Category Archives: Open Science

Evolution: Education and Outreach

The third issue of the Open Access journal ‘Evolution: Education and Outreach’ has been published, and it is again full of good, thought-provoking articles. You can see them (for free, of course) if you click here.

Info about the way OA benefits conservation is itself not OA

How free access internet resources benefit biodiversity and conservation research: Trinidad and Tobago’s endemic plants and their conservation status:

Botanists have been urged to help assess the conservation status of all known plant species. For resource-poor and biodiversity-rich countries such assessments are scarce because of a lack of, and access to, information. However, the wide range of biodiversity and geographical resources that are now freely available on the internet, together with local herbarium data, can provide sufficient information to assess the conservation status of plants. Such resources were used to review the vascular plant species endemic to Trinidad and Tobago and to assess their conservation status. Fifty-nine species were found to be endemic, much lower than previously stated. Using the IUCN Red List criteria 18 endemic species were assessed as Critically Endangered, 16 as Endangered, 15 as Vulnerable, three as Near Threatened, and three as Data Deficient (i.e. insufficient data are available to assess their conservation status). Although such rapid assessments cannot replace in depth research, they provide essential baseline information to target research and conservation priorities and identify specific conservation actions.

Kevin Zelnio:

In a paper just out in the conservation journal Oryx, Van Den Eynden and colleagues discuss how they evaluated plant endemism, conservation status and reserve effectiveness utilizing only freely available online resources from the internet and local Herbaria. There were several conclusions drawn about plant conservation, but here is a tidbit about how free access to information helped in assessing conservation status.

“Research institutes that use information technology to catalogue and distribute information online promote the advancement of knowledge at a global scale. Using such free-access online resources, and advice offered freely by taxonomy experts, a review of the endemic vascular plant species of Trinidad and Tobago and an assessment of their conservation status was carried out in a relatively short time and without significant cost. This in turn has been made freely available online (Van den Eynden, 2006). Such rapid evaluation of conservation status cannot replace the need for in depth field-based monitoring and assessment but it provides valuable baseline information for the identification and targeting of specific conservation and research needs. The methods used can be applied by most countries for initial assessments of plant extinction risks. Lack of resources or research data is no longer an argument not to do so.”

Free information, it werks bitchez.
(Unfortunately their paper was NOT freely accessible, the irony of it all…)

Open Textbooks

Georgia Harper saw an interesting article in USA Today about Open textbooks and, among else, says:

Open access is just one part of a much bigger and more complex picture. I am very optimistic that open access will find its way into the book market (or what we call books today), but again, it’s not like that will cut off the flow of revenues. Quite the contrary. It just makes it possible for a lot more people to benefit from the work of authors while authors and those who help them ready their works for public consumption still reap sufficient financial rewards to make creating worthwhile. Maybe the biggest stumbling block is understanding that as a copyright owner, you don’t have to appropriate every cent of public benefit from your work. There’s viability in skimming off the top and letting some of the benefit go to those who never would have been able to buy your book anyway. That concept seems really counter-intuitive to many authors and publishers, but I think it’s what makes open access a successful competitor — authors and publishers can still get paid (if that’s what they want) but people who would not have had access also derive benefit.
So, back to copyright law: we make and distribute copies of others’ works; we license others’ works; we buy others’ works. We (educators) are very big consumers of and producers of educational, research and scholarly materials. This is big, big business. And it’s got copyright as a major component of its engine. But a bundle of copyrights, no matter how big, becomes worth less and less over time. New works get created every single day. And every single new author has choices today about how to distribute, market and benefit from his or her work that were simply not available even a decade ago. That’s what makes authoring and creating so exciting today: the chance to reach an audience of any size is within reach for many more of us than in the past. How will you handle your copyrights? Open access has an awful lot to recommend it. Look into it! Creative Commons licensing is a good example of how you can make your work widely and freely available while still maintaining the degree of control that fits with your overall goals in writing or creating in the first place.

Amen.
Hat-tip: Gavin Baker

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.

The Graduate Junction

Graduate Junction is a new social networking site designed for graduate students and postdocs. I looked around a bit and found it clean, easy-to-use and potentially useful. This is how they explain it – give it a try and let me know what you think:

The Graduate Junction is a brand new website designed to help early career
researchers make contact with others with similar research interests,
regardless of which department, institution or country they work in. Designed
by two graduate researchers at the University of Durham, The Graduate Junction
has proved very popular with research students and academics alike. Within the
first two weeks after our launch in early May 2008 over 2000 researchers in the
UK had registered and the news had spread across 40 countries.
Currently research students have two main sources of information, published
literature and academic conferences. Whilst published literature is
essential, it can only ever reveal completed work. Relevant academic
conferences provide a forum for students with similar research interest to
interact but occur infrequently. It is very easy to become isolated, overly
focused on the specifics of one’s own work and lose a sense of what other
related work is being done.
The Graduate Junction hopes to prevent that isolation and allow early career
researchers to start forming the networks which can stay with them throughout
their careers. The Graduate Junction aims to provide an atmosphere similar to
that at academic events and through the use of the internet aims to establish
an on-line worldwide graduate research community.
The Graduate Junction is unique because it links researchers based on ‘research
keywords’, promoting interdisciplinary relationships. By simply registering a
few basic details, users can search for fellow researchers by keyword,
institution, department, supervisor or name. Alternatively, users can search
The Graduate Junction’s on-line research groups which allows them to find and
communicate with a number of other researchers sharing their research
interest. The Graduate Junction has been designed to be simple and provide
only information and functionality that is relevant to researchers.
The Graduate Junction is useful for all Master, Doctoral and Postdoctoral
researchers at any stage of the research process, and allows them to start
building networks and stay informed about current developments in their field.
With the addition of conference and postgraduate job listings imminent, The
Graduate Junction aims to be one of the most useful resources available for all
graduate researchers.

Real Science for schools

When I go around proselatizing for Open Access, I always try to remember to point out that the potential users are not just scientists and physicians in the developing world, or researchers at low-tier or community colleges, but also high schools. So, I was very happy to hear about the existence of Real Science, a website that uses the latest freely available research to use in classrooms:

Imagine teaching the latest science on the same day it appears in the newspapers.
Imagine the kick the kids will get when they say to their parents watching the news on TV: “We did that in school today. It’s like this ….”
We get information from sources around the world, sift it to find newsworthy nuggets, then turn these into free teaching and learning resources that grab young people’s interest and hold their attention.
We devise activities that develop understanding, support groupwork and guide pupils to explore the issues – scientific, ethical, environmental – raised by the latest science news.
We provide links to free resources, activities and lesson plans for teachers and online activities for children and young people.

See, for instance how they covered recent papers on cocktail chatter, walking pterosaurs and dinosaur tracks. Do you like it?

Books on Open Access

As expected, most of them are free to download. Peter Suber has all the relevant links:
Open Access Opportunities and Challenges: A Handbook (PDF) by Barbara Malina (ed.).
Science Dissemination using Open Access by Canessa and Zennaro.
Understanding Open Access in the Academic Environment: A Guide for Authors (PDF) by Kylie Pappalardo.
I also have Scholarly Journals Between the Past & the Future by Martin Rundkvist.

OA student projects available

Heather Morrison just finished teaching her class on Open Access and the student projects are now all online for you to see.

More you can see, more you click

That is, in a nutshell, the conclusion of this study. If you have free access to a lot of literature, you are much more likely to click on links and download PDFs (which hopefully means you will read the papers, learn from them, improve your science, and cite them when writing your own manuscripts). If you know that most of the time you will see a “pay $60” page instead, you don’t bother clicking anyway.
Also, this mainly applies to the new papers – the older papers are rarely looked at – so there is no real need to keep archives TA for any lengthy periods of time.
Peter Suber comments.

NIH Public Access Policy instructions on PubMed home page

Thanks to Heather for the heads-up:

Instructions for NIH-funded authors have been prominently placed on the PubMed home page.
There is a link to a list of journals that will manage the submission process with the NIH guidelines on behalf of authors – very handy! – as well as instructions for authors who publish in journals that do not provide this service.

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.

If you thought that OA-evangelism is an intellectual game – think again!

Yes, I know, Gavin is a dear colleague and a friend, but his latest article, Excluding the poor from accessing biomedical literature: A rights violation that impedes global health, is just brilliant. A must-read for all concerned with healthcare, medical information and OA publishing:

In this article, I take a rights-based view of this current crisis of restricted access to the results of scientific and medical research. Such research is conducted in the interests of the public, and yet the results are largely kept out of the public domain by traditional corporate publishers who own them, subject them to extremely tight copyright restrictions, and sell them in a market worth about US$5 billion. The results of biomedical research have unfortunately been privatized, monopolized, and concentrated in the hands of a tiny number of multinational corporations.
This article considers how exclusion from accessing the biomedical research literature harms global public health. I argue that this literature should be considered a global public good and base my argument upon long-standing and recent international declarations that enshrine access to scientific and medical knowledge as a human right. I present an emerging alternative publishing model, called open access, and argue that this model is a more socially responsive and equitable approach to knowledge dissemination. I situate open access publishing within a broader movement that has emerged in the digital era to create a public “knowledge commons,” which can play a crucial role in supporting an informed citizenry in its efforts to promote human rights. Finally, I propose that Health and Human Rights itself, as an open access journal, could help to catalyze the creation of an online “health and human rights commons.”

Open access and the last-mile problem for knowledge

Peter Suber, a thoughtful essay, as always:

In telecommunications the “last-mile problem” is the problem of connecting individual homes and businesses to the fat pipes connecting cities. Because individual homes and businesses are in different locations, hooking up each one individually is expensive and difficult. The term is now used in just about every industry in which reaching actual customers is more difficult than reaching some location, like a store or warehouse, close to customers.
We’re facing a last-mile problem for knowledge. We’re pretty good at doing research, writing it up, vetting it, publishing it, and getting it to locations (physical libraries and web sites) close to users. We could be better at all those things, but any problems we encounter along the way are early- or mid-course problems. The last-mile problem is the one at the end of the process: making individualized connections to all the individual users who need to read that research.
The last-mile problem for knowledge is not new. Indeed, for all of human history until recently it has been inseparable from knowledge itself and all our technologies for sharing it. It’s only of interest today because the internet and OA give us unprecedented means for solving it, or at least for closing the gap significantly.
The problem is not that librarians “warehouse” knowledge in the pejorative sense of that term. On the contrary, they go out of their way to help users find and retrieve what the library has to offer, and often do the same for much beyond the library as well. The problem is to make individualized connections between knowledge, wherever it lies, and users, wherever they are. Even a well-stocked and well-organized library staffed by well-trained librarians can only solve a subset of that problem and connect a subset of users with a subset of knowledge.

Read the whole thing – it is excellent and thought-provoking.

Video Archive from Workshop on New Communication Channels for Biology

All the usual suspects were there (I was supposed to go but I could not possibly fit it into my calendar) and now you can watch all the videos from all the presenters – just click here and choose:

San Diego, CA, June 30, 2008 — More than 20 experts presented their views on the future and use of new media and communications in the biological and other sciences. The New Communications Channels in Biology Workshop at UC San Diego was organized by the Calit2-based Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA) with funding from the Gordon and Betty Moore Foundation. Talks ranged across topics in e-science communications, including science blogs, semantic Web tools, authenticated wiki-like research discussions and analysis, as well as the potential to formalize community-level contributions. Calit2 speakers included CAMERA executive director Paul Gilna and the developer of the Research Intelligence portal, Jerry Sheehan. Calit2 offered a live webcast of the workshop; the individual talks are now archived for on-demand viewing

What should be the new (sub)categories on ResearchBlogging.org?

ResearchBlogging.org is getting ready for a big upgrade, or so I hear. You can be a part of the process by helping shape up the new categories and subcategories – all you need to do is go to this blog post, see what is already there and post your suggestions in the comments.

New issue of the Journal of Science Communication

New issue of the Italian Journal of Science Communication is out with some excellent articles (some translated or abstracted from Italian, all in English):
Cultural determinants in the perception of science:

Those studying the public understanding of science and risk perception have held it clear for long: the relation between information and judgment elaboration is not a linear one at all. Among the reasons behind it, on the one hand, data never are totally “bare” and culturally neutral; on the other hand, in formulating a judgment having some value, the analytic component intertwines – sometimes unpredictably – with the cultural history and the personal elaboration of anyone of us.

Collaborative Web between open and closed science:

‘Web 2.0’ is the mantra enthusiastically repeated in the past few years on anything concerning the production of culture, dialogue and online communication. Even science is changing, along with the processes involving the communication, collaboration and cooperation created through the web, yet rooted in some of its historical features of openness. For this issue, JCOM has asked some experts on the most recent changes in science to analyse the potential and the contradictions lying in online collaborative science. The new open science feeds on the opportunity to freely contribute to knowledge production, sharing not only data, but also software and hardware. But it is open also to the outside, where citizens use Web 2.0 instruments to discuss about science in a horizontal way.

The future of the scientific paper:

Will the use of the Web change the way we produce scientific papers? Science goes through cycles, and the development of communication of science reflects the development of science itself. So, new technologies and new social norms are altering the formality of the scientific communication, including the format of the scientific paper. In the future, as PLoS One is experimenting right now, journals will be online hosts for all styles of scientific contributions and ways to link them together, with different people contributing to a body of work and making science more interdisciplinary and interconnected.

Public domain, copyright licenses and the freedom to integrate science:

From the life sciences to the physical sciences, chemistry to archaeology, the last 25 years have brought an unprecedented shift in the way research happens day to day, and the average scientist is now simply awash in data. This comment focuses on the integration and federation of an exponentially increasing pool of data on the global digital network. Furthermore, it explores the question of the legal regimes available for use on this pool of data, with particular attention to the application of “Free/Libre/Open” copyright licenses on data and databases. In fact, the application of such licenses has the potential to severely restrict the integration and federation of scientific data. The public domain for science should be the first choice if integration is our goal, and there are other strategies that show potential to achieve the social goals embodied in many common-use licensing systems without the negative consequences of a copyright-based approach.

To blog or not to blog, not a real choice there…:

Science blogging is a very useful system for scientists to improve their work, to keep in touch with other colleagues, to access unfamiliar science developed in other fields, to open new collaborations, to gain visibility, to discuss with the public. To favour the building of blog communities, some media have set up networks hosting scientists’ blogs, like ScienceBlogs.com or Nature Network. With some interesting features and many potential uses.

The other books – A journey through science books:

On March 2007 JCOM issue, Bruce Lewenstein made this question: why should we care about science books? Next he analyzed some fundamental roles of science books. As a continuation for that enquiry, this text wants to be a dialogue about science, readers, and books, just a quick look at many of the other books, science books, those that do not find easily their place in bookstores and libraries; these books situated beyond labels like fiction or romance but equally memorable, necessaries and desirables.

….and several other articles, all worth checking out (you need to save and download PDFs of each, though).

More on Historical OA

As making historical papers OA is something I am very interested in, I am watching with great interest, as Jonathan Eisen attempts to make all of his father’s scientific publications freely available. I think we will learn a lot from his experience about copyright, fuzzy laws, attitudes of different publishers, etc., and can use that knowledge to help more old papers see the light of day online for everyone to see, read and use.

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.

Are Academic Journals Obsolete?

An interesting discussion on Slashdot (you may need to log in to see all the comments).

Announcing the Health Commons

Check this out on the Science Commons blog:

Science Commons’ mission is to speed the translation of basic research to useful discoveries, and we believe that a new approach is necessary to find more cures, faster. Today, we’re opening up the Health Commons, a project aimed at bringing the same efficiencies to human health that the network brought to commerce and culture.
————————
The Health Commons proposes a different approach: enabling more companies, foundations, laboratories or even individuals to conduct research on disease targets efficiently, by providing better access to the resources that large pharmaceutical companies assemble and integrate “in house.” To do this, Health Commons will facilitate the emergence of a “virtual marketplace,” or ecosystem, through which participants can more easily access the data, knowledge, materials and services for accelerating research.

Why Toll Access has no legs?

For the same reason snakes have no legs. Or perhaps not. It is difficult to find out.

A really, truly bad article about Open Access

If you are looking for a short, easy-to-understand statement that gets absolutely everything about Open Access completely wrong, you can’t do much better than this: Hidden cost of open access in Times Higher Education. Luckily, the commenters set it straight. So does Peter Suber, who also adds an important point:

The success of the OA movement means that every day newcomers hear about it for the first time. One of the burdens of that success is that many newcomers pick up and spread old myths about it. If Altbach isn’t new to OA issues, then he’s inexcusably careless with them, and his claim about peer review is one of the classic myths that newcomers have been picking up and spreading for years.

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!

Search for PPT slideshows by keyword

Go to http://www.slideworld.org, type in a keyword, and it will do a search of slideshows that contain that word. I typed “circadian” and found a lot….
Hat-tip: Ana

Math is Hard: Impact Factors and other number-crunching of scientific literature

Ethics in Science and Environmental Politics has devoted an entire issue to the question of the use and misuse of bibliometric indices in evaluating scholarly performance. All articles are Open Access. I’d like to see the responses on blogs – let me know if you write/read one, please.
Peter does the first one.

John Stuart Mill on Open Access to scientific papers

Peter Suber goes philosophical:
Open access and the self-correction of knowledge:

Here’s an epistemological argument for OA. It’s not particularly new or novel. In fact, I trace it back to some arguments by John Stuart Mill in 1859. Nor is it very subtle or complicated. But it’s important in its own right and it’s importantly different from the moral and pragmatic arguments for OA we see more often.
The thesis in a nutshell is that OA facilitates the testing and validation of knowledge claims. OA enhances the process by which science is self-correcting. OA improves the reliability of inquiry.
Science is fallible, but clearly that’s not what makes it special. Science is special because it’s self-correcting. It isn’t self-correcting because individual scientists acknowledge their mistakes, accept correction, and change their minds. Sometimes they do and sometimes they don’t. Science is self-correcting because scientists eventually correct the errors of other scientists, and find the evidence to persuade their colleagues to accept the correction, even if the new professional consensus takes more than a generation. In fact, it’s precisely because individuals find it difficult to correct themselves, or precisely because they benefit from the perspectives of others, that we should employ means of correction that harness public scrutiny and open access.
I draw on two propositions from John Stuart Mill. It may seem odd that they don’t come from his philosophy of science, but his short treatise on the freedom of expression, _On Liberty_ (1859). Mill made a powerful argument that freedom of expression is essential to truth-seeking, and in elaborating it pointed out the essential role of opening discussion as widely as possible. Here’s how the two propositions look in their natural habitat:

Read the whole thing…

Historical OA

More and more societies are compiling their ‘classical’ papers.
Here is another one.
And here I wrote, among else:

“In discussions of Open Access, we always focus on brand new papers and how to make them freely available for readers around the world as well as for people who want to mine and reanalyse the data using robots. But we almost never discuss the need to make the old stuff available. Yet we often lament that nobody reads or cites anything older than five years. Spending several years reading everything published in the field in the 20th century up until about 1995 (as well as some 19th century stuff) helped me greatly in my own research. It would help others, I’m sure, especially those who are now revisiting old questions with new techniques. How are the classical papers going to be made available for today’s students?
SRBR is working on it now, and I assume that this will be done piece-meal, with each society doing their own work on making old literature available. What I saw (not yet available for public) is a development of a ChronoHistory website. Yes, people will send in pictures and anecdotes and old posters and stuff (and I hope once that material is online that SRBR will get a professional historian of science to make sense of it all), but the most important part of the site will be a repository of the old papers. Services of a real science librarian have been secured to deal with everything from copyright to technical problems in order to provide copies of many old papers on the site. Probably some of the papers will be available to everyone for free while others, due to copyright, may be available only to SRBR members with a password.”

I discussed this with Peter Suber and he says that we tend to focus on new literature because it’s the low-hanging fruit. Yet he agrees that ‘OA to past literature is highly desirable and that we should start thinking about ways to make it happen’. He wrote an article describing a *partial* solution to this problem: Unbinding Knowledge: A proposal for providing open access to past research articles, starting with the most important.
Peter says: “Ultimately we need all peer-reviewed journals to digitize their backfiles for OA. Some are already doing it. Some are digitizing their backfiles but charging for access. Some can’t afford to digitize their backfiles at all.”
Google is willing to digitize the backfile of any journal. Peter blogged about it in December 2006, although Google still doesn’t have a web page for the program. The Google deal isn’t very good. But for journals that can’t find any other funds to digitize their backfile, Peter thinks it’s better than nothing. Google does not have a website for this, but see this interview (this August 2007 interview – via):

Representing another effort to reach currently inaccessible content, Google Scholar now has its own digitization program. “It’s a small program,” said Acharya. “We mainly look for journals that would otherwise never get digitized. Under our proposal, we will digitize and host journal articles with the provision that they must be openly reachable in collaboration with publishers, fully downloadable, and fully readable. Once you get out of the U.S. and Western European space into the rest of the world, the opportunities to get and digitize research are very limited. They are often grateful for the help. It gives us the opportunity to get that country’s material or make that scholarly society more visible.”

Peter also said (personal communication): “As far as I know, the Open Content Alliance doesn’t (yet) digitize journals, but I hope it will start. However, when Google digitizes print literature it pays all the costs (and slightly restricts use of the results); but when OCA digitizes print lit, it requires the possessor or a donor to pay the costs (and provides full OA to the results).”
What do you all think? What is your Society doing about this, you favourite Journals?

Social Networking for Scientists, Part N

It seems everyone is talking about social networking sites these days. There are interesting thoughts on Richard Grant’s and David Crotty’s blogs (read the comment threads as well). Many of those sites will die, others will adapt, but most, I think, will play a supporting role in a whole network of services surrounding…the actual scientific papers. For instance, surrounding TOPAZ-based PLoS papers, perhaps organized into Hubs. And papers from other journals that join into the system. Thoughts?

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….

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Doing science publicly: Interview with Jean-Claude Bradley

Jean-Claude Bradley and I first met at the First Science Blogging Conference where he led a session on Open Science. We then met at SciFoo and later joined forces on a panel at the ASIS&T meeting and finally met again at the second Science Blogging Conference back in January where Jean-Claude co-moderated a session on Making Data Public. Jean-Claude is famous for being the pioneer of the Open Notebook Science movement. He started posting his daily lab activity and results on his blog Useful Chemistry. Soon, he attracted a lot of feedback and subsequently some excellent collaborators. As the work became more complex, Jean-Claude added more blogs, e.g., UsefulChem Molecules and UsefulChem Experiments, but in the end realized that wiki was a better format for this and started the UsefulChem Wiki where you can see, among else, how one of his students is writing a Masters thesis in real time.
Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Who are you? What is your scientific background? What is your Real Life job?
I am an associate professor of chemistry at Drexel university. I’ve been there since 1996. My Ph.D. is in organic chemistry and I have done postdoctoral work on DNA chips and gene therapy. At Drexel I worked on nanotechnology and scientific knowledge management until 2005 when I started the UsefulChem project, centered on synthesizing new anti-malarial compounds using Open Notebook Science.
What do you want to do/be when (and if ever) you grow up?
I’ve worn many hats in my career and part of the fun is not really being able to predict what makes sense doing several years down the road. I try to concentrate on working on projects that I think will have an important impact and where I am in a unique position to contribute.
When and how did you discover science blogs? What are some of your favourites? Have you discovered any new cool science blogs while at the Conference?
I discovered science blogs just through using various social networking sites and finding like-minded people. Some of the blogs I follow most closely: Cameron Neylon’s Science in the Open, Deepak Singh’s BBGM, Antony William’s ChemSpider, Bill Hooker’s Open Reading Frame, Shirley Wu’s One Big Lab and Peter Murray-Rust’s blog. I don’t like answering these types of questions because I don’t want to leave people out:) There are many others in my blog reader but these are probably my main focus right now because they deal with Open Science issues.
bradleypic.JPGYou are one of the pioneers of Open Notebook Science. Could you, please, explain to my readers what this is?
Open Notebook Science is simply the practice of making one’s laboratory notebook completely public in as close to real time as possible. In organic chemistry this is pretty straightforward – researchers must keep a notebook where they record what they do and observe in an experiment, generally with the intent of making a specific compound. In other fields, records may be kept in different formats but the idea is that the research group doing ONS should strive to do research transparently with as little “insider information” as is reasonable. In organic chemistry this means providing access to all raw data files (spectra for example) so that another researcher can independently verify all observations and conclusions made.
You started your Open Notebook on a blog, but then later moved it to a wiki. Why? What are the advantages and disadvantages of the two platforms?
Yes, initially I started with a blog but realized fairly quickly that it was not sufficient to function as a lab notebook because there is no record of changes made. A wiki is really close to a perfect tool for the actual notebook since all page versions are time-stamped. We use Wikispaces as our hosting service, which has the advantage of providing third-party timestamps on everything recorded or changed.
Doing science is like focusing a lens. At first you have few data points and make some tentative observations. As more data get added and more thinking and talking get done, things become clearer and the notebook is updated accordingly. Sometimes that means errors get fixed and that entire process is tracked by the wiki. I still use the blog as a means of reporting on big picture issues and milestones. I can then link from the blog to the wiki to back up any claims I make.
Very few scientists are doing Open Notebook Science right now – do you see the practice exploding in the near future, with almost everyone doing it? Will this be a generational thing? Or dependent on the scientific discipline?
I don’t see the practice of full ONS becoming used by the majority of researchers very soon, although I do think many more scientist will become more open in some way. For example they may blog more about their current work or make more raw data available after their papers come out. I don’t think the practice should be mandated. Those who choose to do will most likely find it rewarding, if only in meeting new colleagues and collaborators. There may be something to the generational effect – the YouTube generation probably does expect information to be free to consume and share. There is certainly a discipline dependence – where intellectual property is a concern there will be an additional barrier.
When we talk about Science 2.0 and science blogging, we usually discuss science communication, publishing, networking, political action and teaching. But you have performed experiments in Second Life, i.e., Internet is also a tool for actually doing science. Do you see this happening more – people using the Web as a tool in scientific research in the open view of everyone who cares to come by and watch you?
Yes I do see researchers using the web to share their primary research – Gus Rosania and Cameron Neylon are probably the best recent examples. As far as Second Life, it is another tool – with Andrew Lang we are now able to interact with spectra (NMR, IR, etc) simply by “talking” to the display. We can display proteins and molecules in 3D with realistic shapes. Right now, for my work, I view Second Life to be like a website or blog – I can provide basic information about my research and link to the lab notebook on the wiki if people want more information. I have areas on Drexel Island and the American Chemical Society Island to share my lab’s work. My organic chemistry students also do projects for class in Second Life. I think the most useful outcome of using Second Life is meeting new smart people with similar interests. I have met a few wonderful collaborators that way.
Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?
The most memorable event at the conference was probably meeting Moshe Pritsker from the Journal of Visualized Experiments. He offered to send someone over to my lab to record a protocol – I still have to arrange that….
It was so nice to see you again and thank you for the interview. I hope to see you again in January.
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Check out all the interviews in this series.

Social Networking sites for scientists are proliferating….

There is Nature Network, there is Jeff’s Bench, there is Facebook Scibook, Knowble.com is dead, and people are still building new social networking sites aimed at scientists. There is now SciLink (thanks Alex) and now also ResearchGATE (thanks Bertalan). I am joining everything and watching….one of these days, one of these will win. Nobody can guess which one (or perhaps more than one), but perhaps you can tell me which ones you like and dislike and why?

How YOU can help with malaria research

Social networking meets social conscience:

As reported today in the science journal Nature, MalariaEngage.org aims to help in the stuggle against malaria. Rather than throwing buckets of money at big name Western research institutes, the new website aims to give smaller locally-based African projects a bigger profile.
Relying on grass-roots support from people who are concerned about poverty and disease, the website hopes to fund in-country research that would otherwise be overlooked by the big funders such as the Gates Foundation or NIH.
The site provides profiles of projects that individuals (that’s you and me!) can evaluate and choose to support.

The Open Sleep Journal and The Phylogeny of Sleep Database

One of the latest additions (just two days ago, I think) to the Directory of Open Access Journals is a journal that will be of interest to some of my readers – The Open Sleep Journal. The first volume has been published and contains several interesting articles. One that drew my attention is The Phylogeny of Sleep Database: A New Resource for Sleep Scientists (PDF download) by Patrick McNamara, Isabella Capellini, Erica Harris, Charles L. Nunn, Robert A. Barton and Brian Preston. It describes how they built a database that contains information about sleep patterns in 127 mammalian species. The Database itself can be found here and one can search it by species, by what was measured, by physiological or environmental conditions in which sleep was measured, etc. It has links to research on everything from platypus and echidna, through humans and kangaroos, to elephants, giraffes and sloths.
Since one of the stated projects that will come out of the database is a publication of a book on the Evolution of Sleep, I looked around to see if they are interested in anything else apart from mammals. Looking at the Projects page, I see they intend to add birds to the database later on. But that is not enough. Sleep did not suddenly appear full-blown in mammals and separately in birds. There is a long history of sleep research in reptiles, amphibians and fish, as well as – more recently – in insects like cockroaches, honeybees and Drosophila. In order to study the origin, evolution and adaptive function of sleep we have to look at its precursors among the invertebrates, not just focus on mammals and birds.

Open Access to Scholarly Publications (video)

Open Access to Scholarly Publications (Updated May 10, 2008) from Sean Kass on Vimeo.
by Sean Kass (Via).

Open Access in Italy

Recordings from the Open Access panel in Trieste are now available online. The order was a little different – I went last.

The Impact Factor Folly

The latest issue of Epidemiology features a (only somewhat tongue-in-cheek) article by Miguel A. Hernan: Epidemiologists (of All People) Should Question Journal Impact Factors. Well worth reading and thinking about:

Developing a good impact factor is a nontrivial methodologic undertaking that depends on the intended goal of the rankings. Hence, a scientific discussion about any impact factor requires that its goal is made explicit and its methodology is described in enough detail to make the calculations reproducible. Paradoxically, the methodology of the impact factor that is used to evaluate peer-review journals cannot be fully evaluated in a peer-reviewed journal. As illustrated above, a manuscript describing the Thomson Scientific impact factor would be a hard sell for most journals, and hardly acceptable for the American Journal of Epidemiology, the International Journal of Epidemiology, or Epidemiology.

The same issue also features several interesting responses:
Impact Factor: Good Reasons for Concern
How Come Scientists Uncritically Adopt and Embody Thomson’s Bibliographic Impact Factor?
Rise and Fall of the Thomson Impact Factor
The Impact Factor Follies

Open Access Directory (OAD)

Open Access Directory (OAD) is a wiki that contains all the information one may need and want in regard to Open Access Publishing, from jobs to research questions. You should bookmark it and check it out regularly.

Open Humanities Press

Peter Suber relays the announcement (and add some more) of the Open Humanities Press, a collection of seven Open Access journals (a humanities PLoS of sorts) in critical and cultural theory.
Humanities bloggers have been way ahead of science bloggers in regards to posting their own work (including ideas, hypotheses and rough drafts) online, yet official humanities publishing has lagged behind natural sciences and medicine when it comes to adopting Open Access, so this is a very positive move on their part.

UNESCO booklet on Open Access

UNESCO recently published and informative book: Open access to knowledge and information: scholarly literature and digital library initiatives; the South Asian scenario, which, from what I can see, can be easily modified for all other geographic areas as well. Perhaps it can be used as a template for publishing similar booklets for Africa, Eastern Europe, Latin America, etc.

EuroTrip ’08 – Belgrade, Open Access

OK, I posted a lot of pictures of Belgrade and my Mom’s food so far, but the real business was on Tuesday, when I gave two talks about Open Access, PLoS, Science 2.0, the future of the scientific paper, Open Notebook Science and science blogging.
In the morning, I gave a talk in the gallery of the Museum of Contemporary Art in front of about 20 people, mostly specialist librarians. That session was recorded and, as soon as the podcast is available, I will link to it. There were many good questions asked at the end and the excitement was palpable.
Afterwards I gave an interview for Radio Beograd 202 which ran that same afternoon at 5pm as well as again next morning. I will get a CD of the recording and once I get home will turn it into a podcast and post it.
The next day I gave an interview for a popular show about Digital Culture on Radio Belgrade 2 which will run on Monday morning (I think) and will be available online as a podcast at some point in the future). On Tuesday I have to go to the Radio Belgrade 1 station to be on a very hip (they say “cult”) show in the morning – it is a call-in show, I understand, and will be interesting to do. At least by now, my ability to talk about all this in Serbian language has somewhat improved 😉
In the afternoon, I went to the Pediatric Center of the Medical School at the University of Belgrade, where I gave the presentation again, with perhaps less talk about blogs and more emphasis on Open Access publishing, especially in the medical area. There were about 30 people in the amphitheater, including my Mom, her student Vuk, three of my childhood friends (from elementary school and even before) – one of whom is a professor of Psychiatry – and two high school friends: one is a biomedical researcher and the other, Dr.Vera Zdravkovic who organized the event, is a pediatric endocrinologist and also a professor in the med school.
Again, the interest and enthusiasm were huge, with many excellent questions afterwards – we kept talking in the hall for quite a while afterwards. Perhaps the most important immediate result is that local people who can and should help each other – the researchers/physicians and the medical librarians – got to meet each other and understand how they can help each other find, produce, organize and share information. I think that in Serbia librarians will be the key to the move towards modern use of online technology in scientific and medical research and publishing.
Finally, and perhaps most importantly, both groups (librarians and researchers) got to meet Vedran, the guru of everything Open in Serbia who will be able to help them immensely with all aspects of opening their science to the world and managing the scientific and medical information.
The librarian of the Oncology Center, Ana Ivkovic, was at the afternoon talk. She runs a fantastic blog and she took some pictures from the event and posted them on Flickr.
The Director of the Pediatric Center is an amazing woman. I am not at all surprised that, under her leadership, her center is at the cutting edge of the use of technology in comparison to the rest of the Medical School. We had great discussion after the talk in her office and, afterwards, at lunch in the restaurant Frans. Frans is right next to the vet school and I spent many hours there during my vet-school years back in the 80s. It used to be a hole in the wall with a few tables inside and a few outside. Now it is an elite restaurant – and we joked that they made their first million off of me and my friends and all the beer we had there over the years.

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Science and the New Media

Sheril Kirshenbaum will be on a panel on Science and the New Media at the AAAS Forum On Science And Technology Policy on May 9th and, as bloggers tend to do, she is asking for questions, comments and ideas from the readers. If you have some thoughts on the topic – science on the Web, etc., – go and join the discussion in the comments there.

Science 2.0 (repost)

From the ArchivesI think I have a profile on Friendster – I don’t know, I haven’t checked since 2003. I have bare-bones profiles on MySpace, LinkedIn and Change.Org and I will get an e-mail if you “friend” me (and will friend you back), but I do not have time to spend on there. I refuse to even look at all the other social networking sites like Twitter – there are only so many hours in the day.
But I am interested in possible ways of making science communication more interactive and more Webby 2.0, beyond just blogs. Pedro, Carl and Phillip have recently written thoughtful posts about this topic as well.

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Science 2.0

Do you remember when Mitch Waldrop wrote a draft of an article about Science 2.0 and asked for community feedback? He got 125 comments. Using them, he has now finalized the text and it appears in today’s edition of Scientific American: Science 2.0 — Is Open Access Science the Future? Is posting raw results online, for all to see, a great tool or a great risk?

Open Access in Italian

The podcast of the radio interview with Derek Law and me about Open Access is now available online. Most of the show is in Italian, but if you cannot understand it, our interview is in English and it starts at the 22:07 minute point.

Science Communication in the Age of Internet – in Belgrade

Yup, as soon as I land in Belgrade, I will be giving two lectures about Open Access and the Science Communication in the Age of Internet. The first one, this Tuesday at 11am, will be in the beautiful hall of the Museum of Contemporary Art in Belgrade, sponsored by the Serbian Museum Association and the Museum of Contemporary Art. The main target audience are librarians, but I gather that the lecture is open and quite heavily advertised.
The second lecture will be on the same day at 2pm in the Decanate of the Medical school at the University of Belgrade, geared more towards the physicians, students and researchers. More information will follow, as soon as I get it.
Many thanks to Vedran and two of my childhood friends who are now professors in the Medical school, for organizing these events.
You can RSVP on Facebook:

Serbian Museum Association
e-mail: mdsrbije@infosky.net
www.mds.org.yu
i
Salon Muzeja savremene umetnosti
Pariska 14, Beograd
tel/fax: +381 (0)11 2630 940
www.msub.org.yu
Utorak, 22. april 2008. u 11 casova
Predavanje Bore Zivkovica:
KOMUNIKACIJA NAUKE U DOBA INTERNETA
Bora Zivkovic je internet menadzer za Public Library of Science, organizaciju koja objavljuje naucne radove po principu Otvorenog Pristupa (Open Access). Predavanje ce predstaviti najnovije razvoje u komunikaciji nauke na internetu, ukljucujuci naucne blogove i vikije, koncept Javne Laboratorijske Sveske i Otvorenog Pristupa.
Predavanje ce se odrzati u Salonu Muzeja savremene umetnosti.
Molim vas da potvrdite svoje prisustvo na predavanju.
Kontakt osoba:
– Olivera Nastic, predsednik Sekcije bibliotekara i knjiznicara specijalnih bilioteka MDS
Muzej savremene umetnosti, Beograd, 011/3115-713.
Slicno predavanje, istoga dana u 14h, ce se odrzati u sali Dekanata medicinskog fakulteta u Beogradu. Pristup otvoren.

NIH public access law explained

Peter Suber wrote the most clear, brief and to-the-point explanation of the new law (PDF). Worth reading and bookmarking. Along with the explanation of how it works, Peter also provided this handy table of myths about the new law that some of the dinosaur publishers are trying to push – save it, print it out and have it in your pocket when you go to meetings:
suber%20table.JPG

Another competitive edge of Open Access

Niyaz Ahmed did some stats on the Faculty of 1000 and came up with some interesting data:

I did some analyses involving tools at F1000Biology to know how inclined are the opinion leaders in biological sciences about PLoSONE articles given that the Faculty Members of F1000 have been traditionally ‘jumping’ to articles from a few top tier journals such as Nature or Cell. Good to say, the trend is reversing, although slow.
Here is how – I was very much pleased to note PLoS ONE’s visible impact; 55 of the1241 articles (4%) published in PLoS ONE in 2007 have been evaluated and recommended by the experts at F1000Biology. What this means in terms of impact? As a comparison I modeled PLoS ONE statistics alongside one highly established journal, Nature (the only journal with which PLoS ONE can be compared due to its multidisciplinary nature). A total of 349 articles out of 2892 (12%) published by Nature in 2007 were evaluated at F1000Biology. Seemingly, the difference in terms of number of articles evaluated looks large. However, as I mentioned, if we consider the current visible bias of F1000 faculty towards Nature journals and the publishing criteria (at Nature) linked to space (huge rejection rates due to subjective criteria), PLoS ONE stands distinctly tall given the fact that it is just born.
Performances of all other titles were nowhere near. Other 66 Open Access titles (all BMC series + Genome Biology put together) from Biomed Central (4740 articles in 2007) could yield only 47 evaluations at F1000Biology (0.9%) during 2007. Given that BMC titles are also freely available, it is intriguing to know what makes PLoSONE so successful at F1000? In my perception – it is the high quality of the articles plus the ease with which they can be judged on face – PLoSONE sandbox makes it extremely simple for the evaluators to quickly pick the articles based on notes, referee’s comments, ratings, reader responses and community feedback etc.
The future is even brighter – more and more F1000 members are inclined to using open access articles for their benchmarking. It makes life easy. I remember, I once had almost begged for a reprint from an author of a beautiful review article on genome duplications (many authors do not respond to reprint requests in a reasonable time frame). I wanted to have it evaluated at F1000Medicine and the closed access article was costing me USD 60.00 (in India, this equals to a monthly rent for a 2 bedroom house!!) – how shame!
Finally, I do not know how useful will be these initial statistics on F1000 ratings; but, I am sure this could mean a good indicator for the prospective authors at PLoSONE (especially in the absence of any bibliometric index such as Impact Factor) to foresee its reputation and peer-acceptance that the journal has earned in a short time.

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.

The Scientific Paper: past, present and probable future

From the ArchivesA post from December 5, 2007:
Communication
Communication of any kind, including communication of empirical information about the world (which includes scientific information), is constrained by three factors: technology, social factors, and, as a special case of social factors – official conventions. The term “constrained” I used above has two meanings – one negative, one positive. In a negative meaning, a constraint imposes limits and makes certain directions less likely, more difficult or impossible. In its positive meaning, constraint means that some directions are easy and obvious and thus much more likely for everyone to go to. Different technological and societal constraints shape what and how is communicated at different times in history and in different places on Earth.
Technology – Most communication throughout history, including today, is oral communication, constrained by human language, cognitive capabilities and physical distance. Oral communication today, in contrast to early history, is more likely to include a larger number of people in the audience with whom the speaker is not personally acquanted. It may also include technologies for distance transmission of sound, e.g., telephone or podcasts. This is the most “natural” means of communication.

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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.