Category Archives: PLoS

Cameron Neylon on Article Level Metrics

On Vimeo:

Article-level Metrics from PLoS on Vimeo.

Praxis

Open Access and the divide between ‘mainstream’ and ‘peripheral’ science (also available here and here) by Jean-Claude Guédon is a Must Read of the day. Anyone have his contact info so I can see if he would come to ScienceOnline’10?
There is a whole bunch of articles about science publication metrics in the latest ESEP THEME SECTION – The use and misuse of bibliometric indices in evaluating scholarly performance. Well worth studying. On article-level metrics, there are some interesting reactions in the blogosphere, by Deepak Singh, Bjoern Brembs, Duncan Hull, Bill Hooker and Abhishek Tiwari. Check them out. Of course, all of those guys are also on FriendFeed where more discussion occured.
Can someone use FOIA to sneak a peak into your grant proposal and check-out your preliminary data? See the discussion on DrugMunkey blog, on Dr.Isis’ blog and on Heather Etchevers’ blog. My beef: don’t use the term “Open Access” for this as it is not related. This is not even Open Notebok Science – which, and I am on record in several places about this – MUST be voluntary and does not fit everyone.

Gavin Yamey, the Senior Magazine Editor of PLoS Medicine, is currently on sabbatical from the journal after being awarded a “mini-fellowship” from the Kaiser Family Foundation to undertake a project as a reporter in East Africa and Sudan.

His first two posts about this: Reporting from East Africa and Sudan and Far from the reach of global health programs.
The “article of the future” by Cell/Elsevier, analyzed by DrugMonkey, Kent Anderson, Marshall Kirkpatrick and Martin Fenner.

Measuring scientific impact where it matters

Everyone and their grandmother knows that Impact Factor is a crude, unreliable and just wrong metric to use in evaluating individuals for career-making (or career-breaking) purposes. Yet, so many institutions (or rather, their bureaucrats – scientists would abandon it if their bosses would) cling to IF anyway. Probably because nobody has pushed for a good alternative yet. In the world of science publishing, when something needs to be done, usually people look at us (that is: PLoS) to make the first move. The beauty of being a path-blazer!
So, in today’s post ‘PLoS Journals – measuring impact where it matters’ on the PLoS Blog and everyONE blog, PLoS Director of Publishing Mark Patterson explains how we are moving away from the IF world (basically by ignoring it despite our journals’ potential for marketing via their high IFs, until the others catch up with us and start ignoring it as well) and focusing our energies in providing as many as possible article-level metrics instead. Mark wrote:

Article-level metrics and indicators will become powerful additions to the tools for the assessment and filtering of research outputs, and we look forward to working with the research community, publishers, funders and institutions to develop and hone these ideas. As for the impact factor, the 2008 numbers were released last month. But rather than updating the PLoS Journal sites with the new numbers, we’ve decided to stop promoting journal impact factors on our sites all together. It’s time to move on, and focus efforts on more sophisticated, flexible and meaningful measures.

In a series of recent posts, Peter Binfield, managing editor of PLoS ONE, explained the details of article-level metrics that are now employed and displayed on all seven PLoS journals. These are going to be added to and upgraded regularly, whenever we and the community feel there is a need to include another metric.
What we will not do is try to reduce these metrics to a single number ourselves. We want to make all the raw data available to the public to use as they see fit and we will all watch as the new standards emerge. We feel that different kinds of metrics are important to different people in different situations, and that these criteria will also change over time.
A paper of yours may be important for you to be seen by your peers (perhaps for career-related reasons which are nothing to frown about) in which case the citation numbers and download statistics may be much more important than the bookmarking statistics or the media/blog coverage or the on-article user activity (e.g., ratings, notes and comments). At least for now – this may change in the future. But another paper you may think would be particularly important to be seen by physicians around the world (or science teachers, or political journalists, etc.), in which case media/blog coverage numbers are much more important for you than citations – you are measuring your success by how broad an audience you could reach.
This will differ from paper to paper, from person to person, from scientific field to field, from institution to institution, and from country to country. I am sure there will be people out there who will try to put those numbers into various formulae and crunch the numbers and come up with some kind of “summary value” or “article-level impact value” which may or may not become a new standard in some places – time will tell.
But making all the numbers available is what is the most important for the scientific community as a whole. And this is what we will provide. And then the others will have to start providing them as well because authors will demand to see them. Perhaps this is a historic day in the world of science publishing….

PLoS ONE Academic Editor Interview – Peter Sommer

It was hectic during the travels, but I managed to interview Peter Sommer, PLoS ONE Section Editor for Virology anyway – in the age of the Internet, one can be connected everywhere. We posted the interview on everyONE blog yesterday.

Open Access in Belgrade

As you know, I gave two lectures here in Belgrade. The first one, at the University Library on Monday, and the second one at the Oncology Institute of the School of Medicine at the University of Belgrade. As the two audiences were different (mainly librarians/infoscientists at the first, mainly professors/students of medicine at the second) I geared the two talks differently.
You can listen to the audio of the entire thing (the second talk) here, see some pictures (from both talks) here and read (in Serbian) a blog post here, written by incredible Ana Ivkovic who organized my entire Belgrade “tour” this year.
The second talk was, at the last minute, moved from the amphitheater to the library, which was actually good as the online connection is, I hear, much much better in the library. Library got crowded, but in the end everyone found a chair. What I did, as I usually do, was to come in early and open up all the websites I wanted to show in reverse chronological order, each in a separate window. Thus, the site I want to show first is on top at the beginning. When I close that window, the second site is the top window, then the third, etc. Thus I do the talk by closing windows instead of opening them (and hoping and praying that would not take too much time).
Knowing how talks usually go in the States, I prepared to talk for about 50 minutes. But, when I hit the 50 minute mark, I realized that nobody was getting restless – everyone was looking intently, jotting down URLs of sites I was showing, nodding….so I continued until I hit 60 minutes as which time I decided to wrap up and end. Even then, nobody was eager to get up and leave. I was hoping I’d get a question anyway….and sure, I got 45 minutes of questions. Then another 20 minutes or so of people approaching me individually to ask questions….
I used the Directory of Open Access Journals as the backdrop to give a brief history of the Open Access movement, the difference between Free Access and Open Access and the distinction between Green OA and Gold OA.
Then I used the PLoS.org site to explain the brief history of PLoS and the differences between our seven journals. Of course, this being medical school, I gave some special consideration to PLoS Medicine.
Then I used the Ida – Darwinius massillae paper to explain the concept of PLoS ONE, how our peer-review is done and to show/demonstrate the functionalities on our papers, e.g., ratings, notes, comments, article-level metrics and trackbacks.
Then I used the Waltzing Matilda paper to enumerate some additional reasons why Open Access is a Good.Thing.
Trackbacks were also a good segue into the seriousness by which the scientific and medical community is treating blogs these days. I showed Speaking of Medicine and EveryONE blog as examples of blogs we use for outreach and information to our community.
I showed and explained ResearchBlogging.org (which they seemed to particularly be taken with and jotted down the URL), showed and explained the visibility and respect of such blogging networks as Scienceblogs.com and Nature Network and then Connotea as an example of various experiments in Science 2.0 that Nature is conducting.
I put in a plug for ScienceOnline conferences and the Open Laboratory anthologies as yet another proof how seriously Science 2.0 and science blogging is now being taken in the West. Then showed 515 scientists on Twitter, The Life Scientists group and Medicine 2.0 Microcarnival on FriedFeed as examples of the ways scientists are now using microblogging platforms for communication and collaboration. I pointed out how Pawel Szczesny, through blogging and FriendFeed, got collaborations, publications, and in the end, his current job.
Then I described Jean-Claude Bradley’s concept (and practice) of Open Notebook Science and showed OpenWetWare as a platform for such work. I pointed out that Wikipedia and wiki-like projects are now edited by scientists, showing the examples of A Gene Wiki for Community Annotation of Gene Function, BioGPS and ChemSpider and ended by pointing out a couple of examples of the ways the Web allows citizen scientists to participate in massive collaborative research projects
But probably the most important part of the talk was my discussion of the drawbacks of Impact Factor and the current efforts to develop Article-level metrics to replace it – something that will be particularly difficult to change in developing countries yet is essential especially for them to be cognizant of and to move as fast as they can so as not to be left behind as the new scientific ecosystem evolves.

Waltzing Matilda – why were the three Australian dinosaurs published in PLoS ONE?

As I was traveling, I only briefly mentioned the brand new and exciting paleontology paper in PLoS ONE – New Mid-Cretaceous (Latest Albian) Dinosaurs from Winton, Queensland, Australia that was published on Thursday. Bex has written an introduction and will post a Media/Blog coverage (of which there was a lot!) summary probably tomorrow.
The fossils were discovered, cleaned and analyzed by the Australian Age Of Dinosaurs non-profit organization, with a help of thousands of volunteers – the ‘citizen scientists’. You can learn more from their press release.
The importance of the publication of this paper from the angle of its scientific significance has been covered by several bloggers already. Also, several notice how good it is that the paper was published in an Open Access online-only journal. For example, Andy Farke writes:

This paper is a fantastic example of the real benefits of an on-line, open access journal like PLoS ONE. Without page limitations, the authors were allowed to truly monograph the heck out of the bones. Virtually every element is illustrated from multiple angles (with high resolution photos downloadable from the website!) and accompanied by thorough text descriptions and measurements. The editors of most journals would freak out over such a “waste” of precious space – but I have a feeling that future researchers are going to thank the authors for their thoroughness. As a PDF, the paper weighs in at 51 pages – and this doesn’t include the supplementary information!

The lead author Scott Hocknull, in an interview for us, said:

“One of my major motivations for submitting to PLoS ONE was the fact that my research will reach a much wider community, including the hundreds of volunteers and public who gave their time and money to the development of natural history collections. They are the backbone of our work (excuse the pun) and they usually never get to see their final product because they rarely subscribe to scientific journals.”

In the comment on the post at Sauropod Vertebra Picture of the Week, Scott Hocknull said:

This project is almost a 100% volunteer effort, with thousands of volunteer preppers working endlessly to get the bones ready for publication. This was one of my main reasons for choosing PLoS ONE to publish in. One of my others was the opportunity to provide detail images and descriptions (as best I can).
Most of our volunteers have no access to scientific journal subscriptions, therefore having it online and free for them to look at meant that they could see for themselves the fruits of their labours. They need more credit for the beautiful bones than I.

And all of you can read it for free as well – all 51 pages of it, plus all the great images and supplemental information. And you can add ratings, notes, comments and trackbacks on the paper as well.

Banjo, Clancy and Matilda

I am running to the Lindau Harbor for the last day’s trip and will be offline for the next 12 or so hours. So I don’t have time for a long post right now about this cool new dinosaur paper we just published in PLoS ONE.
So please check it out – see what it is all about and read the paper itself.

The winner of the PLoS ONE Blog Pick of the Month for June 2009….

….is – you’ll have to go here to see.

ClockCast #1

A couple of months ago, my SciBling David Dobbs and I recorded about an hour of discussion for Bloggingheads.tv. We talked mainly about science journalism, but also about journalism in general, about the future of the book, etc.
Unfortunately, Dave’s half of the file got broken beyond repair, so the show never aired. I kept my half of the file and did not really know what to do with it. So, recently I downloaded Audacity and tried my hand at editing the audio part of the file, trying to cut out the silences (during which Dave was talking) and dialogues that would be intelligible without Dave’s part of the file.
Here is the very first part, just a brief (1 minute and 38 seconds) introduction to myself and my job. Thus, my very first podcast, which (after popular vote on FriendFeed decided) will be called ClockCast. I will try to find some time (as I am learning to tackle Audacity!) to edit and post the rest of the file in the near future (I am not, for now, promising any kind of regularity for posting these, until I feel comfortable with the medium and the technology):

ClockCast1.wav –

PLoS ONE: Background, Future Development, and Article-Level Metrics

If you are in any way following the developments in the world of science publishing, you have probably heard about the new effort by PLoS to establish article-level metrics for scientific papers (instead of the dreadful and erronoeus Impact Factor).
Today, Peter Binfield, the Managing Editor of PLoS ONE, published a paper entitled “PLoS ONE: Background, Future Development, and Article-Level Metrics” that covers all of that in great detail. The paper is, of course, Open Access, so you can download the PDF for free here and the related PowerPoint slideshow here.
Peter says:

The paper goes into a lot of detail on the history and inner workings of PLoS ONE, and so if you are at all interested in where our journal came from; how it operates; and where it is going in the future, then it is required reading.

I second that! A Must Read!
Also, as this is a peer-reviewed article, if you blog about it, and if you use the BPR3 icon, the link to your blog post will show up on the ResearchBlogging.org aggregator and will thus be eligible for the Blog Pick Of The Month for June.
You can also discuss this article on FriendFeed.

Journal Clubs on PLoS ONE articles

What does it mean – a Journal Club? Read here and, if you want to do one, contact me.

Caryn Shechtman: A Blogger Success Story (an interview with Yours Truly)

You may have noticed a couple of days ago that Caryn Shechtman posted an interview with me on the New York blog on Nature Network. Then, Caryn and Erin and I thought it might be a good idea to have the entire interview reposted here, for those who missed it. So, proceed under the fold:

Continue reading

Speaking of Medicine

If you read this blog even superficially, you are probably aware of everyONE, the community blog of PLoS ONE. The blog has been so successful, that our colleagues at PLoS Medicine have decided to follow our example and start their own community blog.
And, today they are ready to reveal – Speaking of Medicine. Go check it out – click on all the tabs on top for all the additional information. Bookmark and subscribed. Spread the word about it. And come back often and use it – and post comments.

The May Blog Pick Of The Month at PLoS ONE is….

…to be found on the everyONE blog.

Article-Level Metrics (at PLoS and beyond)

Pete Binfield, the Managing Editor of PLoS ONE, presented a webinar about article-level metrics to NISO – see also the blog post about it:

Commenting on scientific papers

There have been quite a few posts over the last few days about commenting, in particular about posting comments, notes and ratings on scientific papers. But this also related to commenting on blogs and social networks, commenting on newspaper online articles, the question of moderation vs. non-moderation, and the question of anonymity vs. pseudonymity vs. RL identity.
You may want to re-visit this old thread first, for introduction on commenting on blogs.
How a 1995 court case kept the newspaper industry from competing online by Robert Niles goes back into history to explain why the comments on the newspaper sites tend to be so rowdy, rude and, frankly, idiotic. And why that is bad for the newspapers.
In Why comments suck (& ideas on un-sucking them), Dan Conover has some suggestions how to fix that problem.
Mr. Gunn, in Online Engagement of Scientists with the literature: anonymity vs. ResearcherID tries to systematize the issues in the discussion about commenting on scientific papers which has the opposite problem from newspapers: relatively few people post comments.
Christina Pikas responds in What happens when you cross the streams? and Dave Bacon adds more in Comments?…I Don’t Have to Show You Any Stinkin’ Comments!
You should now go back to the analysis of commenting on BMC journals and on PLoS ONE, both by Euan Adie.
Then go back to my own posts on everyONE blog: Why you should post comments, notes and ratings on PLoS ONE articles and Rating articles in PLoS ONE.
Then, follow the lead set by Steve Koch and post a comment – break the ice for yourself.
Or see why T. Michael Keesey posted a couple of comments.
You may want to play in the Sandbox first.
I am watching all the discussions on the blog posts (as well as on FriendFeed) with great professional interest, of course. So, what do you think? Who of the above is right/wrong and why? Is there something in Conover’s suggestions for newspapers that should be useful for commenting on scientific papers? What are your suggestions?

My interviews with Radio Belgrade

Last year in May, when I visited Belgrade, I gave interviews with Radio Belgrade, talking about science publishing, Open Access, science communication and science blogging. The podcasts of these interviews – yes, they are in Serbian! – are now up:
Part 1
Part 2
I know that this blog has some ex-Yugoslavs in its regular audience, people who can understand the language. I hope you enjoy the interviews and spread the word if you like them.

Only a few days left…

…until I pronounce the Blog Post Of The Month for May. Make sure your post is aggregated on ResearchBlogging.org. There are 33 entries there so far – make sure yours shows up there by May 31st at midnight EST.

Night, night, Ida…

Some 47 million years ago, Ida suffocated in the volcanic ashes. I feel the same way at the end of this week – I need to get some air. And some sleep.
But watching the media and blog coverage of the fossil around the clock for a few days was actually quite interesting, almost exhilarating – and there are probably not as many people out there who, like me, read pretty much everything anyone said about it this week. Interestingly, my own feel of the coverage was different if I assumed an angle of a scientist, an angle of an interested student of the changes in the media ecosystem, and an angle of a PLoS employee. It is far too early to have any clear thoughts on it at this point.
But if you want to catch up with me, I have put together a sampling of the blog and media coverage over on the everyONE blog.

Wow! Check Google.com

…and you’ll see this:
ida google.JPG

Introducing Ida – the great-great-great-great-grandmother (or aunt)

Another super-cool day at PLoS (one of those days when I wish I was not telecommuting, but sharing in the excitement with the colleagues at the Mothership) – the publication of a very exciting article describing a rarely well-preserved fossil of a prehistoric primate in a lineage to which we all belong as well:
Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology by Jens L. Franzen, Philip D. Gingerich, Jörg Habersetzer, Jørn H. Hurum, Wighart von Koenigswald and B. Holly Smith
The fossil, named Ida (the scientific name is Darwinius masillae, a new genus), was discovered in Messel Pit, Germany and lived around 47 million years ago. The fossil is 95% complete – an incredibly complete fossil for an early primate – and along with the skeleton also contains the outline of the body and the contents of the gut. From such rich information, the scientists were able to deduce that Ida was a herbivorous female of about nine months of age.
Ida fig-s62.jpg
[The image is Fig. S6 of the PLoS ONE article, published under the Creative Commons Attribution License; any reuse should cite the authors and journal.]
Unlike lemurs, Darwinius masillae does not have a “toothcomb” and a “grooming claw,” but like primates in the lineage that also contains humans, Ida has opposable big toes, nail-bearing fingers and toes, and a foot bone called the talus bone.
Check out Bex’s blog post on everyONE for more details as well as the interactive Ida website and, of course, read the paper itself – 27 pages of details, Open Access, thus free for all to see!
As always, you should rate the article, post notes and comments and send trackbacks when you blog about this paper. You can also easily place this article on various social services (CiteULike, Connotea, Stumbleupon, Facebook, Digg and Mendeley) with just one click. Bex and I will collect all the media and blog coverage and post the links to the best on everyONE blog later this week, and that will be linked from the PLoS ONE homepage as well.
I would like to use this opportunity to thank the PLoS ONE production team who did a tremendous job in getting the paper out in record time. Despite the paper being available for only minutes, the mainstream media has already run with the story. I expect that science bloggers, with their expertise, will provide more detailed and in-depth coverage of the paper (and skip the silly “missing link” trope) once they digest the scientific information in the paper.

Continue reading

Trackbacks – the hows and the whys – on PLoS journals’ articles

Just read it here, then bookmark it for the next time you write a blog post about a PLoS paper…

Envelope, please!

Blog Post Of The Month for April 2009 goes to…..

PLoS Medicine is Five

Five years ago, PLoS Medicine, the second journal in the PLoS stable, sent its first call for submissions. It has quickly gained reputation as one of the top medical journals.
In the editorial published last night, the Editors look back at the five years so far, and also look forward into the future:

In the age of the Internet, five years can seem like an eternity. PLoS Medicine issued its first call for papers five years ago and the inaugural issue went live online five years ago this October–for those of you who are nostalgic, check out the original call for papers [1]. Anniversaries often prompt reflection, and over the past few months we’ve taken a close look at our original plans for PLoS Medicine, what’s happened since the journal launched, and most importantly how the journal should evolve in the future. We now propose a refocusing of the journal’s priorities that will, we believe, align them more closely with the world’s health priorities…

So, what is the vision for the future?

The PLoS Medicine editors also emphasize the need to look beyond just the biological causes of disease. As the world faces up to the challenges of a changing climate, a turbulent economic system, continued global conflict – and now a possible influenza pandemic – they now wish to reinforce the important place in health research of work that encompasses the social, environmental, and political determinants of health, as well as the biological.

Semantic Enhancements of a Research Article

In today’s PLoS Computational Biology: Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article:

Scientific innovation depends on finding, integrating, and re-using the products of previous research. Here we explore how recent developments in Web technology, particularly those related to the publication of data and metadata, might assist that process by providing semantic enhancements to journal articles within the mainstream process of scholarly journal publishing. We exemplify this by describing semantic enhancements we have made to a recent biomedical research article taken from PLoS Neglected Tropical Diseases, providing enrichment to its content and increased access to datasets within it. These semantic enhancements include provision of live DOIs and hyperlinks; semantic markup of textual terms, with links to relevant third-party information resources; interactive figures; a re-orderable reference list; a document summary containing a study summary, a tag cloud, and a citation analysis; and two novel types of semantic enrichment: the first, a Supporting Claims Tooltip to permit “Citations in Context”, and the second, Tag Trees that bring together semantically related terms. In addition, we have published downloadable spreadsheets containing data from within tables and figures, have enriched these with provenance information, and have demonstrated various types of data fusion (mashups) with results from other research articles and with Google Maps. We have also published machine-readable RDF metadata both about the article and about the references it cites, for which we developed a Citation Typing Ontology, CiTO (http://purl.org/net/cito/). The enhanced article, which is available at http://dx.doi.org/10.1371/journal.pntd.0​000228.x001 , presents a compelling existence proof of the possibilities of semantic publication. We hope the showcase of examples and ideas it contains, described in this paper, will excite the imaginations of researchers and publishers, stimulating them to explore the possibilities of semantic publishing for their own research articles, and thereby break down present barriers to the discovery and re-use of information within traditional modes of scholarly communication.

Related: Creative Re-Use Demonstrates Power of Semantic Enhancement:

A Review article published today in PLoS Computational Biology describes the process of semantically enhancing a research article to enrich content, providing a striking example of how open-access content can be re-used and how scientific articles might take much greater advantage of the online medium in future.
Dr. David Shotton and his team from Oxford University spent about ten weeks enriching the content of an article published in PLoS Neglected Tropical Diseases, the results of which can be seen online here.
The enhanced version includes features like highlighted tagging which you can turn on or off (tagged terms include disease names, organisms, places, people, taxa), citations which include a pop-up containing the relevant quotation from the cited article, document and study summaries, tag clouds and citation analysis…

PLoS ONE Collections

You may be aware that PLoS ONE has started creating Collections of articles in various areas of research. Two months ago we put together the first such collection – Stress-Induced Depression and Comorbidities: From Bench to Bedside and a month later, we unveiled our second collection – the PLoS ONE Paleontology Collection.
This post overviews what our Collections are all about. It is important to keep in mind that there are two types of Collections at PLoS ONE:
The first type is a one-off, ‘closed’ collection, often associated with a Conference, a Consortium or a Research Center. In this case we ask for, or are offered, a group of manuscripts (in the range 10-40 papers) which are all submitted roughly at the same time, peer-reviewed in the normal fashion, evaluated by the journal according to our normal evaluation process and then, if accepted, published roughly at the same time. The Collection then serves as a Proceedings from the meeting, or a collection of the research output of a Center, Society or Consortium etc.
Papers can still be added over time going forwards (for example, as that research group publishes new content), and so the Collection has the potential to become a ‘living’ Collection of the output from a specific group. Although the closest analogy to a PLoS ONE Collection is a ‘special issue’ of a journal, because of the ability to add new content over time, a PLoS ONE Collection is actually a lot more flexible and powerful than a traditional ‘special issue’. The Stress-Induced Depression and Comorbidities: From Bench to Bedside is an example of this kind of a Collection.
The other kind is different – it is an ‘open’ collection (in the sense that any paper we publish, provided it fits the scope of the Collection, can become part of that Collection). This means that all of our papers to date that deal with the topic (and meet the scope) can be included in the Collection. Furthermore, future articles will be automatically added to the Collection as soon as they are published. The Paleontology Collection is an example of such an open collection and contains all the content we have published in the field of Paleontology.
There may be other types in the future. For instance we may determine (using an expert editor, or using article-level metrics for example) the ‘top’ articles that we have published on a single topic, and highlight them in some sort of ‘best of’ Collection.
The articles in a Collection will always be placed together, prominently displayed and easy to find – just a single click is needed to get there. Each of the articles also prominently displays the link to the Collection it is a part of, so everything is nicely linked together.
It is also important to note that all papers are published as part of the ‘normal’ run of the journal (and so their citation reference is simply the normal citation that any PLoS ONE paper would have). Inclusion in a Collection is simply an attribute of a paper (a ‘tag’ as it were) and so a Collection is simply a way to ‘collect together’ (or ‘aggregate’) published papers on a single topic. Because of this, a single paper can conceivably appear in multiple Collections. It is also worth noting that PLoS ONE Collections can include papers published in other PLoS titles.
We also assume that by placing articles in a topic together, we will highlight to readers the activities (and the broader developments) that are happening in that area. We hope that by seeing this content together in this way, authors and readers will be stimulated to engage in discussions, either using our on-site tools for notes, comments and ratings, or offsite on their personal blogs, sending trackbacks to the articles so they can be easily found there.
If you are organizing a scientific meeting, or are a member of a scientific Society, Consortium or Center, and would be interested in submitting a set of manuscripts for a potential Collection, please contact me at Bora@plos.org.
Cross-posted on everyONE blog.

PLoS sites temporarily down – get your updates here (UPDATED)

The Bay Area experienced telecoms trauma overnight. Rumors of main switch outages, fiber optic cables being cut and telephone coverage being suspended, abound. We hear that the fiber optic cable is the most likely culprit. We’re trying to figure out how long it might take for these big picture issues to get fixed (could be as little as one hour) and at the same time we’re planning on possibly providing another solution via Amazon EC2. Our IT team have been working on the situation since 4.00am.
All the sites that are co-located with United Layer (who are in the Bay Area) are affected, only PLoS Biology is currently working. We advise our users, fans and authors to visit PubMed Central in the meantime.
We’ll be using PLoS Twitter (also Pete Binfield’s and mine), this Facebook page, our FriendFeed room, and everyONE blog to keep you updated. Plus, I will use A Blog Around the Clock for those of you who prefer that route.
Update: We’re back!

Good news, our sites are now live again. Our co-location company, United Layer, have found a work around to the server outages caused by the vandalism of AT&T Fiber Optic Cable lines in the Northern California region.
We have mirror sites that contain all articles on all sites published on or before 17th March 2009 ready to go live on Amazon EC2 should we experience more difficulties. Alternatively, you could use PubMed Central for a complete archive of current content.
We’ll continue to use this site for further updates should we need to, but we have our fingers crossed that the worst is behind us.

Harold Varmus is everywhere!

VarmusBookCover.jpgLook what came in the mail yesterday! The Art and Politics of Science by Harold Varmus and, since he is in some way my boss, with a very nice personal inscription inside the cover. I am excited and already started reading it.
And speaking o Varmus, he seems to be everywhere. See this article in TimesOnline:

A major investment in fighting tropical infections and chronic conditions like heart disease and diabetes in poor countries would transform international perceptions of the US, according to Harold Varmus, who co-chairs the President’s Council of Advisers on Science and Technology.
In an exclusive interview with The Times, Dr Varmus said that American diplomacy had undervalued the role of medicine and science in fostering friendly relations with developing nations.
He is asking President Obama to endorse a plan from the US Institute of Medicine that would almost double annual US support for global health to $15 billion by 2012. ….

Blog Post Of The Month at PLoS ONE

The winner has just been announced – you will need to click to see who it is!

Blog Pick Of The Month at PLoS ONE

If you write blog posts about PLoS ONE papers, you are eligible for a prize every month! I explain in some detail here, but this is the main point:

…every month, I will read all the blog coverage aggregated on ResearchBlogging.org and pick a blog post that, in my opinion, showcases the best coverage of a PLoS ONE article. I know, there is no way to quantify the “quality” of writing, so my picks will be personal. I will be looking for the posts that do the best job at connecting the center of the [science publishing] ecosystem – the paper – to the outside world. I will announce the winner here on the 1st of the following month and we’ll send the blogger a small prize as a sign of our appreciation.

You still have four days to write for the March prize, then keep writing with the April prize in sight…

Welcome to EveryONE

EveryONE? What’s that? It is the new PLoS ONE community blog:

Why a blog and why now? As of March 2009, PLoS ONE, the peer-reviewed open-access journal for all scientific and medical research, has published over 5,000 articles, representing the work of over 30,000 authors and co-authors, and receives over 160,000 unique visitors per month. That’s a good sized online community and we thought it was about time that you had a blog to call your own. This blog is for authors who have published with us and for users who haven’t and it contains something for everyone.

Just launched, this blog will have posts about all aspects of PLoS ONE, from technical to editorial, about Open Access, etc. I will give you more information soon. Join the community and contribute. Chris Patil and Neil Saunders already did.

Latest journal ranking in the biological sciences

Take a look at this picture:
PLoSONEonMendeley.jpg
It shows the top five journals ordered by the numbers of papers that Mendeley users decided are worth keeping for future reference. The discussion of the meaning of these numbers is here. I sure like that #5 there….

LaTeX fan? You can now use your favourite software to submit manuscripts to PLoS ONE

Yesss!!! I know lots of people, especially in math, physics, engineering and computational biology have been yearning for this for a while. And, starting today, you can submit manuscripts to PLoS ONE in LaTeX. Read the formatting instructions carefully, then submit.
The first article submitted in LaTeX was the High-Resolution Map of Science one last week, featured today in New York Times.

Interview with a PLoS ONE frequent author: Seyed Hasnain

Last week, I conducted an e-mail interview with one of the PLoS ONE most frequent authors, Professor Seyed Ehtesham Hasnain . The interview is now live on the PLoS Blog

Harold Varmus on Daily Show last night

Under the fold:

Continue reading

Harold Varmus on Daily Show tonight

So says Jonathan. Will watch.

Fossils! Fossils! Fossils!

You may be aware that PLoS ONE has started making Collections of papers in various areas of research. The older PLoS journals have been making collections for a long time. PLoS ONE is just starting. Last month we put together the first such collection – Stress-Induced Depression and Comorbidities: From Bench to Bedside.
Today, we are happy to unveil our second collection – the PLoS ONE Paleontology Collection!
It is important to keep in mind that there are two types of collections: the first type is a one-off, closed collection, often associated with a conference, where we ask for or are offered a whole set of manuscripts (10-20 papers) which are all submitted roughly at the same time, peer-reviewed in a normal fashion, then, if accepted, published roughly at the same time. Then, the collection is closed – there are no more additions to it.
The Paleontology Collection is different – it is an open collection. This means that all of our papers to date (PLoS ONE only, not other PLoS journals) that deal with fossils in any way, 26 of them so far, are included in the collection. Furthermore, all the future palaeo papers will be automatically added to the Collection as soon as they are published. Thus, such papers will always be placed together, prominently displayed and easy to find – just a single click is needed to get there.
We are hoping that the open style of this Collection will motivate people in the field to submit palaeo papers to us in the future.
A second note: as it’s my job to check all the user activity on PLoS ONE, I have noticed that palaeo folks are unusually willing to use the comments/notes/ratings tools. Several of our fossil papers already have quite a lot of comments, notes, ratings and/or trackbacks (you should go to this blog post to see the examples). So, I would like to use this occasion to try to urge people to register, login and post comments, notes or ratings on palaeo papers, or send trackbacks if their blogging platforms allow it (Blogger.com can’t do it). I think that the palaeo community can be an example to others for the good and vigorous use of these tools. So, if you blog about this new Collection (and I hope you will help us spread the word) I would appreciate it if you would also encourage your blog readers to start using these tools on our fossil papers.
Greg Laden immediatelly understood why Collections are so useful:

PLoS ONE is a veritable fire hose of OpenAccess research. Which is nice, but how do you browse a fire hose?
By using the PLoS ONE collections you can track your favorite topic or delve into the earlier literature or just browse around. And now, starting just moments ago, there is a PLoS collection on paleontology.

Andy adds:

Why should we care? Speaking selfishly, this will allow us to easily access all articles in our field. All future articles are automatically added to the collection. This means that if you don’t want to wade through all of the other contributions on the PLoS ONE list (although there are some very interesting ones!), you can just keep an eye on the paleontology collection for any and all exciting developments. In a broader sense, this collection will help paleontologists to reach an even broader audience.
And once again–take advantage of the comment, note, and rating features at PLoS ONE (as outlined in my previous post). It’s really a unique opportunity to interact with authors, make your thoughts known, and help science march onward. If you have that really cool piece of research, submit your manuscript!

Finally, a word or two on my own musings about this Collection. As these 26 papers were published over the past two years, I knew I personally liked them very much, but only now that they are all in one place I realized why: they are all incredibly inter-disciplinary! These papers are not just simple descriptions of new species. They tend to combine insights and techniques from several disciplines, e.g., comparative anatomy and molecular systematics, biogeography and physiology and more. These are kinds of papers that don’t readily find home in other, more specialized journals, except in Science and Nature. PLoS ONE is, almost by definition, a perfect place for publication of such works. And Open Access ensures that such papers are widely read, covered by media and blogs, and later, hopefully, more often cited than papers hidden behind pay-walls.
So, go ahead and enjoy – introducing the PLoS ONE Paleontology Collection!

Quick check-in from NYC

Mrs.Coturnix and I arrived nicely in NYC last night and had a nice dinner at Heartland Brewery. This morning, we had breakfast at the Hungarian Pastry Shop, where I ordered my pastry using a Serbian name for the cake, and the Albanian woman working in the Hungarian shop understood what I wanted! I forgot to bring my camera with me today, and Mrs.Coturnix did not bring her cable, so the pictures of the pastries will have to wait our return home.
Then, Mrs.Coturnix went for a long walk (it was nice in the morning, got cold in the afternoon), ending up in the Met. I joined my co-panelists Jean-Claude Bradley and Barry Canton and our hosts Kathryn Pope, Rebecca Kennison and Rajendra Bose for lunch at Bistro Ten 18.
Then we walked over to the Columbia campus and got all set up for the Open Science panel. I talked first, giving a brief history of openness in scientific communication, defining Open Access publishing and how it fits in the evolving ecosystem of online science communication, ending with some speculation about the future. Jean-Claude and Barry then followed, describing their own projects, showing how some of that future that sounds so speculative when described in general terms, is already here, done by pioneers and visionaries right here and now.
The panel was followed by a number of excellent questions from the audience – you could follow the discussion blow-by-blow on twitter (several pages of it!), and the video of the entire thing will be posted online in a few days (I will make sure to link to it once it is available).
There were some familar faces in the crowd – including Caryn Shechtman (who already wrote a nice blog post about it), my Overlords Erin and Arikia, Michael Tobis, Talia Page (and her Mom who is writing an interesting book right now), Noah Gray, Hilary Spencer and Miriam Gordon (whose husband does interesting stuff with science education in high schools).
We went for a beer nearby afterwards, where we were re-joined by Mrs.Coturnix. It got really cold, so we went back to the hotel, had some (too) authentic Chinese cuisine for dinner and are trying to rest as tomorrow is another busy day – meeting various famous people for various meals, including the Big Bash at Old Town Bar at 8pm to which you are all invited.

Interview with Dr.Adam Ratner

Last week a did an interview with Dr.Adam Ratner and it is now posted on the PLoS Blog. Go check it out.

User activity on PLoS ONE – an analysis

You may remember some time ago, we gave out the data to a few people in the community to take a look at the commenting function on PLoS ONE. Now, Euan Adie, using crowdsourcing (a big Thank You to 818 people who helped with this project) came up with the most detailed analysis to date. Well worth your time to take a look.

Let’s meet in New York City next week

I will be on a panel, Open Science: Good For Research, Good For Researchers? next week, February 19th (3:00 to 5:00 pm EST at Columbia University, Morningside Campus, Shapiro CEPSR Building, Davis Auditorium). I am sure my hosts will organize something for us that day before and/or after the event, but Mrs.Coturnix and I will be there a couple of days longer. So, I think we should have a meetup – for Overlords, SciBlings, Nature Networkers, independent bloggers, readers and fans 😉
Is Friday evening a good time for this? Or is Saturday better? Let me know.
You can follow the panel on Twitter or Facebook (I am not sure, but the panel may be recorded in some way and subsequently made available online – will check on that), or, if you can, show up in person. More information can be found here:

Open science refers to information-sharing among researchers, and encompasses a number of initiatives to remove access barriers to data and published papers and to use digital technology to more efficiently disseminate research results. Advocates for this approach argue that openly sharing information among researchers is fundamental to good science, speeds the progress of research, and increases recognition of researchers. The panel will discuss frequently raised questions such as “Can open science practices work for researchers who need to establish priority of publication to advance their careers?” and “Is open science compatible with peer review?”

An Awesome Whale Tale

ResearchBlogging.orgWhen I was a little kid, almost nothing was known about evolution of whales. They were huge, they were marine and they were mammals, but their evolutionary ancestry was open to speculation. Some (like Darwin himself) hypothesized that the terrestrial ancestor of whales looked like a bear. Others favored the idea of a hippo-like or even a pig-like ancestor.
Over the decades, two things happened. First, the revolution in molecular biology and computing power allowed scientists to compare many genes of many mammals and thus infer genealogical relationships between whales and other groups of mammals. Second, some smart palaeontologists decided that a good place to look for fossil whales would be Pakistan. The rest is, as they say, history. Digs in Pakistan unearthed a wealth of whale fossils over the years, so many of them, in fact, that the fossil record of prehistoric whales is now one of the best examples of the bushy tree of mammalian evolution in any lineage.
We now know that there were several gradual changes in whales over their evolutionary history from terrestrial animals to a number of branches of aquatic animals – some of these branches went extinct over time, while others have living descendants today. They tended to increase in size. Their front legs evolved into flippers. They gradually lost their hind legs: the large, strong hind legs of early whales were used for swimming by paddling, but later decreased in size as the undulating mode of swimming (and the evolution of the flat horizontal tail) took over. Today’s whales have remnants of hind legs still hidden deep inside their large bodies, in the form of two smalish bones.
While genetics discovers evolutionary relationships, and fossils can tell us about evolution of morphology, it is much more rare that a fossil find allows us to infer much about an extinct animal’s physiology, behavior or ecology. And the discovery of one such fossil was just published in PLoS ONE today: New Protocetid Whale from the Middle Eocene of Pakistan: Birth on Land, Precocial Development, and Sexual Dimorphism (also watch the accompanying video of the fossil). Here is the abstract:

Background
Protocetidae are middle Eocene (49-37 Ma) archaeocete predators ancestral to later whales. They are found in marine sedimentary rocks, but retain four legs and were not yet fully aquatic. Protocetids have been interpreted as amphibious, feeding in the sea but returning to land to rest.
Methodology/Principal Findings
Two adult skeletons of a new 2.6 meter long protocetid, Maiacetus inuus, are described from the early middle Eocene Habib Rahi Formation of Pakistan. M. inuus differs from contemporary archaic whales in having a fused mandibular symphysis, distinctive astragalus bones in the ankle, and a less hind-limb dominated postcranial skeleton. One adult skeleton is female and bears the skull and partial skeleton of a single large near-term fetus. The fetal skeleton is positioned for head-first delivery, which typifies land mammals but not extant whales, evidence that birth took place on land. The fetal skeleton has permanent first molars well mineralized, which indicates precocial development at birth. Precocial development, with attendant size and mobility, were as critical for survival of a neonate at the land-sea interface in the Eocene as they are today. The second adult skeleton is the most complete known for a protocetid. The vertebral column, preserved in articulation, has 7 cervicals, 13 thoracics, 6 lumbars, 4 sacrals, and 21 caudals. All four limbs are preserved with hands and feet. This adult is 12% larger in linear dimensions than the female skeleton, on average, has canine teeth that are 20% larger, and is interpreted as male. Moderate sexual dimorphism indicates limited male-male competition during breeding, which in turn suggests little aggregation of food or shelter in the environment inhabited by protocetids.
Conclusions/Significance
Discovery of a near-term fetus positioned for head-first delivery provides important evidence that early protocetid whales gave birth on land. This is consistent with skeletal morphology enabling Maiacetus to support its weight on land and corroborates previous ideas that protocetids were amphibious. Specimens this complete are virtual ‘Rosetta stones’ providing insight into functional capabilities and life history of extinct animals that cannot be gained any other way.

What does this all mean? Unlike the gradual loss of hind legs, graudal increase in size, gradual evolution of front legs into flippers and gradual evolution of the horizontal tail, we did not have information about the way the prehistoric whales gave birth. We know that all large terrestrial mammals give birth head-first, while all aquatic mammals (not just whales, but also manatees and such) give birth tail-first. But we did not know when did this switch occur.
This paper shows that some early whales, already well along the way of evolving into creatures recognizable as whales but still possessing sizeable hind legs they used for swimming, gave birth head-first. This indicates that these animals, at least on those rare occasions when they were giving birth to their young, had to go up onto dry land. Thus, we now have the timing a little better on the question of when exatly did the whales become completely aquatic, i.e., never coming to land at all, and it is somewhat later than we thought until now.
I tried to explain this in as simple language as possible – suitable for complete laymen or middle-school students, but if you want a little more detail and some better expert opinion on this fossil find and the paper that describes it, please read what others have written about it:
Carl Zimmer
Mike Dunford
Ed Yong
Brian Switek
Greg Laden
Cosmos Magazine
WIRED Science
Philip D. Gingerich, Munir ul-Haq, Wighart von Koenigswald, William J. Sanders, B. Holly Smith, Iyad S. Zalmout (2009). New Protocetid Whale from the Middle Eocene of Pakistan: Birth on Land, Precocial Development, and Sexual Dimorphism PLoS ONE, 4 (2) DOI: 10.1371/journal.pone.0004366

Evolution in PLoS ONE

Evolution is the theme of the month for January at PLoS ONE, so we have picked , for your pleasure, some of our papers for the Top picks in Evolutionary Biology. In conjuction with this, I have also conducted an interview with our Evolution Section Editor Dr.Tom Tregenza.
Dr.Tom Tregenza studies sexual selection and sexual conflict in crickets, both in the lab and in the field, and we discuss some of his research in the interview. He is also involved in a collaborative study of the amazing mimic octopus – see the movie below – so I hope you go and check out the interview:

PLoS ONE seems to be everywhere!

Just check out this list – PLoS ONE papers are apparently on everybody’s ‘Best of 2008’ lists these days. Now, that is impact!

Einstein was smart, but Could He Play the Violin? – the winner of the synchroblogging contest

Happy Anniversary, PLoS ONE!
Today is PLoS ONE’s second anniversary and we’re celebrating by announcing that the winner of the second PLoS synchroblogging competition is SciCurious of the Neurotopia 2.0 blog.
“This fluent post captures the essence of the research and accurately communicates it in a style that resonates with both the scientific and lay community” – Liz Allen, PLoS.
Here is the winning entry, cross posted in its entirety:
====================
Einstein was smart, but Could He Play the Violin?
I already wrote one entry for PLoS ONE’s second birthday, but I’m feeling sparky today, and I think I like this paper better.
I don’t know about you guys, but when I was a sprog, my parents dragged me to music lessons. LOTS of music lessons. As of right now, I have been producing music of some type for the past 21 years straight. And I LOVE it.
Of course, I didn’t always love it. I remember my mother dragging me and my brother to lessons, making us sit down every day and practice (I was, and still am, no good with the practicing), and the fear and shakiness of recitals (heck, I still get that, and it’s been 21 years). In her time, Sci has actually “mastered” (it’s a debatable point), three different instruments (‘instruments’ is a loose term), and still uses one of them professionally on occasion. And if you can guess what they are, Sci will…do something cool. Like send you one of her favorite books. Or perhaps a tshirt with a molecule on it. Or perhaps some of her delicious cookies. Obviously, you can only guess if you don’t KNOW already (that means you, Dad). So there you go, contest open.
Anyway, years and years of music lessons. But the question is: did they do me any good? Does playing ‘Baby Mozart’ really do anything, and is anything achieved by starting your child on Suzuki when they are 2, other than the pain and misery of your child, and possibly an eventual love of music? Can it, perhaps, make me SMARTER?
ResearchBlogging.org Forgeard et al. “Practicing a musical instrument in childhood is associated with enhanced verbal ability and nonverbal reasoning” PLoS ONE, 2008.
And for the record, Einstein did play the violin. Apparently he was quite good.
There actually are several studies out there that show that techniques that you learn can “transfer” to other techniques, giving you a bit of an edge. This works best when you’re performing skills that are very similar to each other (like learning how to estimate the area of a square, and then learning how to estimate the area of a triangle). We know this happens for musicians in the development of fine motor skills. Once you’ve been playing the violin for a while, other things that require fine motor skills will come to you a bit easier (perhaps we should train all would-be surgeons on musical instruments, if you can master playing Rachmaninoff, brain surgery should be a piece of cake).
Of course, most of the studies that have been done are correlational in nature. Kids who play musical instruments have better motor skills. This could be due to the music, or the kids could play music because they have good motor skills. Good motor skills could be a development of things like the higher socio-economic class that often goes along with being taught music as a child, and thus parents are maybe able to put more effort to their development. The possibilities go on. Correlation is NOT causation.
The same thing goes for the correlation between musical learning and IQ. There was a modest correlation, but it could be just the effect of the extra lessons the kids were receiving, resulting in more time spent on focused attention and mastering a skill. Significant correlations have also been shown for music and verbal and language skills. Music lessons have been found to be correlated with increases in reading ability and phonetic comprehension. This actually leads me to a question: if language, reading, and phonetic comprehension are related to the pitch and tone of words, do children who are tone deaf have a harder time mastering reading and verbal skills? I think this might warrant a future PubMed search.
Unfortunately, all the previous tests tended to focus on the “transfer” of skills to not very related fields, like IQ. So in this study, the authors wanted to look at the effects of music learning on “near” transfers, skill closely related to music training: spatial reasoning, verbal abilities, nonverbal, and mathematical. They also looked for VERY closely related skills: fine motor control and auditory skill.
They grabbed a whole bunch of kids around 8-11 years old. Some played musical instruments, some didn’t (one of the problems with this study to me is that the control group is a good bit small than the instrumental group, 41 musicians vs 18 non). Kids were controlled for the socio-economic class of the parents. Average length of music training was close to five years. They also divided the kids up by whether or not they got Suzuki training, but ended up grouping them together, as Suzuki effects were no different from other instrumentalists.
Dang, they didn’t graph their data. Well, I shall fix. Because I can. People should be so grateful I do all their graphing…
graph1.png
There you go. So, as you can see from the graph (the pretty, pretty graph), musical kids scored a lot better on fine motor skills for left and right hand (the first two sets of bars). This is pretty expected, if you’re using fine motor skills a lot, presumably you’ll get better at them. The musical kids also did better when distinguishing tones and following melody lines, though interestingly, they didn’t show any improvements in rhythm. I wonder if this has anything to do with the kids of music the kids were studying. There wasn’t a single drummer in the bunch, it was all either piano or stringed instruments.
And finally, the kids with musical training scored a lot better (I know it doesn’t look like it, but the MANCOVA analysis uncovered a difference) on vocabulary testing. They outperformed their non-musical counterparts in both verbal ability (vocabulary) and non-verbal reasoning skills. They didn’t find any differences in math or spatial reasoning.
The authors hypothesize that music training may transfer skills to some other related domains. The other hypothesis is that music training doesn’t enhance a specific skill set, but rather your general intellectual ability. This would mean they would score higher on every test given. In fact, they DID score higher, but most of the time the scores didn’t reach significance.
Still, remember this is correlation, not causation. Families were of similar socio-ecoomic class and education, but that doesn’t mean they are all similar parents. Kids who take music lessons may have parents that are more involved in their intellectual development. Kids that persist in taking music lessons for a good chunk of time may have superior motivation. Correlation =/= causation.
But it’s still a cool paper, and no matter what, it’s quite clear that music lessons didn’t HURT. Time to tape your poor child to the piano bench!
Marie Forgeard, Ellen Winner, Andrea Norton, Gottfried Schlaug (2008). Practicing a Musical Instrument in Childhood is Associated with Enhanced Verbal Ability and Nonverbal Reasoning PLoS ONE, 3 (10) DOI: 10.1371/journal.pone.0003566

PLoS ONE Second Birthday Synchroblogging Competition – final list of entries

The deadline for the PLoS ONE Second Birthday Synchroblogging Competition is now officially over. Here are all the posts written for the competition – 18 posts, written by 17 people, covering 22 PLoS ONE articles. Liz, Dave, Jason and I will be reading them today and will announce the winner as soon as we can:
Barn Owl of Guadalupe Storm-Petrel: DNA Repair During Spermatogenesis: Gimme a Break! about the article: Deletion of Genes Implicated in Protecting the Integrity of Male Germ Cells Has Differential Effects on the Incidence of DNA Breaks and Germ Cell Loss
Ed Yong of Not Exactly Rocket Science: Predatory slime mould freezes prey in large groups about the article: Exploitation of Other Social Amoebae by Dictyostelium caveatum
Scicurious of Neurotopia (version 2.0): Why Did the Dolphin Carry a Sponge? about the article: Why Do Dolphins Carry Sponges?
Scicurious of Neurotopia (version 2.0): Einstein was smart, but Could He Play the Violin? about the article: Practicing a Musical Instrument in Childhood is Associated with Enhanced Verbal Ability and Nonverbal Reasoning
Allyson of Systems Biology & Bioinformatics (Semantically Speaking) on One way for RDF to help a bioinformatician build a database: S3DB (also cross-posted on The mind wobbles: One way for RDF to help a bioinformatician build a database: S3DB) about the article: A Semantic Web Management Model for Integrative Biomedical Informatics
Simon Cockell of Fuzzier Logic: Contextual Specificity in Peptide-Mediated Protein Interactions about the article: Contextual Specificity in Peptide-Mediated Protein Interactions
Mike Haubrich of Tangled Up in Blue Guy : Small-Bodied Humans on Palau – A Disagreement about the articles: Small-Bodied Humans from Palau, Micronesia and Small Scattered Fragments Do Not a Dwarf Make: Biological and Archaeological Data Indicate that Prehistoric Inhabitants of Palau Were Normal Sized
Martin of The Lay Scientist : Catching Snowflakes: The Media and Public Perceptions of Disease about the article: Medicine in the Popular Press: The Influence of the Media on Perceptions of Disease
Nir London of Macromolecular Modeling Blog: Model for the Peptide-Free Conformation of Class II MHC Proteins about the article: Model for the Peptide-Free Conformation of Class II MHC Proteins
Greg Laden of Greg Laden’s blog: How to make an elephant turn invisible about the articles: Risk and Ethical Concerns of Hunting Male Elephant: Behavioural and Physiological Assays of the Remaining Elephants, Roadless Wilderness Area Determines Forest Elephant Movements in the Congo Basin, Elephant (Loxodonta africana) Home Ranges in Sabi Sand Reserve and Kruger National Park: A Five-Year Satellite Tracking Study and Population and Individual Elephant Response to a Catastrophic Fire in Pilanesberg National Park.
The Neurocritic of The Neurocritic blog: Can You Reread My Mind? about the article: Using fMRI Brain Activation to Identify Cognitive States Associated with Perception of Tools and Dwellings
Moneduloides of Moneduloides blog: A trypanosome and a tsetse walk into a bar… about the article: Factors Affecting Trypanosome Maturation in Tsetse Flies
El-Ho of Pas d’il y’on que nous: The Etiology of Fear about the article: Coupled Contagion Dynamics of Fear and Disease: Mathematical and Computational Explorations
Ian of Further thoughts: Evolution and conservation in Mexican dry forests about the article: Sources and Sinks of Diversification and Conservation Priorities for the Mexican Tropical Dry Forest
Alun Salt of Archaeoastronomy: If you put a snail shell to your ear can you hear the sound of your thoughts? about the article: Climate Change, Genetics or Human Choice: Why Were the Shells of Mankind’s Earliest Ornament Larger in the Pleistocene Than in the Holocene?
Michael Tobis of Only In It For The Gold: The Singularity about the article: Ecosystem Overfishing in the Ocean
PodBlack Cat of PodBlack blog: Pet Ownership – Maybe Not For Better Health, Perhaps Sense Of Humour? about the article: To Have or Not To Have a Pet for Better Health?
Juan Nunez-Iglesias of I Love Symposia!: Randomise your samples! about the article: Randomization in Laboratory Procedure Is Key to Obtaining Reproducible Microarray Results
Not in competition, because Dave Munger of Cognitive Daily is one of the judges: Make sure you get some sleep — or at least some caffeine — before that test about the article: Sleep Loss Produces False Memories

PLoS ONE Second Birthday Synchroblogging Competition – entries so far

The entries for the PLoS ONE Second Birthday Synchroblogging Competition have been coming in all day. Here are the posts I found so far. If you have posted and your post is not on this list, let me know by e-mail. I will keep updating this post and moving it to the top until the competition closes at dawn tomorrow:
Ed Yong of Not Exactly Rocket Science: Predatory slime mould freezes prey in large groups about the article: Exploitation of Other Social Amoebae by Dictyostelium caveatum
Scicurious of Neurotopia (version 2.0): Why Did the Dolphin Carry a Sponge? about the article: Why Do Dolphins Carry Sponges?
Scicurious of Neurotopia (version 2.0): Einstein was smart, but Could He Play the Violin? about the article: Practicing a Musical Instrument in Childhood is Associated with Enhanced Verbal Ability and Nonverbal Reasoning
Allyson of Systems Biology & Bioinformatics (Semantically Speaking) on One way for RDF to help a bioinformatician build a database: S3DB (also cross-posted on The mind wobbles: One way for RDF to help a bioinformatician build a database: S3DB) about the article: A Semantic Web Management Model for Integrative Biomedical Informatics
Simon Cockell of Fuzzier Logic: Contextual Specificity in Peptide-Mediated Protein Interactions about the article: Contextual Specificity in Peptide-Mediated Protein Interactions
Mike Haubrich of Tangled Up in Blue Guy : Small-Bodied Humans on Palau – A Disagreement about the articles: Small-Bodied Humans from Palau, Micronesia and Small Scattered Fragments Do Not a Dwarf Make: Biological and Archaeological Data Indicate that Prehistoric Inhabitants of Palau Were Normal Sized
Martin of The Lay Scientist : Catching Snowflakes: The Media and Public Perceptions of Disease about the article: Medicine in the Popular Press: The Influence of the Media on Perceptions of Disease
Nir London of Macromolecular Modeling Blog: Model for the Peptide-Free Conformation of Class II MHC Proteins about the article: Model for the Peptide-Free Conformation of Class II MHC Proteins
Greg Laden of Greg Laden’s blog: How to make an elephant turn invisible about the articles: Risk and Ethical Concerns of Hunting Male Elephant: Behavioural and Physiological Assays of the Remaining Elephants, Roadless Wilderness Area Determines Forest Elephant Movements in the Congo Basin, Elephant (Loxodonta africana) Home Ranges in Sabi Sand Reserve and Kruger National Park: A Five-Year Satellite Tracking Study and Population and Individual Elephant Response to a Catastrophic Fire in Pilanesberg National Park.
The Neurocritic of The Neurocritic blog: Can You Reread My Mind? about the article: Using fMRI Brain Activation to Identify Cognitive States Associated with Perception of Tools and Dwellings
Moneduloides of Moneduloides blog: A trypanosome and a tsetse walk into a bar… about the article: Factors Affecting Trypanosome Maturation in Tsetse Flies
El-Ho of Pas d’il y’on que nous: The Etiology of Fear about the article: Coupled Contagion Dynamics of Fear and Disease: Mathematical and Computational Explorations
Ian of Further thoughts: Evolution and conservation in Mexican dry forests about the article: Sources and Sinks of Diversification and Conservation Priorities for the Mexican Tropical Dry Forest
Alun Salt of Archaeoastronomy: If you put a snail shell to your ear can you hear the sound of your thoughts? about the article: Climate Change, Genetics or Human Choice: Why Were the Shells of Mankind’s Earliest Ornament Larger in the Pleistocene Than in the Holocene?
Michael Tobis of Only In It For The Gold: The Singularity about the article: Ecosystem Overfishing in the Ocean
PodBlack Cat of PodBlack blog: Pet Ownership – Maybe Not For Better Health, Perhaps Sense Of Humour? about the article: To Have or Not To Have a Pet for Better Health?
Juan Nunez-Iglesias of I Love Symposia!: Randomise your samples! about the article: Randomization in Laboratory Procedure Is Key to Obtaining Reproducible Microarray Results

The U.S. Commitment to Global Health

Listen here to the The December 16, 2008 David E. Barmes Global Health Lecture given by Dr.Harold Varmus:

Harold Varmus, former Director of the National Institutes of Health and co-recipient of a Nobel Prize for studies of the genetic basis of cancer, is President of Memorial Sloan-Kettering Cancer Center in New York City. Dr. Varmus chairs the Scientific Board of the Bill & Melinda Gates Foundation’s Grand Challenges in Global Health program and leads the Advisory Committee for the Global Health Division. He was a member of the World Health Organization (WHO) Commission on Macroeconomics and Health, and is a co-founder of the Public Library of Science, a leading publisher of open access journals. In addition, he serves as co-chair of the Institute of Medicine’s committee on The U.S. Commitment to Global Health. The committee will issue its interim report on the day preceding the lecture.

Synchroblogging contest….

…has started.

PLoS – on Twitter and FriendFeed

Despite online debates – which one is better: Twitter or FriendFeed, sometimes serious, sometimes tongue-in-cheek – the fact is that these are two different animals altogether. Asking one to make a choice between the two is like asking one to make a choice between e-mail and YouTube – those are two different services that do different things. Thus, they are to be used differently.
Twitter is a communications tool (or a ‘human application’). You can broadcast (one-to-many), you can eavesdrop (many-to-one) or you can converse (one-to-one, either in public or through Direct Messages). But most importantly – you have to mix a little bit of all three. If all you do is throw your RSS feed into Twitter, i.e., only broadcast, then you are doing it wrong. In Twitter, you have to engage with others on a regular basis – listening, talking, conversing. Reciprocating. Not building a fan-club, but a network of friends. As I mentioned yesterday:

You will be measured by the size of your network – who is your (mutual – it has to be mutual!) friend.

You know that, after a long time of resistance, I recently succumbed and started using Twitter – find me here. I find it useful and I am trying to balance the three modes (broadcast, eavesdrop, converse) as best I can. I can definitely see the allure, especially for people who use mobile devices (I don’t – I spend too much time online anyway and need to reconnect with the physicalness of the world when I am not at the computer, thus I disabled the online access on my cell phone and have never texted a message in my life).
People who follow me on Twitter, probably all of them, know where I work. One out of 20 tweets or so have something to do with PLoS. My profile links to my blog, on which it is immediately obvious where I work. I don’t need to pull in the RSS feed from PLoS to be effective as a “face of PLoS” on Twitter.
But, even better, I am not alone – Liz Allen is now on Twitter, too, as an “official” face of PLoS. And, if you check out the PLoS twitter profile and click on “Follow”, you will see that she totally groks it. Her tweets do not have that horrible “PR feel” about them that some of the business marketers erroneously use. So I hope you will subscribe.
FriendFeed, on the other hand, is an aggregator. It is as much or as little of a conversation as you want it to be. You do not have to balance the three modes and you can use it in one of the modes only and it can still work for you.
I have joined FriendFeed some time ago and I find it extremely useful. This is where I find half of my “bloggable” material these days – the eavesdropping mode. I do the broadcast mode by importing the feeds from my blog and my Twitter. I use the conversation mode by “liking” and/or commenting on other people’s stuff. As with Twitter, people who follow me mostly know where I work and are used to seeing an occasional PLoS-related entry from me without considering it to be PR spamming.
But what FriendFeed allows me to do in addition, is make a room. You can join the room or not, depending on your interest. But this way I do not have to spam anyone who subscribes to my main feed. You can join the PLoS ONE room if you want to see the PLoS ONE feed imported. Whenever there is a good blog post covering one of the PLoS ONE papers, I add the permalink to that post as a comment on that paper’s feed in the room (feel free to do it yourself if you blog about our papers). Occasionally I may place additional news or links there as well. That way, I can be myself yet still do the marketing for PLoS that I need to do. And nobody’s complained so far. You should give it a try.