Category Archives: PLoS

PLoS ONE is Two – Second Birthday Synchroblogging Competition

Paper number 0000001 was published in PLoS ONE on December 20th 2006 – exactly two years ago. So, we will have various types of celebrations, of course. One of those, the one you can and should participate in, is the Second Birthday Synchroblogging Competition.
So, how does it go? How can you participate?
First, spread the word about it to your own contacts and readers.
Second, if you are not already registered with ResearchBlogging.org, do so ASAP, or on December 17th at the latest (to give them enough time to approve you and to give yourself enough time to look around and familiarize yourself with the way it works).
Third, go to PLoS ONE and browse the articles – there are almost 4000 there so there are plenty to choose from. Pick one that is in your area of interest or expertise, a paper that you find exciting and you can fully understand.
Write a blog post about that paper, using the guidelines of ResearchBlogging.org – once you are registered, look around the forums and the blog there for discussions on exactly what the criteria are.
Now wait – hold on. Don’t post it yet! Make sure that you publish your post on December 18th.
Make sure that your post contains the BPR3 icon and the Reference (both provided by a ResearchBlogging.org automated tool). This will ensure that your post shows up on the ResearchBlogging.org front page aggregator.
If your post does not show up there within a few hours, or if you already know that there is a technical incompatibility between ResearchBlogging.org and your blog, please e-mail me (Bora@plos.org) the permalink of your post. Also, try to make sure that the words “PLoS ONE @ Two” appear in your post or in your tags. I will look at the ResearchBlogging.org aggregator, in my e-mail, at Google Blogsearch and Technorati – that way I will be sure to catch all the entries.
If you are blogging on an “upper-level” platform, e.g., Drupal, Expression Engine, WordPress, MoveableType, Typepad, etc., please send a trackback from your post to the paper itself. You have to make sure that the body of your post contains the link to the paper in this exact form (there are several alternative URLs that will not work):
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000000
Then, in the “outgoing trackbacks” field of your blog, paste the URL of the paper in exactly this form:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0000000/trackback
If you are using Blogspot, LiveJournal, etc. you cannot send trackbacks. But there is no reason why you cannot drop the permalink of your post in a comment on the paper itself.
You should login/register at PLoS ONE and consider posting your brief comments, notes or ratings there as well – after all, you are one of the few people who actually read the paper in great detail and with deep focus – you know more about it than most other people on the planet.
Once everyone’s posted their posts on the 18th, all the entries will be judged by a panel of four judges: Liz Allen of PLoS, Dave Munger of ResearchBlogging.org (and blogger on Cognitive Daily), Jason Stajich from the Department of Plant and Microbial Biology at UC-Berkeley, and myself.
The winner will be announced on December 20th. The winning post will be (with permission) cross-posted on the PLoS ONE Blog and here on A Blog Around the Clock. The author of the post will also receive a bag of swag that includes the new PLoS Water bottle (H2go brand) and a couple of cool PLoS t-shirts.
So, let’a start writing….

Interviews with PLoS ONE authors and academic editors

If you don’t follow the PLoS Blog (you don’t? really?), you may have missed a series of posts we recently started, interviewing some of our authors and academic editors, who reveal the behind-the-scenes thoughts about the process. Check out interviews with Jeremy Farrar, Dario Ringach, Ivan Baxter, Niyaz Ahmed and Tian Kegong.

The usefulness of commenting on scientific papers

Here is a great example by Cameron Neylon:
It’s a little embarrassing…

…but being straightforward is always the best approach. Since we published our paper in PLoS ONE a few months back I haven’t been as happy as I was about the activity of our Sortase. What this means is that we are now using a higher concentration of the enzyme to do our ligation reactions. They seem to be working well and with high yields, but we need to put in more enzyme. If you don’t understand that don’t worry – just imagine you posted a carefully thought out recipe and then discovered you couldn’t get that same taste again unless you added ten times as much saffron.
None of this prevents the method being useful and doesn’t change the fundamental point of our paper, but if people are following our methods, particularly if they only go to the paper and don’t get in contact, they may run into trouble. Traditionally this would be a problem, and would probably lead to our results being regarded as unreliable. However in our case we can do a simple fix. Because the paper is in PLoS ONE which has some good commenting features, I can add a note to the paper itself, right where we give the concentration of enzyme (scroll down to note 3 in results) that we used. I can also add a note to direct people to where we have put more of our methodology online, at OpenWetWare. As we get more of this work into our online lab notebooks we will also be able to point directly back to example experiments to show how the reaction rate varies, and hopefully in the longer term sort it out. All easily done on the web, but impossible on paper, and in an awful lot (but not all!) of the other journals around.
Or we could just let people find out for themselves…

Yes. If you find out after publication that you need to tweak your experimental protocol, the only place where other people interested in using your technique are guaranteed to find the new information is if it is attached to the paper itself.

Bats eat birds – join the discussion

As the month of September is coming to a close, and the topic of the month in PLoS ONE is bats, we decided to end the focus with a Journal Club.
Starting today, and lasting a week, there will be a Journal Club on this PLoS ONE article – Bats’ Conquest of a Formidable Foraging Niche: The Myriads of Nocturnally Migrating Songbirds by Ana G. Popa-Lisseanu, Antonio Delgado-Huertas, Manuela G. Forero, Alicia Rodriguez, Raphael Arlettaz and Carlos Ibanez:

Along food chains, i.e., at different trophic levels, the most abundant taxa often represent exceptional food reservoirs, and are hence the main target of consumers and predators. The capacity of an individual consumer to opportunistically switch towards an abundant food source, for instance, a prey that suddenly becomes available in its environment, may offer such strong selective advantages that ecological innovations may appear and spread rapidly. New predator-prey relationships are likely to evolve even faster when a diet switch involves the exploitation of an unsaturated resource for which few or no other species compete. Using stable isotopes of carbon and nitrogen as dietary tracers, we provide here strong support to the controversial hypothesis that the giant noctule bat Nyctalus lasiopterus feeds on the wing upon the multitude of flying passerines during their nocturnal migratory journeys, a resource which, while showing a predictable distribution in space and time, is only seasonally available. So far, no predator had been reported to exploit this extraordinarily diverse and abundant food reservoir represented by nocturnally migrating passerines.

Folks in the The Kalcounis-Ruppell lab, Hershey lab and O’Brien lab in the Department of Biology at UNC Greensboro, have read and discussed the paper and posted their comments here.
You know what to do – go there, register/login and join the conversation.

Bats, Bats, Bats!

Batman.jpgThis month’s Theme Of The Month in PLoS ONE are bats! Midway between the release of Batman II and Halloween, this sounds like an appropriate choice. Peter Binfield provides more information.
A number of our bat papers have received media and blog coverage (and not just by Anne-Marie!), but it is never too late. Bloggers tend to write about the newest papers, fresh off the presses. But nothing stops you from going back and covering one of the older papers if you find it interesting. Perhaps you were just not aware of it before.
Here are some of our bat papers to date, showcasing the diversity and quality of chiropteran research in PLoS ONE:
Accelerated FoxP2 Evolution in Echolocating Bats
Echolocating Bats Cry Out Loud to Detect Their Prey
Bats Use Magnetite to Detect the Earth’s Magnetic Field
Absent or Low Rate of Adult Neurogenesis in the Hippocampus of Bats (Chiroptera)
The Perils of Picky Eating: Dietary Breadth Is Related to Extinction Risk in Insectivorous Bats
Bats’ Conquest of a Formidable Foraging Niche: The Myriads of Nocturnally Migrating Songbirds
Bats Avoid Radar Installations: Could Electromagnetic Fields Deter Bats from Colliding with Wind Turbines?
bat.gifNutrition or Detoxification: Why Bats Visit Mineral Licks of the Amazonian Rainforest
Paracellular Absorption: A Bat Breaks the Mammal Paradigm
Evidence of Henipavirus Infection in West African Fruit Bats
Temporal Dynamics of European Bat Lyssavirus Type 1 and Survival of Myotis myotis Bats in Natural Colonies
Genomic Diversity and Evolution of the Lyssaviruses
Marburg Virus Infection Detected in a Common African Bat
As always, you should rate the articles, post notes and comments and send trackbacks when you blog about the papers.
And if you work on bats, send your manuscripts to PLoS ONE. It is becoming quite a hub for bat papers and the people around them.

Circadian Biology in PLoS ONE

PLoS ONE has already published a large number of papers in chronobiology. But we want more. Hey, I work there – I want to see more.
So, when I went to the SRBR meeting in May, I did whatever I could to explain how PLoS ONE works and why my colleagues in the field should consider publishing with PLoS.
One thing we neeeded to give potential authors confidence is to add more chronobiologists to our Editorial Board in order to ensure that their mansucripts will be handled (and thus reviewed) by the experts in the field.
So, I am very happy to announce that we have secured editorial services of three excellent chronobiologists: Shin Yamazaki of Vanderbilt University, Michael N. Nitabach of Yale and Paul A. Bartell of Penn State. They WILL understand what your manuscript is all about, I promise 😉
So, if you have a manuscript in the works, consider PLoS ONE and join the revolution in publishing!

ResearchBlogging.org, v.2.0

The cat is out of the bag! The version2.0 of ResearchBlogging.org is ready to go and you can test it out:

After a week of late nights and hard coding, our development team has released the beta version of the site to our entire userbase! You can visit the new site here:
http://72.32.57.144/index.php/
We are planning on launching the site at the researchblogging.org address over the weekend, but you can get a head start now setting up your account, customizing it the way you like, and trying out all our new features. (note: All passwords have been reset, so you’ll need to use the “forgot password?” link to set your password)
There will be much, much more on our official launch date of September 2, but here is a partial list of new features:
* Multiple language support (and 30 new German-language bloggers!)
* Topic-specific RSS feeds
* Post-by-post tagging with topics and subtopics
* “Recover password” feature
* Email alerts when there is a problem with posts
* Users can flag posts that don’t meet our guidelines
* Customized user home pages with bios and blog descriptions
* Blogger photos/other images displayed with each post
* Multiple bloggers per blog
* Multiple blogs per blogger
* Advanced troubleshooting features
We’re super excited that the system is ready to go, and we look forward to seeing you on the new site!

Well, we took a little look at the PLoS HQ and noticed that out of 87 pages of ‘all results’ there are 8 pages of ‘PLoS’ results – implying that about 10% of all the BPR3 posts are on PLoS papers from all seven journals – and of those, 4 pages are just on PLOS ONE papers – which is about 5%. All I can say is w00t! for Open Access – when bloggers can read, bloggers will write.

Post-publication Peer-review in PLoS-ONE, pars premiere

Why is the letter P the most useful for alliterative titles?
But back to the substance. One thing that bugged me for a long time is that I often see on blogs or hear in person a sentiment that “there are no comments on PLoS ONE”. Yet I spend quite some time every week opening and reading all the new comments so I KNOW they are there and that there is quite a bunch of them already. Why the difference in perception? Is it due to the predictable distribution (a few papers get lots of comments, most get one or none, just like blog posts)?
So, when we saw this nice analysis of commenting on BMC journals by Euan Edie, we decided to take a look at our own numbers and see how they compare. We got the data together and sent them to a few people, mostly bloggers, to take a look. As they write their blog posts I will post the links here, especially when they do the nitty-gritty statistical analysis.
But for now, quickly out of the box, two of them have already posted their first impressions they took when they scanned the data.
Deepak Singh writes:

There people post a link and a whole discussion erupts (not always, but often enough). I would throw out this challenge (see the DOI suggestion above). Why should discussion be localized to PLoS One itself. If a paper pubished in PLos One is discussed in 20 other places, it would be considered a success. In other words, we shouldn’t limit our thinking to just on site commenting. Perhaps within the site, we should be focussed on ratings and perhaps tagging and notes.
——————–
So what have we learned from this exercise. Quite frankly, I am not sure. Is the commenting on PLoS One at a level that we hoped it would be? Not quite. Is it as bad as some might like to believe? Not quite. What we have is a very very nascent (no pun intended) effort on the part of the scientific community using web publishing platforms as a communication medium. I’d like to ask those same scientists to think about newsgroups. Most scientists are fairly comfortable participating in newsgroups, and here you essentially have one, with very clearly defined thread titles.

Cameron Neylon says:

In that context, I think getting the numbers to around the 10-20% level for either comments or ratings has to be seen as an immense success. I think it shows how difficult it is to get scientists to change their workflows and adopt new services. I also think there will be a lot to learn about how to improve these tools and get more community involvement. I believe strongly that we need to develop better mechanisms for handling peer review and that it will be a very difficult process getting there. But the results will be seen in more efficient dissemination of information and more effective communication of the details of the scientific process. For this PLoS, the PLoS ONE team, as well as other publishers, including BioMedCentral, Nature Publishing Group, and others, that are working on developing new means of communication and improving the ones we have deserve applause. They may not hit on the right answer first off, but the current process of exploring the options is an important one, and not without its risks for any organisation.

There are also two quick responses on Nascent and Genome-Technology.
What is most interesting is that there are no comments on Nascent and Genome-Technology, only a couple on Deepak’s and Cameron’s posts, yet a very nice long discussion on FriendFeed (very much worth reading, and not just for compliments to me)! What can we learn from that fact alone?
Second, the comment (by ‘comment’ I mean Ratings+Notes+Comments) to article ratio on PLoS ONE has risen from 1.1 a year ago to about 1.5 today. For comparison, my own blog has 1.6. And I get lots of comments – on a few posts, while zero or one on most. And I am prolific with quick/short posts like Quotes, so it is a decent comparison: not every paper is exciting or controversial enough (just like most of my posts are not) to motivate people to say anything.
Also, a blog post usually gets comments immediately. After 24 hours it is deemed stale and people move on to the new stuff. A scientific paper will be expected not to get any for the first few months and to only gradually accumulate them over the years as new information comes in that sheds new light on that paper. And I see this every week – older papers get a nice share of comments every week, while papers published this week do not.
See what I wrote last year about this:

One thing to keep in mind is that a PLoS ONE article is not a blog post – the discussion is not over once the post goes off the front page. There is no such thing as going off the front page! The article is always there and the discussion can go on and on for years, reflecting the changes in understanding of the topic over longer periods of time.
Imagine if half a century ago there was Internet and there were Open Access journals with commenting capability like PLoS ONE. Now imagine if Watson and Crick published their paper on the DNA structure in such a journal. Now imagine logging in today and reading five decades of comments, ratings and annotations accumulated on the paper!!!! What a treasure-trove of information! You hire a new graduate student in molecular biology – or in history of science! – and the first assignment is to read all the commentary to that paper. There it is: all laid out – the complete history of molecular biology all in one spot, all the big names voicing their opinions, changing opinions over time, new papers getting published trackbacking back to the Watson-Crick paper and adding new information, debates flaring up and getting resolved, gossip now lost forever to history due to it being spoken at meetings, behind closed door or in hallways preserved forever for future students, historians and sociologists of science. What a fantastic resource to have!
Now imagine that every paper in history was like that (the first Darwin and Wallace letters to the Royal Society?!). Now realize that this is what you are doing by annotating PLoS ONE papers. It is not the matter so much of here-and-now as it is a contribution to a long-term assessment of the article, providing information to the future readers that you so wished someone left for you when you were reading other people’s papers in grad school and beyond. Which paper is good and which erroneous (and thus not to be, embarrassingly, cited approvingly) will not be a secret lab lore any more transmitted from advisor to student in the privacy of the office or lab, but out there for everyone to know. Every time you check out a paper that is new to you, you also get all the information on what others think about it. Isn’t that helpful, especially for students?

I hope more of you join in the discussion, and I will post links to other posts as they appear over the next week or two.

Max Planck Society to support publication charges for PLoS journals.

This is big! A new agreement was signed between Max Planck Society and Public Library of Science in which the MPS will pay publication fees for its researchers. Mark Patterson explains:

The MPS is one of the world’s leading research organizations whose researchers have an international reputation for scientific excellence. We are delighted to be collaborating with the MPS in this way so that more MPS researchers will be encouraged to publish their work in PLoS journals, and to promote open access to research literature more broadly. For papers accepted in PLoS journals after July 1st, 2008, MPS will pay the publication fee directly to PLoS for all articles where the corresponding author is affiliated with a Max Planck Institute.
In 2003 MPS was the co-initiator of the Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities and ever since then, MPS has demonstrated consistent and strong leadership in the promotion of open access to research results.
With the ever-expanding range of open access options available to authors, we encourage other research funders to set up funds to cover publication fees in open access journals or to include such expenses within their grants and research awards.

The Max Planck Society issued a press release about this as well:

In accordance with its commitment to ensure public availability of its research output, the Max Planck Society (MPS) has reached an agreement with the Public Library of Science (PLoS) for the central funding of publication fees of MPS scientists without burdening the budget of single Max Planck Institutes.
Like many Open Access journals, PLoS journals charge a fee for publication. For papers accepted in PLoS journals after July 1st, 2008, MPS will pay the publication fee directly to PLoS from central funds for all articles where the corresponding author is affiliated with a Max Planck Institute.
“PLoS is a top quality Open Access publisher. We are pleased to support a seminal publication model with this collaboration and thus facilitate publishing for our scientists in this interesting spectrum of titles”, said Ralf Schimmer, head of the Department of Scientific Information Provision of the Max Planck Digital Library.
PLoS is a nonprofit organization of scientists and physicians committed to making the world’s scientific and medical literature a freely available public resource. PLoS applies the Creative Commons Attribution License (CCAL) to all published articles. Under the CCAL, authors retain ownership of the copyright for their article, but allow anyone to download, reuse, reprint, modify, distribute, and/or copy articles in PLoS journals, so long as the original authors and source are cited. No permission is required from the authors or the publishers. Thus, the contents of the seven Open Access journals of PLoS are freely accessible for the reader worldwide via internet.
Collaboration for promoting Open Access
“The Max Planck Society is one of the world’s leading research organizations whose researchers have an international reputation for scientific excellence. We are delighted to be working with MPS so that more MPS researchers will be able to publish their work in PLoS journals, and for the broader promotion of Open Access to research literature”, said Mark Patterson, Director of Publishing at PLoS.
The research institutes of the Max Planck Society perform basic research in the interest of the general public in the natural sciences, life sciences, social sciences, and the humanities. As co-initiator of the Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities (2003) MPS has actively supported change in scientific publishing in accordance with Open Access principles. MPS is advocating the position that research funding should include allocations for making research results freely available.”

PLoS ONE on FriendFeed

Last night I made another room in FriendFeed – PLoS ONE in the Media/Blogs. I made it primarily for my own use, linking to the media and blog coverage of PLoS ONE papers so I can have everything in one place.
But this should not stop you from using it, as well as from adding to it – if you read (or write yourself) a good article or blog post about one of the PLoS ONE papers, old or new, please place the link there and help me in my work. See the ‘Green Sahara’ example for the format I prefer (use the title and link of the paper, then add URLs of posts/articles in comments).

When science bloggers publish, then blog about it ;-)

On Tuesday night, when I posted my personal picks from this week’s crop of articles published in PLoS ONE, I omitted (due to a technical glitch on the site), to point out that a blog-friend of mine John Logsdon published his first PLoS ONE paper on that day:

It’s a updated and detailed report on the ongoing work in my lab to generate and curate an “inventory” of genes involved in meiosis that are present across major eukaryotic lineages. This paper focuses on the protist, Trichomonas vaginalis, an organism not known to have a sexual phase in its life cycle.

Here is the paper (and check John’s post for his experiences publishing in PLoS ONE):
An Expanded Inventory of Conserved Meiotic Genes Provides Evidence for Sex in Trichomonas vaginalis:

Meiosis is a defining feature of eukaryotes but its phylogenetic distribution has not been broadly determined, especially among eukaryotic microorganisms (i.e. protists)–which represent the majority of eukaryotic ‘supergroups’. We surveyed genomes of animals, fungi, plants and protists for meiotic genes, focusing on the evolutionarily divergent parasitic protist Trichomonas vaginalis. We identified homologs of 29 components of the meiotic recombination machinery, as well as the synaptonemal and meiotic sister chromatid cohesion complexes. T. vaginalis has orthologs of 27 of 29 meiotic genes, including eight of nine genes that encode meiosis-specific proteins in model organisms. Although meiosis has not been observed in T. vaginalis, our findings suggest it is either currently sexual or a recent asexual, consistent with observed, albeit unusual, sexual cycles in their distant parabasalid relatives, the hypermastigotes. T. vaginalis may use meiotic gene homologs to mediate homologous recombination and genetic exchange. Overall, this expanded inventory of meiotic genes forms a useful “meiosis detection toolkit”. Our analyses indicate that these meiotic genes arose, or were already present, early in eukaryotic evolution; thus, the eukaryotic cenancestor contained most or all components of this set and was likely capable of performing meiotic recombination using near-universal meiotic machinery.

Happy, er, conception-day?

Two years ago on this day, PLoS ONE opened for submissions (and surprisingly many manuscripts – 70 – got submitted immediatelly).

PLoS ONE theme of the month

For August, the theme is Natural and Synthetic Vision: Neuronal Mechanisms for Vision, Network Properties and Modeling, and Visual Psychophysics and Perception.

Happy birthday, PLoS Genetics!

PLoS Genetics is celebrating its third birthday this month! Let’s see what’s new this week, among else…
PLoS Genetics Turns Three: Looking Back, Looking Ahead:

PLoS Genetics is three years old this month–a milestone worth celebrating! As we do, and as we recognize all who have helped us reach this point in time, we thought this would be a good opportunity to share with you a summary of our brief history and a look ahead.
Our original intent was to provide an open-access journal for the community that would “reflect the full breadth and interdisciplinary nature of genetics and genomics research by publishing outstanding original contributions in all areas of biology.” Now, three years later, all of us on the Editorial Board are very pleased with the breadth of topics covered and with the diversity of approaches, organisms, and systems. Going forward, PLoS Genetics will continue to be a journal by and for the entire genetics and genomics community.

The Status of Dosage Compensation in the Multiple X Chromosomes of the Platypus:

Dosage compensation equalizes the expression of genes found on sex chromosomes so that they are equally expressed in females and males. In placental and marsupial mammals, this is accomplished by silencing one of the two X chromosomes in female cells. In birds, dosage compensation seems not to be strictly required to balance the expression of most genes on the Z chromosome between ZZ males and ZW females. Whether dosage compensation exists in the third group of mammals, the egg-laying monotremes, is of considerable interest, particularly since the platypus has five different X and five different Y chromosomes. As part of the platypus genome project, genes have now been assigned to four of the five X chromosomes. We have shown that there is some evidence for dosage compensation, but it is variable between genes. Most interesting are our results showing that there is a difference in the probability of expression for X-specific genes, with about 50% of female cells having two active copies of an X gene while the remainder have only one. This means that, although the platypus has the variable compensation characteristic of birds, it also has some level of inactivation, which is characteristic of dosage compensation in other mammals.

Pain Genes:

Pain, which afflicts up to 20% of the population at any time, provides both a massive therapeutic challenge and a route to understanding mechanisms in the nervous system. Specialised sensory neurons (nociceptors) signal the existence of tissue damage to the central nervous system (CNS), where pain is represented in a complex matrix involving many CNS structures. Genetic approaches to investigating pain pathways using model organisms have identified the molecular nature of the transducers, regulatory mechanisms involved in changing neuronal activity, as well as the critical role of immune system cells in driving pain pathways. In man, mapping of human pain mutants as well as twin studies and association studies of altered pain behaviour have identified important regulators of the pain system. In turn, new drug targets for chronic pain treatment have been validated in transgenic mouse studies. Thus, genetic studies of pain pathways have complemented the traditional neuroscience approaches of electrophysiology and pharmacology to give us fresh insights into the molecular basis of pain perception.

Stable in a Genome of Instability: An Interview with Evan Eichler:

We like to think that our genome is rock-solid, that it is dependable, there for us when we need it. The truth is far from that. By fits and starts, our species’ collective genome is undulating, reshaping itself with eruptions of genomic lava and clashes of sequence tectonics, at once both marvelous and unsettling. We are unaware of this tumult within us until we are confronted with disease in ourselves, our friends, or our family.
Evan Eichler is a man obsessed with this process, and to speak with him is a study in contrasts (Image 1). An unassuming Canadian, Eichler is a student of genomic architecture, the arrangement of sequences in our genome, and their evolution. Eichler grew up on a farm in Manitoba, married his college sweetheart, and now lives together with her and their four children in the mountains east of Seattle. As we walked up the hill to my office during his recent visit to UCSF, he talked about being an early riser, taking his son to band practice before school, and then driving the 30 miles to work in his Toyota. Eichler is a man bristling with excitement for his discoveries, but holding it in check by a tradition of modesty. He has consistently followed his own path, chosen career opportunities that were dictated not by politics or peer pressure but rather by what feels like a good fit for him.

Nice shirt, Eric!

I am currently reading – and enjoying very much – The Carbon Age: How Life’s Core Element Has Become Civilization’s Greatest Threat by Eric Roston.
He was recently interviewed for DC Examiner and they ran a picture of him wearing a familiar t-shirt 😉
Eric%20with%20a%20shirt.JPG
Recently, Eric was quoted in TIME and lambasted by Rush Limbaugh, which, as Tom notes, means that Eric made it Big Time!

TOPAZ upgrade

TOPAZ software, the one that hosts five out of seven PLoS journals (ONE, Pathogens, Neglected Tropical Diseases, Genetics and Computational Biology) has just been upgraded. There is not much new in the terms of functionality visible to readers, but the upgrade should greatly increase the stability of the sites and the speed of loading of papers, comments and other pages.
Give it a test-drive: search and browse papers, download PDFs, post comments/notes/ratings, send trackbacks, and if you notice any glitches, let us know exactly where you were, what you were trying to do, and what happened (there is usually a “contact” or “report” button somewhere on each page, but you can also just e-mail me).

On the PLoS ONE publishing model

Now that the spirited debate about the comparative business models of Nature and PLoS has died down, it is nice to take a little break from it all, and then start a new round – this time about publishing models, not business, and what it means for the future of the scientific paper – how the peer-review, impact factors, researcher evaluation, etc. are changing. Of course I am biased, but I love what Cameron Neylon just posted on his blog: What I missed on my holiday or Why I like refereeing for PLoS ONE:

To me the truly radical thing about PLoS ONE is that is has redefined the nature of peer review and that people have bought into this model. The idea of dropping any assessment of ‘importance’ as a criterion for publication had very serious and very real risks for PLoS. It was entirely possible that the costs wouldn’t be usefully reduced. It was more than possible that authors simply wouldn’t submit to such a journal. PLoS ONE has successfully used a difference in its peer review process as the core of its appeal to its customers. The top tier journals have effectively done this for years at one end of the market. The success of PLoS ONE shows that it can be done in other market segments. What is more it suggests it can be done across existing market segments. That radical shift in the way scientific publishing works that we keep talking about? It’s starting to happen.

Read the whole thing and let Cameron (and me) know what you think.

Gene Expression in PLoS ONE

As you probably know by now, we have monthly themes in PLoS ONE. This month, the topic is Gene Expression, where there are more than 140 articles already, mainly looking at genome-wide expression and epigenetics. Of course, we want more. And I am still looking for a group to do a Journal Club on one of the related papers, so if you are interested, let me know.

On the Nature of PLoS….

I know that you know that I work for PLoS. So, I know that a lot of you are waiting for me to respond, in some way, to the hatchet-job article by Declan Bucler published in Nature yesterday. Yes, Nature and PLoS are competitors in some sense of the word (though most individual people employed by the two organizations are friendly with each other, and even good personal friends), and this article is a salvo from one side aimed at another. Due to my own conflict of interest, and as PLoS has no intention to in any official way acknowledge the existence of this article (according to the old blogospheric rule “Do Not Feed The Trolls”), I will only send you to the responses by others who felt compelled to comment about the article. You can also, if you wish, post a comment on the article itself.
Peter Suber:

Declan Butler last used tax records to investigate PLoS’ finances in June 2006. See some of the comments (first set, second set) generated by his investigation.

DrugMonkey:

Since they are in science however, we can expect Nature to be totally objective and to eschew blatantly self-serving editorials and news focus pieces that gratuitously bash the competition. Can’t we? Yeah right.

Jonathan Eisen:

So why is the success of PLoS One a problem? Well, because it allows Nature to do the old good cop bad cop routine and to write, again, about the “failings” of the PLoS publication model. Now, mind you, the article does not quote a single source for what the PLoS publication model is. But they do say it has failed.

Vanya:

Hmmm…but tell us how you really feel. In case you’re wondering, the “bulk, cheap publishing of lower quality papers” takes place in PLoS ONE. Sigh. I’m an author on one such “lower quality paper”. I’d break down and cry if it weren’t for the feedback, citations and media coverage we received on that paper.
In the words of my labmate who chooses to go unnamed:
“maybe Nature, at the end of their articles, should write Competing Interests: The authors have declared that competing interests exist and we like to talk bad about a competitor’s economic model”
Seriously though, I wonder if Nature realises that their article comes across as being extremely one-sided and very childish.

Greg Laden:

Some will say that the Nature piece by Butler is negative or even cynical regarding PLoS. Maybe. But on close examination, perhaps Butler is just doing his job as a journalist, asking questions, probing, seeking clarity. In the mean time, PLoS clearly stands up well against these questions.
One thing that does bother me a bit about the Nature piece is this: To the extent that it can be seen as negative, it must be seen as negative about a competitor. Normally one would expect a discloser statement indicating that where PLoS loses financially, Nature gains. The sources cited by Butler who have negative things to say about PLoS are also either competitors or simply anti-OpenSource.
I am absolutely confident that Butler and Nature will address (or even redress) this apparent misstep.

Razib:

I won’t really get into the details here. I think the article makes some good factual points, but they’re stitched together in a manner to depict PLoS in a rather unfavorable light. The kicker of course is that Nature has some major conflicts of interest here.’

Razib:

PLoS, does it suck? (check the comments thread)

GrrlScientist:

Wow, have you read Declan Butler’s nasty little hatchet job that was just published in Nature about the Public Library of Science (PLoS)? My jaw hit the top of the table in my little coffee shop where I am ensconced — why would Nature demean their journal by publishing such a snotty little screed where they attack the normal, but probably painful, financial ups-and-downs of a new journal?

Alex Holcombe:

Nature has published a news item by Declan Butler on the finances of one of its competitors: the open-access PLoS journals, using language that puts the organisation and its journals, especially PLoS ONE, in a negative light.
The fact that PLoS does not meet its costs exclusively from the author publication fees, as Nature focuses on, is interesting, especially from the point of view of an organization like Nature Publishing Group, whose purpose is to make a profit. But….

Mike Dunford:

A story that fairly examined what PLoS ONE has done so far, how it’s perceived by other scientists (or even how aware other scientists are of it), and whether the increased number of articles appearing there means that more scientists are using the journal’s articles as resources would be an interesting read. It’s sad that Butler and the editors at Nature decided to go with the snide hatchet job instead.

PlausibleAccuracy:

Ok, so I think I agree that the article is sort of unnecessarily rude and demeaning, but I wouldn’t really expect anything different from a for-profit publisher. The worst part is that everything Dr. Butler tries to imply is a failing of PLoS has been done many times over in the closed-access for-profit journal community. Right, so let’s try to look past the blatant attack and take a look at the actual facts, shall we?

Insilico:

Nature has some news to tell the world about their rival PLoS (Public Library of Science). Open source publishing by PLoS thrives on charity funding. Does the business model needs a redesign of it’s aims, goals and strategies? Or is it a cheap trick from scared Nature publishing? Judge yourself….

Bill Hooker:

This clumsy hatchet job from Nature reporter Declan Butler is beneath him, a poor excuse for journalism and an affront to the respect with which many of his colleagues are regarded by the research community.
Let’s start with the title: “PLoS stays afloat with bulk publishing”. Loaded rhetoric, anyone? The clear implications are that PLoS is floundering (Butler’s own numbers show otherwise!), and that “bulk” is somehow inferior (to, one presumes, “boutique” or some such). PLoS is “following an haute couture model of science publishing” sniffs our correspondant, who goes on to clarify: “relying on bulk, cheap publishing of lower quality papers to subsidize its handful of high-quality flagship journals”.
This emphasis on “quality” and the idea that the same somehow equates with scarcity continues throughout: “the company consciously decided to subsidize its top-tier titles by publishing second-tier community journals with high acceptance rates”, “the flood of articles appearing in PLoS One (sic)”, “difficult to judge the overall quality”, “because of this volume, it’s going to be considered a dumping ground”, “introduces a sub-standard journal to their mix”.
The intent is obvious, and the illogic is boggling. Where does Butler think the majority of science is published? Even if you buy into this nebulous idea of “quality” (one knows it when one sees it, does one not old chap? wot wot?) there can be no “great brand” journals without the denim-clad proletarian masses. All the painstaking, unspectacular groundwork for those big flashy headline-grabbing (and, dare I say it, all too often retracted) Nature front-pagers has got to go somewhere.

Greg Laden:

My own criticism of “peer review” is really meant to be a broader critique of the publishing process overall. Furthermore, my belief is NOT that the situation with science publishing is totally screwed up, but rather, that there are some real problems that must be addressed, and PLoS as Open Access and PLoS as on line is an important model for what I see as a good approach to solving some of these problems.

Dave Munger:

My goodness! PLoS has received $17 million in grants! This is obviously a signal that things are going badly for the revolutionary open-access publisher. They’re resorting to handouts! When a charitable organization continues to earn the respect of more and more foundations, increasing its bottom line year after year, it’s clearly a sign of impending doom!
——————-
Clearly this demonstrates that Harvard is in dire circumstances, just like PLoS. Don’t let Harvard and PLoS’s impeccable reputations fool you. When granting institutions and other donors want to give non-profits large sums of money, it’s a sign of their inevitable decline. Fortunately we have private institutions like Nature, the University of Phoenix, and DeVry University to take their place.

ocmpoma:

Several blogs over at ScienceBlogs are discussing a recent review of PLoS, a major open access organization, in Nature. Their opinions of the piece are not very high. Here’s Gene Expression, whose post lists out several others on the subject; here’s Greg Laden’s Blog, which brings a broader discussion of peer review into the discussion; and here’s Living the Scientific LIfe, which has what I think is the best summary of the main points in the review, and the problems with them.

janeblum:

Personally, I think Nature has as much right as any business to take potshots at the competition. Whether they are wise to do so remains to be seen. I doubt that true believers on either side of the open access movement are going to persuaded by the article or the reactions to it, so it’s difficult to see what they gain. And as Britannica learned when it challenged wikipedia, such challenges can come back to haunt you later. Britannica endured an extended comparison of the accuracy of its articles versus those in Wikipedia, and now includes wikipedia-like features. Will we see Nature Publishing Group journals change as a result of this discussion?

SciCurious:

I wouldn’t know one thing or another about PLoS’ financial status. I can barely keep my own bills straight without looking at other people’s. But I do know that there’s no shame to be had in publishing in one of PLoS’ “lower level” journals. They’re pretty well respected in my department. As for PLoS ONE, my own advisor told me just yesterday that she’d LOVE to have a PLoS ONE article. Grad students in my department present PLoS ONE articles in Journal Clubs, and many of the respected people in my field send papers there.

Richard:

Nature does really well at the first section but does it really ensure that the results are rapidly disseminated to the public throughout the world? Or does charging for access fulfill the ‘fashion that conveys their significance’? if you pay for something does that enhance its significance?
Interestingly, Nature did not make a profit for more than 30 years:

juniorprof:

In closing, I’d just like to say a few words about science in developing countries and open access. I hope that as scientists we can all recognize the important role that science and researchers can play in helping developing countries achieve their goals. Research is a powerful tool in the repertoire of education. Moreover, many developing countries have urgent research needs that don’t register on the radar of countries that have reached industrialized status. Even if institutions in developing countries receive discounted access to pay journals it is money spent that could be dedicated to other aspects of research or education. These researchers must have access to literature to succeed and they must also have as many research dollars as they can get their hands on. Open access can be a powerful tool in this fight. My personal opinion is that open access journals, and PubMed Central in particular, can and should be key aspects of how we can bring science, education and research to developing countries. Think about that when you’re putting off depositing your papers in PubMed Central or when you’re considering the appropriate venue for your next publication

Bruce Sterling:

I also really love it when scientists abandon all reserve and objective dignity and start backstabbing and eyegouging in public.

Bjoern Brembs:

It needs to be pointed out here that publishing in these “non-light” journals decides over grants, tenure, promotions and thus peoples’ careers and livelyhoods. So one could paraphrase the current system of publishing in science in the following way: If the scientific community were a large corporation, it would be out-sourcing it’s hiring and firing to a group of ex-employees who either left the corporation because they didn’t like it or were fired themselves. Now how many managers would implement such a system in their company?
Instead, we should have one single, decentralized, publicly accessible database where the current assessment by editors (i.e., the “non-light” component of peer review in e.g. Nature) comes after publication as one of many measures of post-publication review and assessment. The first review should be done by scientists on the science – whatever happens to the paper afterwards is open to debate. I, for one, value the input of professional editors and their expert judgement of scientific newsworthyiness and would not want to miss it.

John Dupuis:

As most science librarians, I am somewhat critical of Nature’s tendency to charge boatloads of money for their journals and journal backfiles, but I do accept that what they do costs money and that they have a right to run their company as they see fit. I don’t have a problem paying for stuff that has real value.
However, I do have to say I am very disappointed with this turn of events. Notwithstanding their journal business, I have always been very impressed by the web group at Nature and the fine work they have done on products like Scintilla, PostGenomic, Precedings, Connotea, Nature Network and others. Those are, for the most part, fine products that are really pushing the edges and trying new and exciting things. They are of of the few commercial publishers that really seems to get doing science on the web and I’ve been happy to promote those products and services in my community here and to present about them to a wider audience. Of course, OA is a very important piece of the puzzle of doing science on the web and PLoS is also trying new and exciting things and really seems to get it. There’s a real conflict there. Perhaps Nature’s left hand should be telling it’s right hand what’s really going on out here.

Hank (this one is difficult to understand as it is full of misunderstandings of who the players are, how they operate, what the relationships between them are, etc. – the tacit knowledge that people on the inside take for granted and do not realize sometimes that people on the outside do not know – yet sometimes those on the outside feel compelled to comments as if they know – welcome to the blogosphere, this is what makes it vibrant and good! Who knows, someone may take time out of the holidays and go there and explain the complex networks of publishers, bloggers, etc, and who is who, and how Nature works, how PLoS works, etc., though all that information is findable on the web via, for instance, Google search):

Should Nature writers with integrity be a fan of all open access publications? Well, no, not if it is a free-for-all just to make money. Nor should we. Declan Butler taking what he knew what would be an un-popular stand, especially given his employer and the claims of bias it would engender, is to be applauded. Not saying anything would have been the easier, diplomatic road. And completely wrong.

Timo Hannay:

To look on the bright side, none of this may matter very much in the longer run since truly widespread open access to scientific content is coming about through funder-mandated archiving, not open-access publishing. Nevertheless, the ironies and misunderstandings are just too stark to pass them by without comment.

Greg Laden:

A number of bloggers, including myself, had suggested that Delcan Butler’s anti-PLoS writup in nature constituted an attack of one company against another. How silly of us to have done so. Here’s what we should have been thinking instead:

PhysioProf:

Notice how this dude unquestioningly equates the “lowness” or “highness” of a journal with the quantity of “editorial input”? This is totally fucking ridiculous. Journal editors do the best job when they identify good reviewers who understand the importance and reliability of a particular piece of work, and then stay the fuck out of the way.

Michael Meadon:

I like open access. In my opinion, the serials crisis is an absolute travesty and, despite my ‘capitalist’ instincts, the spectacle of huge companies making profits from the efforts of academics who (a) are not in the companies’ employ and (b) are funded (largely) by taxpayers, utterly disgusts me. So it rather pisses me off that the august Nature magazine (which, I should note, I have difficulty accessing because my institution can’t afford the subscription fee) has published a bloody screed against PLoS, the best known open access suite of journals. The screed opens thusly:

Greg Laden:

The flap that started with the ill advised commentary by Delcan Butler started out looking like it MIGHT be an Orwellian, perhaps Nixononian attempt by a well established publishing icon in the fields of science to damage an up and coming competater, the Public Libary of Science in particular, and the Open Access Movement more generally. As time goes by, however, I start to get the impression that it does not merely look this way, but may actually be this way.

Lars Juhl Jensen:

I want to be the first to point out the caveats of this analysis. First, the analysis above did not take into account that each journal does not publish the same number of papers. However, weighting the journals by number of papers when calculating average impact factors shifts the balance in favor of PLoS (9.79 for PLoS vs. 9.46 for NPG). Second, the journal PLoS ONE does not have an impact factor yet and was thus not included in my analysis. Third, the criticism by Declan Butler was mainly targeting the fact that much of PLoS’ revenue is due to PLoS ONE. However, until NPG chooses to make available detailed financial reports like PLoS does, it is impossible to tell how much of their revenue comes from lower-impact journals.

Greg Laden:

The House of Commons (U.K.) Select Committee on Science and Technology investigated Open Access publishing alternatives, and pursuant to this obtained written evidence from Nature Publishing Group consisting of answers to specific questions about “pay to publish.” Here are excerpts from the document. Given the current discussion on Open Access publishing, this may be of interest to you.

Mike Dunford:

Timo Hannay just responded, over at one of Nature’s blogs, to the hordes of bloggers who were somewhat displeased with the tone and content of Declan Butler’s recent Nature article. Now that someone from Nature has returned fire, and other bloggers have fired back, it’s likely that this whole thing is going to turn into one of those multi-day, multi-article kerfuffles that do so much to maintain blogging’s reputation as the WWE of the scientific world. Which is cool, as far as I’m concerned. It’s been a while since I’ve grabbed a folding chair and climbed into the Cage of Death. I’m ready to go.

Pedro Beltrao:

Going back to one of Timo’s main points, I don’t agree that PLoS creates barriers to market entry to other OA publishers. At least certainly not because they used philanthropic grants until they reached break even point. If there are barriers in the market they are due to perception of quality and strong brand name. Here OA publishers have the added advantage that creating a strong brand is easier when most people perceive OA as something good. From the example of PLoS and to some extent BMC there are now clear paths for any publisher (specially one with a strong brand name) to set up a viable business OA model.

Mario Pineda-Krch:

It’s nice to hear Timo Hannay’s view of open content (actually rather refreshing after reading Declan Butler’s tantrum piece). I am a bit puzzled, however. Does Hannay’s views represent the view of the Nature Publishing Group as a whole or do they represent only his own views? And, how does all of this fits in with the Nature vs. PLoS runaway train of Declan Butler that has been whipping up a storm in the blogosphere over the last few days (see Bora’s post for a succinct summary). The pieces by Declan Butler (he actually has two stories, the second and the first) unequivocally give a impression that Nature is (as Timo puts it in the clip) on of those “hostile” and “reactionary” publishers that are in a “defensive mode” towards the Open Access publishing model that “give the whole industry a disservice”.

floatingnotes:

Many critics are complaining about either the appropriateness of Nature criticizing a competing journal (without explicitly discussing conflict of interest) or for criticizing open-access in general. I think it is entirely appropriate for Nature to write well-argued, well-reasoned articles on science publishing, even discussing competing models critically, but the Butler article under question does not pass these criteria IMO.

Niyaz Ahmed:

I found the overall tone and spirit of the news article quite disturbing and distasteful. Especially, their painting of PLoS ONE journal as a ‘dumping ground’ and mention of its peer review process as ‘light’ is not at all correct and ignores facts. I see it as an unsuccessful attempt to dump all the ground-breaking work that PLoS ONE has been publishing since its launch in 2006 (see these posts for exmple; here, here and here). As I said in my response to the story, it is a simple fact that the ~300 scientists who publish in PLoS ONE every month and the 500 Editors who devote their time on rounds of peer reviewing are certainly not the fools out there.

Zen:

My only comment for now is to repeat the mantra that led me to start this website. Ideas that spread, win.

Stevan Harnad:

Nature’s reply states that “Nature isn’t anti-open access,” but it neglects to mention that Nature back-slid in 2005 — from having at first been Green on OA self-archiving by its authors to rejoining instead the minority of journals who still try to embargo access. Nature’s reply also misses the real growth region of Green OA mandates, which is now institutional and departmental mandates like Southampton’s, QUT’s, Minho’s, CERN’s, Liege’s, and now Harvard’s and Stanford’s, rather than just funder mandates.

Greg Laden:

The following are excerpts from the journal Nature regarding the Public Library of Science. These were located with a simple search for the phrase “Public Library of Science.” For each item, I provide the source, and a selected bit of text. I have no selection criteria to report, but I do have a reason for doing this: To give an interesting view of the history of PLoS as a concept and an entity, and to some extent, the reactions to PLoS from various quarters.

Peter Suber:

Stevan is right to correct the impression that all OA is gold OA (through journals), and to remind everyone of green OA (through repositories). But “free online access” is itself only part of the story. Stevan links from that phrase to a more complete discussion. But because he doesn’t elaborate in his post, I’ll elaborate a little. The term “OA” is now used in at least two ways: (1) to remove price barriers alone (“free online access” or gratis OA) and (2) to remove both price and permission barriers (libre OA, which includes BBB OA). The gratis/libre distinction is not the same as the gold/green distinction. The former is about rights or freedoms, and the latter is about venues. Gold OA can be gratis or libre, and green OA can be gratis or libre. Just as we can’t afford to forget about green OA, we can’t afford to forget libre OA.

Oca sapiens:

Cosa gli ha preso a Declan Butler sull’ultimo Nature, di attaccare in quel modo la Public Library of Science? Che il gruppo open access non faccia profitti, si sa, ma davvero PLoS ONE rastrella qualunque articolo, senza tener conto del suo valore? O pubblica risultati interessanti e qualche volta discutibili, ma dando la possibilità a tutti di discuterne? Commenti.
Be’, vado a Modena, dove “Oltre i giardini” mi ha messa nella sezione scienza, ma dev’essere un errore.

ob:

Mittwoch publizierte der renommierte NatureNews-Redakteur Declan Butler eine – allgemein als nasty bezeichneten – Artikel über PLoS: PLoS stays afloat with bulk publishing: Science-publishing firm struggles to make ends meet with open-access model. Die Kommentare dort sind mehr oder weniger einhellig der Ansicht, dass Nature einen Wettbewerber “gedisst” hätte. Stellvertretend hier zwei Kommentare:

Bjoern Brembs:

Editors of schorarly, peer-reviewed journals often claim that somehow their choosiness is the most important verdict on the quality of a scientific manuscript. Points in case are Nature Neuroscience’s peer-review policy, a recent Nature News article or a follow-up on the Nature blog “Nascent”. However, data on the ‘impact’ or quality of papers published in these very choosy journals varies greatly. Therefore, I have a suggestion on how to judge the performance of an editor. My suggestion requires that all peer-reviewed scientific primary literature is deposited in some database before any subjective editorial choice has been made. An example would be PLoS One, but any such database would do. Then, editors can thumb up or thumb down papers after they have been vetted by peers and promote or demote papers according to their judgement, very similar to acceptance and rejections in so-called high-end journals of today. Since all choices (also rejections!) are recorded, each editor (or goup of editors) will establish a track record. In a way, this is similar to the concept of the Faculty of 1000. Obviously, this will provide a great incentive to maximize their reliability as gatekeepers of scientific quality. How can their performance be measured? By counting downloads, citations, trackbacks, comments, ratings, media coverage, Fac1000 mention or any other measure deemed relevant of the papers they accepted/rejected.
That way, everybody would get their cake and eat it too: seemingly objective performance measures for both scientists and editors. Wouldn’t that be fair?

Ricardo Vidal:

What I find to be the most notorious aspect in this whole string of events is that there is quite a large community of science bloggers that are ready to offer their “peer-review” in situations such as these. Is this a good thing? I would like to believe so…

Philip Davis:

In an expository news piece released in last week’s issue of the journal Nature, Declan Butler describes how the Public Library of Science is attempting to stay afloat by using lower-cost, “bulk publishing” with PLoS One to offset mounting costs of publishing PLoS Biology and PLoS Medicine.

Bjoern Brembs:

I’m sure nobody ending up on this obscure blog could have missed the current frenzy about a Nature news article by Declan Butler attacking PLoS. In the meatime, there has been a follow-up by Nature publishing director Timo Hannay, also with comments and a reply by Timo. I think what we see here are the labor pains of a new scientific publishing model. People realize that things are not working effectively, some would maybe even claim that the entire system is broken and needs to be replaced. A good overview can be had from Coturnix in his post, but there are also comments worth noting individually such as Pedro Beltrao, Greg Laden, Lars Jensen, Mario Pineda-Krch, DrugMonkey or Bill Hooker.

Mike the Mad Biologist:

That’s why I almost never review articles for these journals anymore (as opposed to Open Access journals, which I do–two in the last month alone, and that’s during grant season). Seriously, if they ever did want me to review, then they have to pay me just like any other business who wanted to consult my expertise would. If enough of us did that, well, things would get very interesting….

donham nise:

If you haven’t already, take a look at the PLoS Biology or the new journal PLoS One (a direct competitor for Nature since it accept all sorts of articles). From an occasional reader perspective, the articles are authoritative, attractive, and visually appealing.
While Nature remains one of two pre-eminent science journals (the other is Science), it is clear that “the times they are a changin.” The Nature editorial staff clearly recognizes this-and maybe they are a bit worried.

DrugMonkey:

A recent foofaraw (including offerings from YHN and PhysioProf) arose over an ill-advised tone struck in an attack editorial thinly veiled as an analytical news item published in Nature. The discussion has brought Open Access science [several tomes on OA linked here] back to the blog-table for discussion. I have another thought, beyond my reaction to the sneering tone of the aforementioned attack editorial. One of the ways I think the Nature piece may possibly have gone astray is in not recognizing the depth to which their customers, research scientists, are reflexively sympathetic to the notion that our product–the primary scientific observation–should be freely available to all. I have been interested to hear some perspectives on why Open Access trips the trigger from some bloggers not previously on the OA Nozdrul or wackaloon lists.

John Wilbanks:

And, speaking as an entrepeneur, criticizing a startup for high-flying rhetoric and missed revenue projections in its first five years of operations is kind of ridiculous. If we did this kind of fisking on every web company – or even on Nature’s web 2.0 operations, which I doubt pay their own bills with ads and revenue – we wouldn’t have very many startups left to kick around.
——————-
The final takeaway is that everybody involved probably needs a deep breath or five. The article wasn’t that bad. Inartful, yes. Inaccurate, probably not. But the real story here is that the data in the article tell us PLoS is figuring out a path to making it, and has investors in it for the long run. How can that be bad?

Greg Laden:

This item is to be found at the blog called The Scholarly Kitchen. This is a blog of the “Society for Scholarly Publishing” … which is presumably a trade organization supporting the evil, pirate-like publishers. The piece makes a couple of absurd points and one major, major mistake. I have visited the blog and corrected it. They may not like it.

My Biotech Life:

I like the idea of PLoS as a startup that is keeping to it’s original goal while trying to work out the kinks regarding the open-access publishing model. And I agree, they have produced high quality peer reviewed science.

Stevan Harnad:

In other words, while appearing to be doing OA a service, this Nature policy is actually doing Nature a service and only giving OA the minimal due that is already inherent in the NIH and kindred mandates.

Anders Norgaard:

One perspective which has been overlooked a bit, as far as I can tell is that Nature has managed to frame the debate. Intentionally or not.
The framing can be summarized as “the problem is that top tier journals can’t be profitable as open access – author pays, in competition with Toll-Access journals”. This framing is advantageous to Nature as it implies that “the author-pays principle must generate all revenue for OA journals – subsidies are not ok”. Equally advantageous is it when “top-tier journal” is defined not only as “high rejection-rates” but also “high overheads”. Nature has an interest in making the two things seem inseparable.
For society and everyone who is not Nature (or other Toll-Access, high overhead journals) the framing does not make sense. The debate is part of a broader debate of the future of scientific publishing. And it is unreasonable to assume that a future of efficient digital publishing must be hobbled to serve to needs of businesses adapted to the past of high cost of paper distribution. Or that it must be measured by the same criteria of success (high profit from monopoly priviledges) as old businesses.

Georgia Harper:

Well, I will leave it to all of you to figure out if you have sufficient “rights” to read the article itself, but do go read the comments. Too bad about whatever data supports the whole conversation. We pobrecitos don’t have access to that, just to the rants about the results. Ah, transitions.
Of course, I could spend some of my very limited time today clicking my way through the variety of screens I must click through to get to my library’s walled garden where I suspect this article is cached away. Maybe it’s worth it. Maybe not. Today it’s not. It’s summer, I’m on vacation. Only minimally attentive to tedious things like journal article search interfaces. And why is it that publishers do this to libraries? Oh, yes, I’m so sure they have their very good reasons. And I have mine for ignoring authors and their writings whose publishers make their work hard to find and read. So much to read, watch, listen to. So little time. There’s the basic fundamental of Open Access. The business models will follow.

David Crotty:

It’s certainly good news that PLOS has found a way to cover their costs and continue the noble experiment they’ve undertaken. I’m not sure how good the news is for other publishers interested in experimenting with open access and author-pays models. Publishers and societies may not be able to drum up the large amount of donation funding needed to keep a highly selective journal in the black. They may not be all that interested in running streamlined, higher-volume journals to cover costs. It’s also very unclear how many of these type journals the market will bear-if every publisher starts one, will there be enough material/interest to continue to cover costs in other ventures?

Corie Lok:

Reading through some of the comments and blog posts about the article reminded me of a real-live discussion I sat in on at Scibarcamp back in March in Toronto. One senior, high-profile physicist at the event said how disillusioned he was with the science blogosphere. He said he’s been really turned off by the nastiness and divisiveness he’s seen. He said the science blogosphere has not fulfilled its promise of being a forum for serious scientific discussion. (Not to say that all blog posts and comments about the Nature article were mud-slinging; I saw some very good discussions. And not to say that all science bloggers engage in ranting. I’ve seen plenty of blogs that do engage in high-quality conversations but I’m sure many bloggers have stories to tell about the nastiness they’ve read or experienced online.)
Now, maybe it’s a generational thing. Those of us who didn’t ‘grow up’ with blogs might be more easily taken aback by what goes on in them. Those of us who did grow up with them perhaps have learned to take the bad with the good.
But still, I wonder how many other scientists out there would agree with this physicist? If there is a critical number of them out there agreeing with him, what does this mean for science blogging?

Charles W. Bailey, Jr.:

What the Nature article misses is that the scholarly evaluation of PLoS ONE articles does not end with the initial screening review for compliance with the stated Criteria for Publication. Rather, it begins there. PLoS ONE is using a radically different model of peer review than traditional journals. Whether it is a success or failure is not primarily determined by how many articles it publishes, but by the effectiveness of its post-publication review system in assessing the value of those papers.
If PLoS can reduce costs in what the article terms its “second-tier community journals” by using larger academic editorial staffs, there does not appear to be anything intrinsically wrong with that. To the contrary. The issue is not the editorial strategy, rather it’s whether the author fees are unjustifiably high in relation to journal costs and whether the excess profit is being siphoned off to support other publications. Although comparative author fee data is given in the article, there is not enough economic evidence presented in the article to make any informed judgment on the matter.
Regarding grant support, I presume that Jerram understands the issue better than outsiders, and, if he believes that PLos can become self-sustaining in a few years, then there is no reason to doubt it, barring unforeseen circumstances.

Annalise Paaby:

Perhaps I am biased–perhaps my work is generally free of serious methodological flaws–but my experience revealed the PLoS One editorial process to be the most rigorous of the three journals to which I sent my first paper.
It was disappointing to get rejected twice before publishing in PLoS One. But the real frustration was that of the five reviews from the first two journals, three of the referees did not understand the work. (One was downright insulting.) The two reviews from PLoS One, however, were thorough, detailed and clearly by researchers who understood the work. A reflection of an editorial process of high integrity, certainly, and not an unusual one.

ob:

Da kann man als Wettbewerber wirklich neidisch werden und als Bibliothek durchdrehen… War Nature nicht auch derjenige Verlag, der seine kürzlichen exorbitanten Preisanstiege (40% in einem Jahr, gnädig verteilt auf 2-3 Jahre für Konsortien) mit dem Argument verteidigte, man wäre mit zu niedrigen Preisen am Markt eingestiegen und müßte diese nun nach oben anpassen, weil man sein Marktziel (sprich Profitmarge) nicht erreicht hätte. Oh, könnte ich nur mit meinem Dekan auch mal so sprechen!! Aber dafür muß man wohl 3 Jahre auf eine Sprachschule für Marketingdeutsch…

Joseph J. Esposito:

Declan Butler’s recent piece on the PLOS business model was cited
on this list. I think Butler is attempting to hold PLOS to a
standard that few publishers attain, including Butler’s own
employers at the Nature Publishing Group.
What PLOS is doing (whether you like the practice or not) is
simple brand extension. There are highly presitigious and
selective PLOS publications, whose aura is being transferred to a
new program, PLOS One, which has a different editorial
methodology. We are all familiar with this; most members of this
list work with Microsoft Windows, Microsoft Internet Explorer,
Microsoft Word, and Microsoft Excel; renegades may own an iMac,
iPod, and and iPhone. The Nature Publishing Group has been among
the most aggressive STM publishers in extending its brand to new
publications. Indeed, a rival of Nature wryly remarked to me
(enviously, perhaps?) that Nature had put its name onto so many
publications that he was awaiting the announcement for “Nature
Nature.”
PLOS is not above criticism, but let’s not insist that an OA
service compete with toll-access publishers on what are truly
spurious grounds.

Tobias Maier:

In einem Nature Artikel der vergangenen Woche wurde der Rivale PLoS hart angegangen. Nature behauptet, PLoS (sieben unterschiedliche Journals werden von PLoS ausschliesslich open-access verlegt) würde ihr Konzept damit finanzieren, dass sie Artikel niederer Qualität ohne ausreichenden peer-review Prozess für einige Magazine akzeptieren, um mit Hilfe der so eingesammelten Publicationfees ihre Flagship – Journals PLoS Biology und PLoS Medicine, finanzieren zu können.
Einen guten Überblick über die Blogreaktionen zu der Debatte auf der ScienceBlogs.com Schwesterseite bietet Bora Zivkovic, Online Community Manager des kritisierten PLoS Jounrnals, hier auf seinem Blog around the Clock.
Mein Kollege Anders Norgaard liest viel auf ScieceBlogs.com, und hat einen besseren Überblick über die Debatte als ich. Er findet, dass Nature mit der Debatte eigentlich aussagen möchte, dass es für profitable high-profile Journals nur ein gutes Konzept gibt, nämlich das von Nature. Er ist damit nicht einverstanden:

Juan Carlos Lopez:

First, having previously commented on open-access publishing in this forum, I explicitly want to distance my journal and myself from any pejorative descriptors that might have been applied to the science published by the PLoS journals. I’m not an advocate of open access, but the quality of what open-access journals publish has never been an issue I have cared to discuss in public.

Avian Journal Club in PLoS ONE!

As part of the monthly focus on birds, there is a new Journal Club in PLoS ONE this week.
Dr.Elizabeth Adkins Regan from Cornell and her postdoc Dr Joanna Rutkowska from Jagiellonian University have already posted their first comments on the paper by Keith Sockman (here at UNC): Ovulation Order Mediates a Trade-Off between Pre-Hatching and Post-Hatching Viability in an Altricial Bird.
You should all join in the discussion!

Impact Factors 2007

If anyone is interested, Thompson has just released the new Impact Factors for scientific journals. Mark Patterson takes a look at IFs for PLoS journals and puts them in cool-headed perspective.
One day, hopefully very soon, this will not be news. What I mean by it is that there soon will be better metrics – ways to evaluate individual articles and individual people in way that is transparent and useful and, hopefully, helps treat the “CNS Disease”. Journals will probably have their own metrics based on the value they add, but those metrics will not affect individual researchers’ careers the way they do now.

Birds In PLoS ONE!

If you are an astute watcher of the PLoS ONE homepage (or the PLoS Blog, or my blog for that matter), you may have noticed that PLoS ONE now has something like a ‘theme of the month’, i.e., a single, broad topic that we highlight in several different ways on the homepage, blog, in e-mails, etc. We check out the most viewed and downloaded papers on the topic and interview the authors and Academic Editors of those papers, etc. Last month, in May, the theme was Cell Signaling. This month, June ’08, the overarching theme is The Birds!
If you search PLoS ONE for bird + avian (keep clicking ‘Next’ at the bottom of the page again and again), you will see that PLoS ONE has published several dozen interesting articles on various aspects of bird biology. Those articles can be roughly classified into three categories:
– evolution/ecology/conservation
– physiology/neuroscience/behavior
– avian flu
Some papers span two or even all three of the topics (e.g., on the way ecology and behavior of migratory birds affects the epidemiology of bird flu). When we checked the stats to see which bird-related papers have been viewed the most, these articles emerged as our Top 5:
Coevolution of Male and Female Genital Morphology in Waterfowl. Interviews with the author and the Academic Editor of this paper can be found here.
A Visual Pathway Links Brain Structures Active during Magnetic Compass Orientation in Migratory Birds (there is also a brief blurb by the author at the above link).
Cross-Clade Protective Immune Responses to Influenza Viruses with H5N1 HA and NA Elicited by an Influenza Virus-Like Particle
Leg Disorders in Broiler Chickens: Prevalence, Risk Factors and Prevention
Cross-Protection against Lethal H5N1 Challenge in Ferrets with an Adjuvanted Pandemic Influenza Vaccine
There will be something new about Birds In PLoS every Tuesday night on the ONE homepage this month, as well as one or two Journal Clubs on bird-related papers (do you want to do one of these – call me). As I am a bird-man myself, this makes me happy. I hope you like what we have as well.

Facebook update

As it grew too big, and the functionality was lacking, the PLoS Facebook group has been closed and moved to a PLoS Facebook page instead. Join in.

Radiation-eating fungi beat vacuum-cleaner dinos and Steve’s crocs

Recent discussions about potential use of downloads in place of other bibliometric measures (including Impact Factor) made us think. So, we took a look at PLoS ONE stats to see which papers are the most visited to date. The results are here – the most visited ONE paper is Ionizing Radiation Changes the Electronic Properties of Melanin and Enhances the Growth of Melanized Fungi, which got quite a lot of coverage in the media and on blogs (including BoingBoing, Slashdot, Rhosgobel, to point to just a few) when it first came out a year ago.
In second place is Paul Sereno’s Structural Extremes in a Cretaceous Dinosaur (you can get the taste for the media and blog coverage at the bottom of this post), as you may have expected.
The Top 5 also include: Resistance Exercise Reverses Aging in Human Skeletal Muscle by Melov et al., Intense Sweetness Surpasses Cocaine Reward by Lenoir et al., and the late Steve Irwin’s last paper, Satellite Tracking Reveals Long Distance Coastal Travel and Homing by Translocated Estuarine Crocodiles, Crocodylus porosus.
This was not downloads but traffic, but still, it is an interesting result to ponder….Perhaps those papers that have cool pictures can skew the numbers!

LOL PLoS

First LOL PLoS images are now on Flickr and Facebook. If you use the correct tag in Flickr, yours will be added to the set. Please link to the original paper when you do this.

Taxonomy in PLoS ONE

Kevin Zelnio and Alex Wild note that PLoS ONE published its first Taxonomy paper this week – A Revision of Malagasy Species of Anochetus Mayr and Odontomachus Latreille (Hymenoptera: Formicidae) by Brian Fisher and Alex Smith. Kevin explains the paper in detail and explains why this brave move by PLoS is good and important especially considering how many new species are discovered and described each year.

LOL PLoS

Every now and then I have some fun and LOL-cat-ize an image from a PLoS ONE paper. See, for instance, LOLdinosaur, LOLtortoise, LOLtasmaniantiger and LOLpterosaur. Folks at the mothership love these. So, if a number of you are up to this I’ll make a Flickr set or Facebook group, or a linkfest. Pick your favourite PLoS papers, grab images, LOLcatize them (here) and send them to me, or give me the links. Ideally, if you post these on your blogs, provide also a link to the paper itself or at least let me know which paper they came from.
This is not what I have in mind, but it is a LOL and a PLoS and a cat….

What I learned at SRBR meeting last week

A couple of days have passed and I had a lot of work-related stuff to catch up with, but I thought I better write a recap now while the iron is still hot and I remember it all. Here we go….

Continue reading

Cell Signaling in PLoS ONE

Peter Binfield, the new Managing Editor of PLoS ONE, did some analysis of the content of the journal so far, and realized that the single most frequent Category our authors use is ‘Cell Signaling’. And, as he writes in his blog post, those are some impressive papers….and we want more of them!

Microbial genomics in PLoS

Considering this I am kinda baffled by this. There is tons of microbial metagenomics and genomics in PLoS journals.

Harold Varmus on NPR’s Science Friday

Tomorrow at noon, tune into NPR’s Science Friday, as you do every week anyway, I know, and you do not need to be told by me, but this time, make sure you hear Harold Varmus being interviewed about the implementation of the new NIH law and the editorial he wrote in PLoS Biology.
If I remember correctly, NPR Science Friday posts podcasts of the shows a few hours after they air live, so if you miss the show in real time you can come back to it and hear it later.

NIH public access law is now being implemented

As many of you may be aware, yesterday was the first day of the implementation of the new NIH law which requires all articles describing research funded by NIH to be deposited into PubMed Central within 12 months of publication. Folks at SPARC have put together a list of resources one can consult when looking for answers about the implementation of the access policy.
Bloggers on Nature Network as well as here on Scienceblogs.com will write posts about the NIH bill and its implementation throughout the week (the ‘OA week’), informing their readers about the implementation, the next steps to be worked on in the future, and related topics. NIH is collecting public comments on the policy until May 1 so feel free to chime in yourself.
This law is not something that just appeared out of thin air a couple of months ago. As Liz Allen explains:

It’s been a long and winding road to get to this point and PLoS has been closely involved from the very beginning. Inspired by the desire to harness the potential of the internet to foster faster, freer exchange of biomedical knowledge, Harold Varmus, then director of the National Institutes of Health, proposed an electronic publishing site called E-biomed that would provide barrier-free access to the peer-reviewed and pre peer-reviewed scientific literature. After a period of public review (during which E-biomed met with fierce opposition from established publishers, sound familiar?), Dr. Varmus announced the creation of PubMed Central. Launched in February 2000, PMC is the NIH’s free digital archive of biomedical and life sciences journal literature and is the repository into which all NIH funded research articles must be deposited from today.

Of course, if you publish with PLoS, you do not have to worry about any of this – we know what to do and we do it for you automatically. The moment your paper is published, it is immediatelly deposited in PubMed Central, so you can go on with your work without worrying about the new law. In today’s issue of PLoS Biology, Harold Varmus exlains:

In contrast, open-access journals, like those published by PLoS or BioMed Central, make their articles immediately and freely available in PMC, eliminating any extra work by the authors and any delay before the articles are fully accessible. Furthermore, these journals permit far greater use of their articles, by allowing readers to explore and reuse the texts under the terms of a Creative Commons license. These degrees of freedom are possible because access and use do not diminish revenues: open-access publishers recover their costs upfront, frequently by charging a publication fee that is paid from research expenses, rather than with subscription charges to libraries and readers. Thus the distribution and reuse of open-access content can be without limit, just as scientists and the public would wish.

Welcome the new Managing Editor of PLoS ONE

There is a change in the command center of PLoS ONE this month. The transition will be seamless. The new editor, Peter Binfield has joined us a couple of weeks ago and has assumed the Big Kahuna position on the 1st of April. The outgoing editor, Chris Surridge will remain in advisory role for the remainder of the month. I am excited to see them both next week in Cambridge, so we can start plotting the strategy to take over the world together (over a Guinness or two, I hope). And, perhaps important to those who complain that ONE is too biologically oriented, Peter is a physicist, so you know we have never abandoned the mission of ONE to be a place for papers in ALL areas of science.

TOPAZ update

The IT/Web team has been hard at work to make TOPAZ, the platform for 5 out of 7 PLoS journals work smoothly again.

Congratulations to K.T.Vaughan

For becoming the 1000th member of the PLoS Facebook group. I think some swag will be going her way… 😉

Peopling of the Americas – add your thoughts

There is an ongoing Journal Club on the PLoS ONE article A Three-Stage Colonization Model for the Peopling of the Americas. You’ll see that the first comments there have been posted by people you know – bloggers like Martin Rundkvist and Greg Laden and Kambiz Kamrani. Now it’s your turn to add your thoughts. Or, if this is not a topic you are interested in, it is never too late to add your commentary to one of the previous Journal Clubs or to just any PLoS ONE article you are interested in.

TOPAZ Upgrade and other Big News from PLoS

It was a heroic (and sometimes nerve-wrecking) couple of months for the IT/Web team at PLoS, but the fruits of their labor will shortly be visible to all. PLoS Computational Biology, PLoS Genetics and PLoS Pathogens will soon migrate onto the TOPAZ platform. You are familiar with TOPAZ already as PLoS ONE, PLoS Neglected Tropical Diseases and the PLoS Hub for Clinical Trials are already on this platform. The remaining two journals, the two biggies (PLoS Biology and PLoS Medicine) will migrate later this year as well.
Mark Patterson explains in detail what this will mean for you: authors and readers of these three journals – the process will be easier, faster and will help these journals attain financial self-sufficiency. The five journals and one hub hosted on TOPAZ will be better integrated with each other as well. And the interactivity features will enable readers and authors to communicate with each other on the papers and to continue the discussion and review of the work after its publication. For bloggers: you will be now able to send trackbacks to articles in these journals whenever you post about them.
Richard Cave, head of our Web team provides a detailed summary of changes in the TOPAZ platform, made in preparation for the migration of the three journals. After this time, if you open any article in the five journals and one Hub hosted on TOPAZ you will see some differences. For instance, what used to be called a ‘discussion’ will then be called a ‘comment’ – a much more common term that everyone is familiar with. What used to be called an ‘annotation’ will then becalled ‘note’, a shorter, sweeter term (and it reminds you of a Post-It Note, I hope). Furthermore, there will then be more than one types of Note. You will still be able to make a regular note, displayed as a blue mark on the text of the article. But there will be two additional options: a minor correction, displayed as a red mark on the text, or a formal correction displayed on the top of the article. Both will require a review by the editors and will make corrections faster to implement and also make sure that the corrections and the articles are literally on the same page.
Richard describes several more improvements to TOPAZ in his post, but one many people will probably like the most is the vastly improved Search. Go check it out.

PLoS Biology 2.0 – Congratulations to Jonathan!

This is an exciting day at PLoS and, after having to keep my mouth shut for a couple of months about it, I am really happy to be free to announce to the world that my friend and excellent science blogger Jonathan Eisen is now officially the Academic Editor-in-Chief of PLoS Biology.
The editors have written an article that explains his role and how and why it was Jonathan who was chosen. In a separate article, Jonathan gives us a touching and thrilling story of his conversion to Open Access and his vision for the future of PLoS Biology.
You should go and congratulate him in the comments of this blog post.

How to have your papers deposited into PubMed Central

Are you confused with the new NIH Policy and unsure as to what you need to do? If so, Association of Research Libraries has assembled a very useful website that explains the process step by step. But the easiest thing to do is to publish with a journal that does the depositing for you free of charge and here is the list of such journals. Of course, PLoS automatically does that for you as well.

EEB in PLoS ONE

ONE%20publish_center.jpgThe word ‘ONE’ in PLoS ONE indicates that the journal publishes articles in all areas of science. This is not as easy as it sounds, of course. The majority of papers published so far have some kind of biomedical connection to them, which is not a surprise as the biomedical community was the first to embrace PLoS and as the other six PLoS journals are either specifically targeting this community (PLoS Medicine, Pathogens and Neglected Tropical Diseases) or are welcoming to such papers (PLoS Biology, Genetics and Computational Biology).
The support of patient advocate groups, PLoS openness and non-acceptance of advertising from the pharmacological industry, led to a wealth of articles describing clinical trials, leading to our first PLoS Hub – Clinical Trials where the community can post comments on these papers.
But we want PLoS ONE to go beyond and to, eventually, publish equally in all areas of science. We have to do it incrementally. We understand that it is not easy to be the pioneer, the ice-breaker, the first person in one’s field to publish in PLoS ONE and subsequently get asked “you published WHERE?”. Such people, we understand, have to be at a secure point in their careers, as well as strong proponents of Open Access. And such people are key to our success – they tell their colleagues about us and provide the seed – that first paper in the field that gives the others the opening to also submit their manuscripts to us. If you recognize yourself in this description, contact me ASAP!
Eventually, in a year or two, we may see a lot of physics, astronomy, math and chemistry published in ONE. Areas like geology, meteorology and archaeology may come before that. But the best way to expand is to work with what we have – ask people to publish papers that are somewhat related to papers we have already published. So, we may go from biomedical science through Computational Biology to Mathematics, or from biomedical science through Biophysics to Physics.
So, we took a look to see which areas of the Life Sciences have already gravitated to PLoS ONE and it was obvious that we have quickly (in only one year and 1600 papers) become quite a journal-of-choice for the EEB community – that is: Ecology-Evolution-Behavior.
We have already published 159 papers in the Ecology category (see this for a good recent one).
There are already 269 articles tagged as Evolutionary Biology and those include forays into anthropology, invertebrate and vertebrate paleontology and even philosophy of evolutionary biology (we are also capable of publishing taxonomical new-species-description monographs).
Finally, Behavioral Biology (which probably deserves its own category) can be found under the ecology and evolution tags, as well as among the 250 articles categorized as Neuroscience. Check out some cool papers on the behavior of fruitflies, honeybees, iguanas, birds, bats, pikas, chimps and humans, to point out just a few.
Those are large numbers! And we want more! Look around those categories – is there something that is somewhat similar to your own research? If so, why not publish with us?

Viruses in the Oceans: join the latest Journal Club

Brendan Bohannan, Richard W. Castenholz, Jessica Green and their students and postdcos at the Center for Ecology and Evolutionary Biology at University of Oregon are currently doing a Journal Club on the PLoS ONE article The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples, which is part of the PLoS Global Ocean Sampling Collection. Please join in the discussion.

PLoS Blog update

Last week, we made a little upgrade to the PLoS Blog.
If you look at any individual post you will see that we added the “e-mail this page” and “Printer-friendly version” buttons on the bottom of each post.
We have also started allowing trackbacks on our posts. Just like comments, trackbacks will be moderated due to large amounts of spam that are still attacking our system. We check the approval cue for comments and trackbacks on the blog regularly, so yours will show up after a short lag (and if it does not, give me a heads-up by e-mail).
Now look at the right side-bar, where we have made some re-arrangements, some features got new names, and new features have been added.
We have added a new Channel – In The News – where we will highlight the media and blog coverage of our most popular articles.
We have added a Technorati widget so you can see who links to the blog.
Finally, we also added the Blogroll. At the moment, the front page will showcase five from our very long list of favorite blogs and we’ll rotate them to eventually give them all their time in the sun. If you want to make suggestions for our list you can let me know.
This is just the first set of small changes on the PLoS Blog. Keep an eye on it as more changes will be coming in the future, making the blog better, prettier and easier to use.

New Journal Club on PLoS ONE – Chimps exchange fruit for sex

A paper published back in September – Chimpanzees Share Forbidden Fruit by Hockings et al. is getting renewed attention these days.
Rebecca Walton has compiled links to the recent media and blog coverage of the paper (including those by my SciBlings Afarensis, Greg Laden and Brian Switek), the peer-reviewer’s comments have been added to the paper, and The Animal Cognition Research Group at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany has posted a series of comment as part of a Journal Club on this paper.
Now, all you need to do is join in the conversation – log in (or register if you have not done it already) and add your thoughts about chimps sharing forbidden fruit to the comments, ratings and annotations on this paper. If you decide to write a blog post, please send a trackback or, if that fails, leave us the link to your post in the comments on Rebecca’s blog post.

New Journal Club!

Members of the Rodriguez lab and the Otero lab, both of Instituto de Neurociencias de Alicante (CSIC-Universidad Miguel Hernandez. Spain) have just posted their first Journal Club commentary on the PLoS ONE article High-Pass Filtering of Input Signals by the Ih Current in a Non-Spiking Neuron, the Retinal Rod Bipolar Cell.
Check their discussion and join in – respond to their comments or post your own discussions, annotations and ratings and keep the conversation going!
Also, it is never too late to add your thoughts to the previous Journal Clubs.

The most exciting job in science publishing can be yours!

PLoS ONE is the first and (so far) the most successful scientific journal specifically geared to meet the brave new world of the future. After starting it and bringing it up from birth to where it is now one year later, Chris Surridge has decided to move on.
Do you think you have the skill and experience to pick up where he leaves off? Do you want to be at the cutting edge of scientific publishing? If so, take a look at the new job ad for the Managing Editor of PLoS ONE:

The overall responsibility of this position, which will be located in the San Francisco office, is to lead the editorial staff and editorial board who run PLoS ONE — a ground-breaking online-only publication covering the full breadth of scientific and medical research. PLoS ONE was launched one year ago, and is already publishing over 150 peer-reviewed research articles each month.

While other PLoS journals have a narrower scope (Biology, Medicine, Pathogens, Genetics, Computational Biology, Neglected Tropical Diseases), ONE is supposed to be the ONE place for all areas of science. Thus, your scientific background does not necessarily have to be in biomedical research to be eligible and welcome for this job, if your experience and organizational skills are a perfect match for the job.

Clocks and Migratory Orientation in Monarch Butterflies

Blogging on Peer-Reviewed Research

I had no time to read this in detail and write a really decent overview here, perhaps I will do it later, but for now, here are the links and key excerpts from a pair of exciting new papers in PLoS Biology and PLoS ONE, which describe the patterns of expression of a second type of cryptochrome gene in Monarch butterflies.
This cryptochrome (Cry) is more similar to the vertebrate Cry than the insect Cry, also present in this butterfly. The temporal and spatial patterns of expression of the two types of Cry suggest that they may be involved in the transfer of time-information from the circadian clock to the brain center involved in spatial orientation during long-distance migration.
The PLoS Biology paper looks at these patterns of expression, while the PLoS ONE paper identifies a whole host of genes potentially implicated in migratory behavior, including the Cry2. Here is the PLoS Biology paper:
Cryptochromes Define a Novel Circadian Clock Mechanism in Monarch Butterflies That May Underlie Sun Compass Navigation:

During their spectacular fall migration, eastern North American monarch butterflies (Danaus plexippus) use a time-compensated sun compass to help them navigate to their overwintering sites in central Mexico. The circadian clock plays a critical role in monarch butterfly migration by providing the timing component to time-compensated sun compass orientation. Here we characterize a novel molecular clock mechanism in monarchs by focusing on the functions of two CRYPTOCHROME (CRY) proteins. In the monarch clock, CRY1, a Drosophila-like protein, functions as a blue-light photoreceptor for photic entrainment, whereas CRY2, a vertebrate-like protein, functions within the clockwork as the major transcriptional repressor of the self-sustaining feedback loop. An oscillating CRY2-positive neural pathway was also discovered in the monarch brain that may communicate circadian information directly from the circadian clock to the central complex, which is the likely site of the sun compass. The monarch clock may be the prototype of a clock mechanism shared by other invertebrates that express both CRY proteins, and its elucidation will help crack the code of sun compass orientation.

Here is the editorial synopsis:
In Monarchs, Cry2 Is King of the Clock:

Back in the brain, the authors showed that Cry2 was also found in a few dozen cells in brain regions previously linked to time-keeping in the butterfly, and this Cry2 underwent circadian oscillation in these cells, but not in many other cells that were not involved in time keeping. By taking samples periodically over many hours, they found that nuclear localization of Cry2 coincided with maximal transcriptional repression of the clockwork, in keeping with its central role of regulating the feedback cycle. This is a novel demonstration of nuclear translocation of a clock protein outside flies.
Finally, the authors investigated Cry2’s activity in the central complex, the brain structure that is believed to house the navigational compass of the monarch. Monarchs integrate information on the position of the sun and the direction of polarized light to find their way from all over North America to the Mexican highlands, where they spend the winter. Cry2, but not the other clock proteins, was detected in parts of the central complex where it undergoes strong circadian cycling. Some cells containing Cry2 linked up with the clock cells, while others projected toward the optic lobe and elsewhere in the brain.
Along with highlighting the central importance of Cry2 in the inner workings of the monarch’s clock, the results in this study suggest that part of the remarkable navigational ability of the butterfly relies on its ability to integrate temporal information from the clock with spatial information from its visual system. This allows the monarch to correct its course as light shifts across the sky over the course of the day. Other cues used for charting its path remain to be elucidated.

This is the PLoS ONE paper:
Chasing Migration Genes: A Brain Expressed Sequence Tag Resource for Summer and Migratory Monarch Butterflies (Danaus plexippus):

North American monarch butterflies (Danaus plexippus) undergo a spectacular fall migration. In contrast to summer butterflies, migrants are juvenile hormone (JH) deficient, which leads to reproductive diapause and increased longevity. Migrants also utilize time-compensated sun compass orientation to help them navigate to their overwintering grounds. Here, we describe a brain expressed sequence tag (EST) resource to identify genes involved in migratory behaviors. A brain EST library was constructed from summer and migrating butterflies. Of 9,484 unique sequences, 6068 had positive hits with the non-redundant protein database; the EST database likely represents ~52% of the gene-encoding potential of the monarch genome. The brain transcriptome was cataloged using Gene Ontology and compared to Drosophila. Monarch genes were well represented, including those implicated in behavior. Three genes involved in increased JH activity (allatotropin, juvenile hormone acid methyltransfersase, and takeout) were upregulated in summer butterflies, compared to migrants. The locomotion-relevant turtle gene was marginally upregulated in migrants, while the foraging and single-minded genes were not differentially regulated. Many of the genes important for the monarch circadian clock mechanism (involved in sun compass orientation) were in the EST resource, including the newly identified cryptochrome 2. The EST database also revealed a novel Na+/K+ ATPase allele predicted to be more resistant to the toxic effects of milkweed than that reported previously. Potential genetic markers were identified from 3,486 EST contigs and included 1599 double-hit single nucleotide polymorphisms (SNPs) and 98 microsatellite polymorphisms. These data provide a template of the brain transcriptome for the monarch butterfly. Our “snap-shot” analysis of the differential regulation of candidate genes between summer and migratory butterflies suggests that unbiased, comprehensive transcriptional profiling will inform the molecular basis of migration. The identified SNPs and microsatellite polymorphisms can be used as genetic markers to address questions of population and subspecies structure.

Here is an article written after the press release, which, as such articles usually do, greatly overstates the extent of the findings:
Clocking monarch migration:

In previous work, Reppert and his team showed that pigment-producing genes in the monarch eye communicate with the butterfly’s circadian clock. As part of the new study, Reppert and his team also found, in an area of the monarch brain called the central complex, a definitive molecular and cellular link between the circadian clock and the monarch’s ability to navigate using the sun. Briscoe said that Reppert’s study was “really going to overturn a lot of views we had about the specific components of circadian clocks.”

The spatial and temporal patterns of expression make Cry2 the most serious candidate for the connection between the clock and the Sun-compass orientation mechanism. Much work, both at the molecular and at higher levels of organization needs to be done to figure out the exact mechanism by which this animal, during migration, compensates for the Sun’s movement across the sky during the day, and thus does not stray off course. Cry2 appears to be a good molecular “handle” for such studies.
For background, see my older post on the initial discovery of Cry2 in Monarch butterflies by the same team.

How would you like to work at PLoS Medicine?

If you are a doctor, or a post doctoral researcher in a relevant area, and you want to spend 6 months to a year working at a medical journal, this is a great opportunity for you – PLoS Medicine is looking for an intern:

PLoS Medicine, the flagship medical journal of the Public Library of Science, is pleased to announce that it is accepting applications for its first editorial intern.
We are looking for someone with a keen interest in medical publishing and open access who wants to join the PLoS Medicine editorial team.
You’ll need to be a medical graduate with a minimum of 3-4 years post residency/house officer experience or a science graduate with a PhD or equivalent in an appropriate biomedical discipline. You’ll need to be able to live and work in the UK or the US at either our Cambridge, UK or San Francisco offices.
In return, you’ll work as an integral part of the PLoS Medicine editorial team. You’ll get a thorough insight into the workings of a cutting edge international general medical journal and will be trained to handle peer review, commission magazine articles, and write editorials, blogs, editors’ summaries and press releases.
The position is for 6 months in the first instance from early 2008, renewable for a further 6 months.

Read the entire ad here.

ONE is One!

On This Day In History:
The very first article in then brand-new journal PLoS ONE was published on December 20th, 2006. And the Earth trembled (literally – there was an earthquake in San Francisco on that day). And the world of scientific publishing was never the same since.
You can imagine the celebratory mood at the mothership 😉
And there is a lot to celebrate: more than 1300 articles have been published during the first year, attracting more and more fans, more and more (and more famous) authors, more and more community commentary that the TOPAZ tools allow, the birth of the first Hub, and gradually greater and greater scope of the journal, from clinical trials to animal behavior to mathematics, from neuroscience to palaentology to ecology, from genomics to philosophy of science, with more yet to come.
For this celebratory day, the Web team gives you all a birthday present – a completely redesigned PLoS ONE homepage that should make it even easier for you to find what you are looking for in PLoS ONE and its sister journals. Go and see for yourself!

Zotero Translator for PLoS Articles

Zotero is a Firefox plug-in that allows you to manage and cite research papers. They just announced that Zotero now works with PLoS papers. If you have no idea what I am talking about, Rich Cave explains.

Boston – Part 2: Publishing in the New Millennium

It’s been a while since I came back from Boston, but the big dinosaur story kept me busy all last week so I never managed to find time and energy to write my own recap of the Harvard Conference.
Anna Kushnir, Corie Lok, Evie Brown, Kaitlin Thaney (Part 2 and Part 3) and
Alex Palazzo have written about it much better than I could recall from my own “hot seat”. Elizabeth Cooney of Boston Globe has a write-up as well. Read them all.
So, here is my story, in brief….and pictorial, just like the first part (under the fold).

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