptions. This kind of post-publication critique is an important factor in making sure the body of knowledge that a scientific community is working to build is well-tested and reliable — important quality control if the community of science is planning on using that knowledge or building further research upon it.
The idea that the journal here seems to be missing is that they have a duty to their readers, not just to the authors whose papers they publish. That duty includes transmitting the (peer reviewed) concerns communicated to them about the papers they have published — whether or not the authors of those papers respond to these concerns in a civil manner, or at all. Indeed, if the authors’ response to a Comment on their paper were essentially. “You are a big poopyhead to question our work!” I think there might be a certain value in publishing that Reply. It would, at least, let the scientific community know about the authors’ best responses to the objections other scientists have raised.

Example 2: Instant replication of results
About a month ago, a paper came out in the Journal of the American Chemical Society, which suggested that a reductant acted as an oxidant in a particular chemical reaction.
Paul Docherty, of the Totally Synthetic blog, posted about a different paper from the same issue of the journal the day it came out. The very second comment on that post pointed out that something must be fishy about the reductant-as-oxidant paper. And then all hell broke lose in the comments!
Carmen Drahl, in the August 17 issue of C&EN describes what happened next:

Docherty, a medicinal chemist at Arrow Therapeutics, in London, was sufficiently intrigued to repeat one of the reactions in the paper. He broadcast his observations and posted raw data on his blog for all to read, snapping photos of the reaction with his iPhone as it progressed. Meanwhile, roughly a half-dozen of the blog’s readers did likewise, each with slightly different reaction conditions, each reporting results in the blog’s comment section.

The liveblogging of the experiment by Paul and commenters is here. Every single one of them failed to replicate the findings and they came up with possible reasons why the authors of the paper got an erroneous result. The paper, while remaining on the Web, was not published in the hard-copy version of the journal and the initial authors, the journal and the readers are working on figuring out exactly what happened in the lab – which may actually be quite informative and novel in itself.
Compare and contrast
So, what happened in these two examples?
In both, a paper with presumably erroneous data or conclusions passed peer-review and got published.
In both, someone else in the field noticed it and failed to replicate the experiments.
In both, that someone tried to alert the community that is potentially interested in the result, including the original authors and the journal editors, in order to make sure that people are aware of the possibility that something in that paper is wrong.
In the first example, the authors and editors obstructed the process of feedback. In the second, the authors and editors were not in a position to obstruct the process of feedback.
In the first example, the corrector/replicator tried to go the traditional route and got blocked by gatekeepers. In the second example, the corrector/replicator went the modern route – bypassing the gatekeepers.
If you had no idea about any of this, and you are a researcher in a semi-related field moving in, and you find the original paper via search, what are the chances you will know that the paper is being disputed?
In the first example – zero (until last night). In the second example – large. But in both cases, in order to realize that the paper is contested, one has to use Google! Not just read the paper itself and hope it’s fine. You gotta google it to find out. Most working scientists do not do that yet! Not part of the research culture at this time, unfortunately.
If the Comment was published in the first example, chances that a reader of the paper will then search the later issues of the journal seeking comments and corrections are very small. Thus even if the Comment (and Reply by authors) was published, nobody but a very small inner circle of people currently working on that very problem will ever know.
Back in grad school I was a voracious reader of the literature in my field, including some very old papers. Every now and then I would bump into a paper that seemed really cool. Then I would wonder why nobody ever followed up or even cited it! I’d ask my advisor who would explain to me that people tried to replicate but were not successful, or that this particular author is known to fudge data, etc. That is tacit knowledge – something that is known only by a very small number of people in an Inner Circle. It is a kind of knowledge that is transmitted orally, from advisor to student, or in the hallways at meetings. People who come into the field from outside do not have access to that information. People in the field who live in far-away places and cannot afford to come to conferences do not have access to that information.
Areas of research also go in and out of fashion. A line of research may bump into walls and the community abandons it only to get picked up decades later once the technological advances allow for further studies of the phenomenon. In the meantime, the Inner Circle dispersed, and the tacit knowledge got lost. Yet the papers remain. And nobody knows any more which paper to trust and which one not to. Thus one cannot rely on published literature at all! It all needs to be re-tested all over again! Yikes! How much money, time and effort would have to be put into that!?
Now let’s imagine that lines of research in our two Examples go that way: get abandoned for a while. Let’s assume now that 50 years from now a completely new generation of scientists rediscovers the problem and re-starts studying it. All they have to go with are some ancient papers. No Comment was ever published about the paper in the first Example. Lots of blogging about both afterwards. But in 50 years, will those blogs still exist, or will all the links found on Google (or whatever is used to search stuff online in 50 years) be rotten? What are the chances that the researchers of the future will be able to find all the relevant discussions and refutation of these two papers? Pretty small, methinks.
But what if all the discussions and refutations and author replies are on the paper itself? No problem then – it is all public and all preserved forever. The tacit knowledge of the Inner Circle becomes public knowledge of the entire scientific community. A permanent record available to everyone. That is how science should be, don’t you think?
You probably know that, right now, only BMC, BMJ and PLoS journals have this functionality. You can rate articles, post notes and comments and link/trackback to discussions happening elsewhere online. Even entire Journal Clubs can happen in the comments section of a paper.
Soon, all scientific journals will be online (and probably only online). Next, all the papers – past, present and future – will become freely available online. The limitations of paper will be gone and nothing will prevent publishers from implementing more dynamic approaches to scientific publishing – including on-paper commentary.
If all the journals started implementing comments on their papers tomorrow I would not cry “copycats!” No. Instead, I’d be absolutely delighted. Why?
Let’s say that you read (or at least skim) between a dozen and two dozen papers per day. You found them through search engines (e.g., Google Scholar), or through reference managers (e.g., CiteULike or Mendeley), or as suggestions from your colleagues via social networks (e.g, Twitter, FriendFeed, Facebook). Every day you will land on papers published in many different journals (it really does not matter any more which journal the paper was published in – you have to read all the papers, good or bad, in your narrow domain of interest). Then one day you land on a paper in PLoS and you see the Ratings, Notes and Comments functionality there. You shake your head – “Eh, what’s this weird newfangled thing? What will they come up with next? Not for me!” And you move on.
Now imagine if every single paper in every single journal had those functionalities. You see them between a dozen and two dozen times a day. Some of the papers actually have notes, ratings and comments submitted by others which you – being a naturally curious human being – open and read. Even if you are initially a skeptical curmudgeon, your brain will gradually get trained. The existence of comments becomes the norm. You become primed….and then, one day, you will read a paper that makes you really excited. It has a huge flaw. It is totally crap. Or it is tremendously insightful and revolutionary. Or it is missing an alternative explanation. And you will be compelled to respond. ImmediatelyRightThisMoment!!!11!!!!11!!. In the old days, you’d just mutter to yourself, perhaps tell your students at the next lab meeting. Or even brace yourself for the long and frustrating process (see Example 1) of submitting a formal Comment to the journal. But no, your brain is now primed, so you click on “Add comment”, you write your thoughts and you click “Submit”. And you think to yourself “Hey, this didn’t hurt at all!” And you have just helped thousands of researchers around the world today and in the future have a better understanding of that paper. Permanently. Good job!
That’s how scientific self-correction in real time is supposed to work.


A run-down of good recent stuff, highly recommended for your weekend reading and bookmarking:
PLoS One: Interview with Peter Binfield:

…In my view PLoS ONE is the most dynamic, innovative and exciting journal in the world, and I am proud to work on it.
In many ways PLoS ONE operates like any other journal however it diverges in several important respects. The founding principle of PLoS ONE was that there are certain aspects of publishing which are best conducted pre-publication and certain aspects which are best conducted post-publication. The advent of online publishing has allowed us to take a step back and re-evaluate these aspects of how we publish research, without the burden of centuries of tradition. In this way, we have been able to experiment with new ways of doing things which may result in dramatic improvements in the entire process of scholarly publication.
The most important thing which has come out of this premise is that unlike almost every other journal in the world, we make no judgment call whatsoever on the ‘impact’ or ‘significance’ or ‘interest level’ of any submission. What this means is that if an article appropriately reports on well-conducted science, and if it passes our peer review process (which determines whether it deserves to join the scientific literature) then we will publish it. In this way, no author should ever receive the message that their article is scientifically sound but ‘not interesting enough’ for our journal, or that their article is ‘only suited to a specialized audience’. As a result, we short circuit the vicious cycle of “submit to a ‘top tier’ journal; get reviewed; get rejected; submit to the next journal down the list; repeat until accepted” and we are therefore able to place good science into the public domain as promptly as possible, with the minimum of burden on the academic community….

The evolution of scientific impact (also a good FriendFeed thread about it):

What is clear to me is this – science and society are much richer and more interconnected now than at any time in history. There are many more people contributing to science in many more ways now than ever before. Science is becoming more broad (we know about more things) and more deep (we know more about these things). At the same time, print publishing is fading, content is exploding, and technology makes it possible to present, share, and analyze information faster and more powerfully.
For these reasons, I believe (as many others do) that the traditional model of peer-reviewed journals should and will necessarily change significantly over the next decade or so.

A threat to scientific communication (read excellent responses by Peter Murray-Rast and Bjoern Brembs and a thread on FriendFeed):

Sulston argues that the use of journal metrics is not only a flimsy guarantee of the best work (his prize-winning discovery was never published in a top journal), but he also believes that the system puts pressure on scientists to act in ways that adversely affect science – from claiming work is more novel than it actually is to over-hyping, over-interpreting and prematurely publishing it, splitting publications to get more credits and, in extreme situations, even committing fraud.
The system also creates what he characterises as an “inefficient treadmill” of resubmissions to the journal hierarchy. The whole process ropes in many more reviewers than necessary, reduces the time available for research, places a heavier burden on peer review and delays the communication of important results.

Why do we still publish scientific papers?:

I agree with the need to filter papers, but I want to be in control of the filter. I don’t want editors to control my filter and I definitely don’t want a monopolist like Thomson to muck up my filter. I don’t care where something is published, if it’s in my direct field I need to read it, no matter how bad it is. If a paper is in my broader field, I’d apply some light filtering, such as rating, comments, downloads, author institute, social bookmarks, or some such. If the paper is in a related field, I’d like to only read reviews of recent advances. If it’s in an unrelated field, but one I’m interested in nonetheless, I’d only want to see the news-and-views article, because I wouldn’t understand anything else anyway. For everything else, titles, headlines or newsreports are good enough for browsing. All of this can be done after publishing and certainly doesn’t require any artificial grouping by pseudo-tags (formerly called journals).

Science Jabberwocky (how to read/understand a scientific paper when you don’t know the technical terms):

I have to confess that in areas outside mine, there seems to be a terrible array of words no more obvious than ‘brillig’ and ‘slithy’. And words that look familiar, like ‘gyre and gimble’, but which don’t look like they are supposed to mean what I’m used to them meaning.

Media tracking:

The theropod behaviour paper that I have been boring you all with this last week or so has been the first time I have had decent control over the media access to my work and by extension the first time I have had a good idea of what happened to the original press release. I know what I sent to whom and when and thus can fairly easily track what happened afterwards to record the spread and exchange of information from that origin. In the past on the Musings I have targeted inaccuracies in news reports of scientific stories but without knowing the exact details of a story (I may have access to the press release but without knowing who it went to). Well, not so this time and as a result the pattern of reporting I can see is both interesting and informative both from understanding how the media works and knowing how to get your own work publicised.

Rapid evolution of rodents: another PLoS ONE study in the media:

Although media attention and coverage is not, and should certainly not be, the only criterion for scientific “quality” (whatever that is!), it is further testimony of the advantage to publish in “Open Acess”-journals in general, and PLoS ONE in particular. This study is also interesting because it shows the value of museum collections as a source for ecological and evolutionary research, a point that Shawn Kuchta has repeatedly emphasized in our lab-meetings (and which I completely agree with, of course).

20 Quick Points from ‘The World Is Open: How Web Technology Is Revolutionizing Education’:

9. Open Access Journals (Opener #5): The publishing world is increasing becoming open access. Open access journals in the healthcare area provide invaluable information to those in the developing world. The Public Library of Science (PLoS) offers free peer-reviewed scientific journals. Scientists who publish in PLoS journals might present their work in SciVee. SciVee allows the user to hear or see the scientist explain his or her research in what is known as pubcasts.

Pedagogy and the Class Blog:

I’ve been using blogs in my teaching for several years now, so I wanted to share a few ideas that have worked for me. I’m no expert and I’m still casting about for solutions to some of the more nagging problems, but after thirteen course blogs spread across seven semesters (I just counted!), I have obtained a small measure of experience. In other words, I keep making mistakes, but at least not the same ones over and over.

Practicing Medicine in the Age of Facebook:

In my second week of medical internship, I received a “friend request” on Facebook, the popular social-networking Web site. The name of the requester was familiar: Erica Baxter. Three years earlier, as a medical student, I had participated in the delivery of Ms. Baxter’s baby. Now, apparently, she wanted to be back in touch…..

Are young people of today Relationally Starved?:

The more I toss it around, I’m not so sure that our students are “relationally starved.” I just think that relationships look much different today than they have in generations past. Their relationships are more fluid and maybe a little more fragile. It is obvious that advances in technology have changed the way relationships are built and maintained (it has for me). This doesn’t mean that children aren’t in need of the same nurturing and love that we might have had, but there are other layers that we need to ask them about. And I think that might be the key, ASK THEM!

The New Yorker vs. the Kindle:

Now, let’s imagine for a moment that we are back in the 15th century, to be precise just shortly after 1439, when Johannes Gensfleisch zur Laden zum Gutenberg invented movable type printing. I can only imagine the complaints that Baker would have uttered in the local paper (which was, of course, copied by hand from the original dictation). What? Only one title on the catalog? (The Bible.) Oh, and the fonts are sooo boring compared to handwriting. And no colors! And the quality of the drawings, simply unacceptable. This movable type printing thing will never ever replace the amanuenses, it will simply die as yet another “modern invention” and things will keep being just the same as they have been throughout what they at the time didn’t yet call the Middle Ages.

The New Yorker & The News Biz:

After many years, I am finally subscribing to the New Yorker again. Not in print, but via their Digital Reader. I’m blogging about it because I like their model: the Digital Reader adds something I wouldn’t get from the library version, and I feel like this new model bears watching as we migrate from print to online.

The psychology of reading for pleasure:

According to a neurological study that Nell performed, processing demands are higher with books than other media (movies, television) but that also means that when you are absorbed in a book, you are more likely to block out distractions. While readers describe being absorbed in a book as “effortless,” their brains are actually intensely active. As one critic said, this is not an escape from thinking, it’s an escape into thinking – intensely, and without distraction.

How Twitter works in theory:

The key to Twitter is that it is phatic – full of social gestures that are like apes grooming each other. Both Google and Twitter have little boxes for you to type into, but on Google you’re looking for information, and expecting a machine response, whereas on Twitter you’re declaring an emotion and expecting a human response. This is what leads to unintentionally ironic newspaper columns bemoaning public banality, because they miss that while you don’t care what random strangers feel about their lunch, you do if its your friend on holiday in Pompeii.
For those with Habermas’s assumption of a single common public sphere this makes no sense – surely everyone should see everything that anyone says as part of the discussion? In fact this has never made sense, and in the past elaborate systems have been set up to ensure that only a few can speak, and only one person can speak at a time, because a speech-like, real-time discourse has been the foundational assumption.
Too often this worldview has been built into the default assumptions of communications online; we see it now with privileged speakers decrying the use of anonymity in the same tones as 19th century politicians defended hustings in rotten boroughs instead of secret ballots. Thus the tactics of shouting down debate in town halls show up as the baiting and trollery that make YouTube comments a byword for idiocy; when all hear the words of one, the conversation often decays.

Blogging Evolution (PDF):

I describe the general characteristics of blogs, contrasting blogs with other of WWW formats for self-publishing. I describe four categories for blogs about evolutionary biology: “professional,” “amateur,” “apostolic,” and “imaginative.” I also discuss blog networks. I identify paradigms of each category. Throughout, I aim to illuminate blogs about evolutionary biology from the point of view of a
user looking for information about the topic. I conclude that blogs are not the best type of source for systematic and authoritative information about evolution, and that they are best used by the information-seeker as a way of identifying what issues are of interest in the community of evolutionists and for generating research leads or fresh insights on one’s own work.

What Do Mathematicians Need to Know About Blogging?:

Steven Krantz asked me to write an opinion piece about math blogging in the Notices of the American Mathematical Society. I asked if I could talk about this column on my blog, and even have people comment on drafts of it before it comes out in the Notices. He said okay. So, just to get the ball rolling, let me ask: what do you think mathematicians need to know about blogging?

Five Key Reasons Why Newspapers Are Failing and Five Key Reasons Why Newspapers Are Failing, pt. 2:

Journalists are pretty good at working the scene of a disaster. They’ll tell you what happened, who did it, and why.
But when it comes to the disaster engulfing their own profession, their analysis is less rigorous. An uncharacteristic haze characterizes a lot of the reporting and commentary on the current crisis of the industry.
It could have been brought on by delicacy, perhaps romanticism. And since it is not just any crisis, but a definitive one–one that seems to mean an end to the physical papers’ role in American life as we have come to know it–perhaps there’s a little bit of shell-shock in the mix as well.

Online Community Building: Gardening vs Landscaping:

The Gardener creates an ecosystem open to change, available to new groups, and full of fresh opportunities to emerge naturally. The approach is focused on organic collaboration and growth for the entire community. The gardener is simply there to help, cultivate, and clear the weeds if/when they poke up.
The Landscaper creates an ecosystem that matches a preconceived design or pattern. The approach is focused on executing a preconceived environment, regardless of how natural or organic it may be for the larger area. The landscaper is there to ensure that everything stays just as planned.

Don’t Be Such a Scientist: Talking Substance in an Age of Style (book review):

So I end up feeling a bit torn. He’s telling us “Don’t be such a scientist”, and it’s true that there are many occasions when the scientific attitude can generate unnecessary obstacles to accomplishing our goals. At the same time, though, I want to say “Do be such a scientist”, because it’s part of our identity and it makes us stand out as unusual and, like Randy, interesting, even if it sometimes does make us a bit abrasive. But, you know, some of us revel in our abrasiveness; it’s fun.

This has also been in the news a lot last week:
Threats to science-based medicine: Pharma ghostwriting
Wyeth, ‘Ghost-Writing’ and Conflict of Interest
More On Ghostwriting, Wyeth and Hormone Replacement Therapy
Wyeth’s ghostwriting skeletons yanked from the closet
Ghostwriters in the sky
Quickie Must-Read Link … (probably the best commentary of them all).
Several recent posts on the topic dear to my heart – the so-called “civility” in public (including online) discourse:
How Creationism (and Other Idiocies) Are Mainstreamed:

One of the things that has enabled the mainstreaming of various idiocies, from altie woo, to creationism, to global warming denialism is mainstream corporate media’s inability to accurately describe lunacy. For obvious reasons, ‘family-friendly’ newspapers and teevee can’t call creationists, birthers, or deathers batshit lunatic or fucking morons. This is where ‘civility’ (beyond the basic norms of decency when dealing with the mentally ill) and pretensions of ‘balance’ utterly fail.

Weekend Diversion: How to Argue:

You are, of course, free to argue however you like. But if you want to argue on my site, you’re really best off remembering this hierarchy, and staying as high as possible on it. Most of you do pretty well, but this has served me well in general, and I hope it helps you to see things laid out like this. And if not, at least you got a great song out of it!

When an image makes an argument:

Along similar lines to a frequentist interpretation of the strata, maybe this pyramid is conveying something about the ease or difficulty inherent in different types of engagement. It doesn’t take a lot of effort to call someone an asshat, but understanding her argument well enough to raise a good counterexample to it may take some mental labor. If this is the rhetorical work that the pyramidal layout does here, it may also suggest a corresponding hierarchy of people who have the mental skills to engage in each of these ways — making the people at the tippy-top of the pyramid more elite than those using the strategies from lower strata.

How to Argue…:

White men are sufficiently privileged enough to demand that they be treated respectfully while white women, at best, can expect to be presented with contradiction and counterargument. When I saw the category “responding to tone” I thought of the “angry black man” who, although perhaps right, is castigated for his anger and lack of civility for not conforming to the norms of white society. If you’re a non-white woman? Then, the best you can do is hope to not be denied food and shelter if you don’t fuck your husband enough (h/t to Free-Ride for pointing this article out), but you only expect to be part of the discussion if you’re allowed to be.
The call to civility is a frequent tactic to derail the discussion and is as much of an ad hominem attack as calling someone a cocknozzle. It fails to recognize the perspective of the other party or appreciate why they might be angry.

More on the topic:
Dr. Isis Learns to Argue:

I am lucky to have such thoughtful commenters. When I wrote the previous post I had no idea that bleeding from my vagina was clouding my judgement. Then, just when I thought I had cleared enough of the estrogen from my girl brain to understand, I learned that this was all a carefully planned tactic to teach me a lesson. Damn! I hate when that happens!

Weekend Diversion: How to argue…and actually accomplish something:

Here we arrive at the meat of the matter. Once having accomplished more than about 300 ms worth of consideration of a given topic, people are highly resistant to the idea that their rationale, conclusions and evidence base might actually be wrong. And the wronger the consideration might be, the more resistant to acknowledgment is the individual. We might think of this as the intrapersonal Overton window.

A Tale of Two Nations: the Civil War may have been won by the North, but in truth the South never emotionally conceded.:

The Civil War may have been won by the North, but in truth the South never emotionally conceded.
The Town Hall mobs, the birthers, the teabaggers are all part of that long line of “coded” agitators for the notions of white entitlement and “conservative values.”
Of course, this conservative viewpoint values cheap labor and unabated use of natural resources over technological and economic innovation. It also – and this is its hot molten core – fundamentally believes that white people are born with a divine advantage over people of other skin colors, and are chosen by God to lead the heathen hordes.
That a Town Hall mob is itself a heathen horde would never occur to the economically stressed whites who listen to the lies of the likes of Glenn Beck, Sean Hannity, Rush Limbaugh and Lou Dobbs. Lies that confirm an emotionally reinforcing worldview – however heinous – become truths for those in psychological need of feeling superior and chosen.

I remember an America where black men didn’t grow up to be President.:

And all of them are asking for their America back. I wonder which America that would be?
Would that be the America where the Supreme Court picks your president instead of counting all the votes? Would that be the America where rights to privacy are ignored? Would that be the America where the Vice President shoots his best friend in the face? Or would that be the America where an idiot from Alaska and a college drop-out with a radio show could become the torchbearers for the now illiterate Republican party?
I fear that would not be the America they want back. I fear that the America they want back is the one where black men don’t become President.
I remember that America. In that America people screaming at public gatherings were called out for what they were – an angry mob. Of course, they wore sheets to cover up their bad hair. Let’s be clear about something: if you show up to a town hall meeting with a gun strapped to your leg, the point you are trying to make isn’t a good one. Fear never produced anything worthwhile.

In America, Crazy Is a Preexisting Condition:

The tree of crazy is an ever-present aspect of America’s flora. Only now, it’s being watered by misguided he-said-she-said reporting and taking over the forest. Latest word is that the enlightened and mild provision in the draft legislation to help elderly people who want living wills — the one hysterics turned into the “death panel” canard — is losing favor, according to the Wall Street Journal, because of “complaints over the provision.”

Two oldies but goodies:
Atheists and Anger:

One of the most common criticisms lobbed at the newly-vocal atheist community is, “Why do you have to be so angry?” So I want to talk about:
1. Why atheists are angry;
2. Why our anger is valid, valuable, and necessary;
And 3. Why it’s completely fucked-up to try to take our anger away from us.

Atheists and Anger: A Reply to the Hurricane:

Now my replies to the critics. I suppose I shouldn’t bother, I suppose I should just let it go and focus on the love. But I seem to be constitutionally incapable of letting unfair or inaccurate accusations just slide. So here are my replies to some of the critical comments’ common themes.

The Privilege of Politeness:

One item that comes up over and over in discussions of racism is that of tone/attitude. People of Color (POC) are very often called on their tone when they bring up racism, the idea being that if POC were just more polite about the whole thing the offending person would have listened and apologized right away. This not only derails the discussion but also tries to turn the insults/race issues into the fault of POC and their tone. Many POC have come to the realization that the expectation of politeness when saying something insulting is a form of privilege. At the core of this expectation of politeness is the idea that the POC in question should teach the offender what was wrong with their statement. Because in my experience what is meant by “be polite” is “teach me”, teach me why you’re offended by this, teach me how to be racially sensitive and the bottom line is that it is no one’s responsibility to teach anyone else. And even when POC are as polite as possible there is still hostility read into the words because people are so afraid of being called racist that they would rather go on offending than deal with the hard road of confronting their own prejudices.

Open Access, Achievements and Looking Forward (video)

Ginny Barbour, Part 5: Open Access, Achievements and Looking Forward from PLoS on Vimeo.

PLoS Medicine’s Fifth Anniversary and Future Plans (video)

Ginny Barbour, Part 4: PLoS Medicine’s Fifth Anniversary and Future Plans from PLoS on Vimeo.

Open Access to Health Information (video)

Ginny Barbour, Part 3: PLoS Medicine Open Access to Health Information from PLoS on Vimeo.

PLoS ONE Blog Pick of the Month

It is time to announce the July winner. To see who won this time, you’ll have to go here.

Refocusing PLoS Medicine’s Editorial vision (video)

Launching and Running PLoS Medicine (video)