Monthly Archives: October 2012

Halloween Highlights: Crushing Jaws!

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Happy Halloween to those goblins and ghouls amongst you! Before you go trick-or-treating tonight, let’s wrap up our month-long series on creepy critters and things that go bump in the night with one final critter and its modern-day cousin.

The unassuming reptile pictured above is the tuatara. The tuatara are found only in New Zealand, and are often called “living fossils” because of their physiological similarities to their ancient ancestors.

In research published today in PLOS ONE, researchers led by Dr. Oliver Rauhut discovered the fossil remains of an ancient relative of the tuatara, Oenosaurus muelheimensis. The species is named in honor of the Franconian Alb, the wine-growing region in Germany where the fossil was discovered, and the German village of Mühlheim.

Pictured to above is the Oenosaurus’ lower jaw, which in life featured a set of ever-growing tooth plates and multitudinous “pencil-like” teeth. Researchers posit that the arrangement and morphology of the lower jaw suggests that it moved in a crushing motion.

We recently invited Dr. Oliver Rauhut, the corresponding author of the paper, to share the group’s thoughts on their new findings. He writes:

The incentive for our research was the find of a new specimen of a rhynchocephalian from the Late Jurassic of Germany, which we name Oenosaurus muelheimensis. Rhynchocephalians are an ancient group of reptiles, today only represented by the Tuatara that lives on small islands off the coast of New Zealand and is regarded as a classic example of a living fossil. The new fossil has an extremely unusual dentition, and at first we were all at a loss as to what kind of animal this was, with ideas ranging from a chimeran fish to a rhynchosaur -[a] pig-like reptile that lived in the Triassic (which, incidently, is also reflected in the name…). After identifying the animal as a rhynchocephalian, we had a closer look at the dentition, which is unique amongst tetrapods in presenting large, continuously growing tooth plates. Such an extreme adaptation in a Jurassic rhynchocephalien contradicts the traditional idea that these animals were conservative and evolutionary inferior to lizards. Thus, we challenge the current opinion that the decline of rhynchocephalians during the later Mesozoic was mainly caused by selection pressure by radiating lizards and early mammals; instead climate change in the wake of continental break-up at that time might have been responsible.

This concludes our month-long celebration of some the spooktacular science you can find on PLOS ONE. If you are interested in learning about other creepy critters that we have covered in past years, please visit these links.

Have a safe and happy Halloween!

 

Citations:

Rauhut OWM, Heyng AM, López-Arbarello A, Hecker A (2012) A New Rhynchocephalian from the Late Jurassic of Germany with a Dentition That Is Unique amongst Tetrapods. PLoS ONE 7(10): e46839. doi:10.1371/journal.pone.0046839

http://en.wikipedia.org/wiki/Tuatara

The first image is provided courtesy of Helmut Tischlinger and can be found accompanying the institution’s press release.

The second image is Figure 2F in the manusript.

Create. Attract. Deposit.

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The Scholar Electronic Repository of the New Bulgarian University was presented among the winning institutions on the Open Repositories 2012 7th International Conference of the Open Repositories event.

 

The first institutional open-access repository – the Scholar Electronic Repository of the New Bulgarian University (SER of NBU), has been launched in 2005. The project was endorsed by the Library and realized with the financial support from HESP Program of OPEN SOCIETY Institute, Budapest, Hungary.

 

Basic objective of the University is to stimulate creativity and spur of research within academic community and postgraduate students. 

 

A transformation in maintaining policy has raised deposit activity. Better level of training, assistance, and appraisal are achieved by adopting inovative methods and techniques – interactive tutoring, Web 2.0 tools, 3G networking and real time interaction.

Why Green OA Needs To Come Before Gold OA: A Reply to Jan Velterop

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Jan Velterop wrote:

(1) Stevan trades off expected speed of achieving OA against quality of the resulting OA. It’s his right to do that. I just point out that that’s what it is. That’s my right. He calls it ‘deprecating green OA’; I prefer to call it ‘comparing outcome’.

(2) My ‘jumping with a closed parachute’ is not in any way a criticism of green OA or advocating green OA. It is a criticism of presenting green OA (in which the publication of articles being paid for by subscriptions) as the only way until all scholarly literature is available as green OA, and only then consider alternatives to the subscription system. I consider that deeply unrealistic, utterly unfeasible and not viable, and I favour developing gold OA as a replacement of the subscription system alongside green OA, gradually replacing the subscription system.

(3) The agreement reached at the BOAI to pursue both strategies (later called green and gold) proved short-lived. This has been most unfortunate, in my view. Stevan has introduced the idea that gold and green are rivalrous. They aren’t. They both contribute to growing OA. They both come with a transition price. In one case the price is lower quality of the resulting OA; in the other it is money.

Green vs. Gold is not a question of rivalry, it’s a question of priority.

The reason Green has to come first is very simple: (i) Gold OA journal publishing is vastly over-priced today and (ii) the money to pay for it (even once it has been downsized to a fair, affordable price) is still locked into institutional journal subscriptions.

Besides providing 100% OA, Green OA (which is now only 25% when unmandated, but can be increased to 100% when mandated) provides the way both to release the subscription money to pay for Gold OA and to force journals to downsize to a fair, affordable, sustainable price for Gold OA (namely, the price of managing peer review alone, as a per-review (sic) service: no more print edition; no more online edition; all access-provision and archiving offloaded onto the worldwide network of Green OA institutional repositories):

Institutions can only cancel subscriptions when the subscribed content is available as Green OA. Until then they can only double-pay (whether for hybrid subscription/Gold journals or for subscription journals plus Gold journals).

And publishers will not unbundle and cut costs to the minimum (peer review service alone, nothing else) until cancellations force them to do so.

And (before you say it): If a new Gold OA journal enters the market today with a truly rock-bottom price, for the peer-review service alone, the money to pay for it is still over and above what is being paid for subscriptions today, because the subscriptions cannot be cancelled until most journals (or at least the most important ones) likewise downsize to the bare essentials.

And most journals are not downsizing to the bare essentials.

And institutions and funders cannot make journals downsize.

All institutions and funders can do is pay them even more than what they are paying them already (which is exactly what the publisher lobby has managed to persuade the UK and the Finch Committee to do).

I do not call that a “parachute” toward a “soft landing”: I call it good publisher PR, to preserve their bottom-lines. And for most institutions and funders, it not only costs more money, but it is even more unaffordable and unsustainable than the serials status-quo today (which is reputedly in crisis).

The promise from hybrid Gold publishers to cut subscription costs in proportion to growth in Gold uptake revenues, even if kept, is unaffordable, because it involves first paying more, in advance; and all it does is lock in the current status quo insofar as total publisher revenue is concerned, in exchange for OA that researchers can already provide for themselves via Green, since publication and its costs are already being fully paid for — via subscriptions.

Nor is “price competition” the corrective: Authors don’t pick journals for their price but for their quality standards, which means their peer-review standards. It would be nothing short of grotesque to imagine that it should be otherwise (think about it!).

The corrective is global Green OA mandates: That — and not “price competition” between Gold OA journals — will see to it that the huge, unnecessary overlay of commercially co-bundled products and services that scholarly journal publishing inherited from the Gutenberg (and Robert-Maxwell) era is phased out and scaled down, at long last, to the only thing that scholars and scientists really still want and need in the online era, which is a reliable peer review service, provided by a hierarchy of journals, in different fields, each with its own established track record for quality — hence selectivity — at the various quality levels required by the field.

So what’s at issue is not a trade-off of “speed” vs. “quality” (whether peer review quality, or re-use/text-mining rights) at all, but a trade-off of speed vs. the status quo.

And yes, that’s speed, in the first instance, toward 100% free online access (Gratis OA) — of which, let us remind ourselves, we currently have only about 25% via Green and maybe another 12% via Gold — because that is what is within immediate reach (although we have kept failing to grasp it for over a decade).

The rest of the “quality” — Gold OA and Libre OA — will come once we have 100% Green OA, and publishers are forced (by Green-OA enabled subscription cancelations, making subscriptions no loner sustainable) to downsize and convert to Gold.

But not if we keep playing the snail’s-pace game of double-paying pre-emptively for Gold while research access and impact keeping being lost, year upon year — all in order to cushion the landing for the only ones that are comfortable with the status quo (and in no hurry!): toll-access publishers.

And please let’s stop solemnly invoking the BOAI as a justification for continuing this no-sum, no-win game of no-OA unless you double-pay.

Publication costs are being paid, in full (and fulsomely) today. What’s missing is not more revenue for publishers, but OA.

And Green OA mandates will provide it.

The rest will take care of itself, as a natural process of adaptation, by the publishing trade, to the new reality of global Green OA.

Stevan Harnad

Food Science & Nutrition Publishes its First Articles on Early View

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Food Science & Nutrition CoverWe are delighted to announce that Food Science & Nutrition has published its first articles on Early View.  Food Science & Nutrition opened for submissions in May 2012 and we have received a high number of submissions related to all aspects of human food and nutrition, as well as interdisciplinary research that spans these two fields.  The first articles are now live on Wiley Online Library. Read all our open access articles here!  Food Science & Nutrition is an open acces, fully peer-reviewed journal providing rapid dissemination of research in all areas of food science and nutrition.

We hope that next time your are preparing a manuscript you will consider submitting to the journal. Among the first papers available online are:

purple_lock_open Supplementing long-chain n-3 polyunsaturated fatty acids in canned wild Pacific pink salmon with Alaska salmon oil by Trina J. Lapis, Alexandra C. M. Oliveira, Charles A. Crapo, Brian Himelbloom, Peter J. Bechtel and Kristy A. Long
Abstract: Establishing n-3 polyunsaturated fatty acid contents in canned wild Alaska pink salmon products is challenging due to ample natural variation found in lipid content of pink salmon muscle. Supplementing canned wild Alaska pink salmon with salmon oil reduces variability in product composition, and this facilitates accurate disclosure of the n-3 fatty acid content per serving size in the product package.

purple_lock_open Effects of agriculture production systems on nitrate and nitrite accumulation on baby-leaf salads by Alfredo Aires, Rosa Carvalho, Eduardo A. S. Rosa and Maria J. Saavedra
Abstract: We studied the effect of agricultural practices on toxic compounds accumulation. Nitrates and nitrites were detected at lower levels, within the EC regulations. Benefits of ready-to-eat vegetables consumption are discussed.

If you would like to know when new articles and issues appear online sign up for eToC alerts on the Food Science & Nutrition website >

UCT Open Access Week Resources Now Available

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Open access has been showed by numerous studies to increase citation to scholars’ work of all kinds. The online environment also means that new forms of impact can be measured and in new ways. Alternative metrics (ALTmetrics) provide a new approach to analysing impact beyond that of tradition citations, considering other indicators such as downloads and references in social media. The internet has shrunk the world and allows scholars to connect and collaborate across the globe in real time.  

In this digital world, opening up access to not just journal articles but all outputs and information has incredible power to transform academia and society as a whole.  Academics  at UCT had the opportunity last week to engage with these issues and more through several events being run by the OpenUCT Initiative. 

All the presentations have been made available for viewing and download:

1. Demystifying Open Access
2. Exploring ‘Impact’: An introduction to new tools and approaches for alternative scholarship metrics
3. Finding Open Stuff
4. Creative Commons Practical Workshop
5. Academics’ online presence: assessing and shaping your online visibility

Halloween Highlights: Carnivorous Plants

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Plants may not generally be associated with the spooky sentiments of Halloween, but put the right Hitchcock soundtrack with the video below and it could have come straight out of a Hollywood horror film.

Carnivorous plants have inspired many creative minds over time, perhaps most memorably in the cult classic, Little Shop of Horrors which featured a fictitious new hybrid that thrived only on human blood. The real plants may not be so scary to us but for insects, they’re certainly something to be wary of.

The video above  shows the particularly dramatic “active” trapping mechanism employed by one carnivorous species the Drosera glanduligera, a sundew that feeds on insects. Even the abstract of the study “Catapulting Tentacles in a Sticky Carnivorous Plant” conjures cryptic images:

Prey animals walking near the edge of the sundew trigger a touch-sensitive snap-tentacle, which swiftly catapults them onto adjacent sticky glue-tentacles; the insects are then slowly drawn within the concave trap leaf by sticky tentacles.

“Passive” trapping mechanisms used by other carnivorous plants can be equally creepy when documented close up (and paired with the right soundtrack). Take a look at Video S1 and S3, below, of a paper published in 2007 investigating the digestive fluid of the Nepenthes rafflesian, a pitcher plant that relies on its unique shape and a pool of  highly viscoelastic fluid to trap insects for digestion. The first video shows how easily a fly can escape a pool of water, while the second video shows the distinct advantage the digestive fluid gives the plant. Both demonstrate the classic horror film qualities science can evoke!

 

 

Citation: Poppinga S, Hartmeyer SRH, Seidel R, Masselter T, Hartmeyer I, et al. (2012) Catapulting Tentacles in a Sticky Carnivorous Plant. PLoS ONE 7(9): e45735. doi:10.1371/journal.pone.0045735

Citation: Gaume L, Forterre Y (2007) A Viscoelastic Deadly Fluid in Carnivorous Pitcher Plants. PLoS ONE 2(11): e1185. doi:10.1371/journal.pone.0001185

Richard Poynder Interviews Ian Gibson About 2004 UK Select Committee Green OA Mandate Recommendation

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Another brilliant (and timely) OA whodunnit by Richard Poynder!

Yet the plot thickens, with the mystery of the outcome of the 2004 UK Select Committee deliberations still not altogether dispelled.

Ian Gibson is clearly brilliant, and his heart is clearly in the right place. But although his 2004 Gibson Committee Report clearly had (and continues to have) enormous (positive) ramifications for OA worldwide, Ian himself just as clearly does not fully grasp those ramifications!

Journal and Author Selectivity. Ian still thinks that OA is about somehow weaning authors from their preferred highly selective journals (such as Nature), even though the cost-free Green OA that his own Report recommended mandating does not require authors to give up their preferred journals, thereby mooting this issue (and even though the ominous new prospect of double-paying publishers for hybrid Gold OA out of shrinking research funds favoured by the Finch Committee Report does not require authors to give up their preferred journals either).

Research access, assessment and affordability are being conflated here. Green OA does not solve the affordability problem directly, but it sure makes it much less of a life/death matter (since everyone has Green access, whether or not they can afford subscription access). And of course that in turn makes subscription cancelations, publisher cost-cutting, downsizing and conversion to Gold much more likely — while also releasing the institutional subscription cancelation windfall savings to pay the much lower post-Green Gold OA cost many times over. This leaves journals’ peer-review standards and selectivity up to the peers — and journal choice up to the authors — where both belong.

Giving up authors’ preferred journals in favour of pure Gold OA journals was what (I think) BMC’s Vitek Tracz and Jan Velterop had been lobbying for at the time (and that is not what the Gibson Report ended up recommending)!

Emily Commander. So I think if you really want to get to the heart of the mystery of how the Gibson Report crystallized into the epochal recommendation for all UK universities and funders to mandate Green OA you will have to dig deeper, Richard, and interview its author, Emily Commander, who — as Ian indicates — was the one who crafted the text out of the cacophony of conflicting testimonials.

Don’t ask Emily about the bulk of the report, which is largely just ballast, but about how she arrived at its revolutionary core recommendation (highlighted in boldface below). That’s what this is all about…


Select Committee on Science and Technology
Tenth Report
(2004)

Summary
[boldface added]

Academic libraries are struggling to purchase subscriptions to all the journal titles needed by their users. This is due both to the high and increasing journal prices imposed by commercial publishers and the inadequacy of library budgets to meet the demands placed upon them by a system supporting an ever increasing volume of research. Whilst there are a number of measures that can be taken by publishers, libraries and academics to improve the provision of scientific publications, a Government strategy is urgently needed.

This Report recommends that all UK higher education institutions establish institutional repositories on which their published output can be stored and from which it can be read, free of charge, online. It also recommends that Research Councils and other Government funders mandate their funded researchers to deposit a copy of all of their articles in this way. The Government will need to appoint a central body to oversee the implementation of the repositories; to help with networking; and to ensure compliance with the technical standards needed to provide maximum functionality. Set-up and running costs are relatively low, making institutional repositories a cost-effective way of improving access to scientific publications.

Institutional repositories will help to improve access to journals but a more radical solution may be required in the long term. Early indications suggest that the author-pays publishing model could be viable. We remain unconvinced by many of the arguments mounted against it. Nonetheless, this Report concludes that further experimentation is necessary, particularly to establish the impact that a change of publishing models would have on learned societies and in respect of the “free rider” problem. In order to encourage such experimentation the Report recommends that the Research Councils each establish a fund to which their funded researchers can apply should they wish to pay to publish. The UK Government has failed to respond to issues surrounding scientific publications in a coherent manner and we are not convinced that it would be ready to deal with any changes to the publishing process. The Report recommends that Government formulate a strategy for future action as a matter of urgency.

The preservation of digital material is an expensive process that poses a significant technical challenge. This Report recommends that the British Library receives sufficient funding to enable it to carry out this work. It also recommends that work on new regulations for the legal deposit of non-print publications begins immediately. Failure to take these steps would result in a substantial breach in the intellectual record of the UK.

The market for scientific publications is international. The UK cannot act alone. For this reason we recommended that the UK Government act as a proponent for change on the international stage and lead by example. This will ultimately benefit researchers across the globe.

OPUSeJ Project

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OPUSeJ (Open-access Peer-reviewed Universal Scholarly electronic Journal) at www.opusej.org. is a new site, still in an incubation state, which is our answer to “Set the default to OPEN ACCESS”. OPUSeJ is an academic article sharing site designed to handle all scholarly articles. Any article, by any author, on any subject, in any language, in any format could be submitted for peer-review to be published for free online access by all. Any article (or a pre-reviewed version of the article) that has already been published after peer-review, in any journal, could be registered at OPUSeJ as a Forum article. This is a site in which the author acts as a moderator for open comments and can post addendum, erratum and citations forward.

OPUSeJ is strictly electronic, run by volunteers and is peer-produced, so costs are low. Author registration fees would be nominal and are currently not being charged. All are welcome to view the site and consider contributing a new manuscript or registering an already published article. For more info read the editorial, Scholars without Borders at http://www.opusej.org/2012/07/12/editorial-scholars-without-boarders/.

Sincerely,

Donato Pezzutto

Editor OPUSeJ 

Why CC-BY will sometimes be a violation of research ethics: weight loss ad on bus example

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This example is meant to illustrate one of the reasons why I recommend AGAINST CC-BY as a default for open access. CC-BY is the Creative Commons – Attribution Only license, giving blanket permission, in advance, for anyone to re-use a work, including making derivatives, as long as the work is attributed. From the user’s perspective, this is great! However, it is important to note that CC-BY opens up possibilities that are both positive and negative. I am focusing on the negative, because so many of my colleagues in the open access movement appear to focus exclusively on the positive. Here is one illustration of why CC-BY is not always a good idea.

Picture a research subject in an obesity study, who agrees to allow the researcher to use their picture in a published research article. The researcher, following traditional protocols for working with research subjects, will probably have said something about the publication. However, it is at present very unlikely that the researcher has told the subject that they plan to publish with a CC-BY license, which means that their picture will be available for anyone, anywhere, to use for commercial purposes, including making derivatives. A weight loss company could take this picture and use it in an advertisement on the side of a bus, a use of a CC-BY licensed work that is arguably quite appropriate. If this kind of consequence of publishing with CC-BY (very different from traditional academic publishing) is not explained to the subject in the process of requesting permission to publish the picture, then the researcher does not have informed consent, and will be in violation of research ethics protocol if the picture is published CC-BY.

In a case like this, there are legal as well as moral issues to consider. A research subject in this position might well want to sue someone – that someone could be the researcher, the university, the journal, and/or a research funder if the policy of the latter was the reason for publishing CC-BY.

This could happen without CC-BY. However, CC-BY makes this more likely – a commercial entity might well gather CC-BY licenses to create a database of images to sell (Springer Images already does this). A CC-BY-NC and/or ND license (NC = noncommercial, ND = no derivatives) would signal to a potential user of the image that a usage like this would be appropriate, and would protect the researcher, university, etc. from legal risk by making a lawsuit less likely (with CC-BY-NC and/or ND, the fault is clearly that of the weight loss company, so they are more likely to be sued), and gives a strong argument in the case that a lawsuit does proceed.

The BOAI 10 recommendation of CC-BY is one of the reasons that I cannot support BOAI 10 as a whole. This is not a small disagreement about priorities or preferences, but rather one element of BOAI 10 that I regard as a serious error to be avoided.

Updated October 27 correcting typos and some minor proofreading.

This post is part of the Creative Commons and Open Access critique series.

Worth a Thousand Words

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How many arrows are depicted in the photo above? How many can you find? One? Five?

The answer is 118.

In research published last week, researchers digitally compiled 118 different lithic points from the Patagonia region of South America. All samples date back to the Late Holocene period and — the researchers posit — were made using other arrows, spears, and points. The study examined the design of these points and aimed to determine whether they can be seen as working in a modular system comprised of the blade (e.g., the arrow) and the stem (e.g., the arrow shaft).

The image above is Figure 1 in the manuscript. And as you can see, the researchers labeled twenty-four parts, or “landmarks”, of the composite image. These points or landmarks helped in measuring the image’s shape, angles, and proportions.

To learn more about this image and read the full text of the study, click here.

Citation: González-José R, Charlin J (2012) Relative Importance of Modularity and Other Morphological Attributes on Different Types of Lithic Point Weapons: Assessing Functional Variations. PLoS ONE 7(10): e48009. doi:10.1371/journal.pone.0048009

http://en.wikipedia.org/wiki/Modular_design

ALWAYS MORE Splendid Stuff: postcards, football, Muppets frm Digital Repository at U Maryland

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To celebrate Open Access Week 2012 Oct. 21-28 DuraSpace will post a new “For Your Repository Viewing Pleasure” each day (and beyond) to highlight the “splendid stuff in YOUR repository”.

The University of Maryland Libraries, a DuraSpace Silver Sponsor and long-time user of Fedora and DSpace, are continuing to add to digitize and add valuable collection material to their repository daily.

DRUM (Digital Repository at the University of Maryland) <http://drum.lib.umd.edu>, currently holds close to 13,000 digital objects, including all of the theses and dissertations produced by students at the University of Maryland since 2003.

Digital Collections <http://digital.lib.umd.edu> is home to the University’s digitized special collections, and includes a rich array of content, appealing to students, alumni, and scholars. 

Even when it’s not football season, take some time to view one of the over 700 University of Maryland football films dating from 1946-1989, recently digitized and made freely available via the University AlbUM digital collection <http://hdl.handle.net/1903.1/1773>.  Or, if planning a road trip this summer, pick a state and browse the National Trust Library Historic Postcard Collection’s over-4,000 historic postcards for attraction ideas <http://hdl.handle.net/1903.1/3711>. In the past year, we have digitized several hundred manuscripts to assist in research relating to the history of the Civil War and slavery in Maryland  <http://hdl.handle.net/1903.1/1716>. Into espionage? Digital Collections is also an excellent place to read other people’s diaries, whether you’re interested in heartfelt confessions from a young Maryland widow in 1859 <http://hdl.handle.net/1903.1/2613> or  a war diary detailing aspects of the attack on Pearl Harbor <http://hdl.handle.net/1903.1/5910>.

If tempted to visit campus, the University of Maryland Libraries’ Digital Collections contain a number of resources that are restricted to campus use due to licensing restrictions.  The collections include over 70 digital videos documenting the work of Jim Henson <http://hdl.handle.net/1903.1/419>, over 800 digital educational films <http://hdl.handle.net/1903.1/420>;, and a growing collection of digitized Japanese children’s books from the post-WWII years, 1946-1949 <http://hdl.handle.net/1903.1/3301>.

The University of Maryland Libraries have been actively adding content to their Fedora repository since 2007, and will continue to do so.  The treasures located there are used for fun, for research, and for educational purposes, and we hope, for reasons that we have not even imagined.

Thanks to Jennie Levine Knies, Manager, Digital Stewardship, McKeldin Library, University of Maryland, for submitting this information.

Please continue to send descriptions of the “Splendid Stuff” that can be found in YOUR Open Access repository. DuraSpace will highlight availability throughout year. Please contact Carol Minton Morris cmmorris@duraspace.org for more information.