Branding vs. Freeing

C P Chandrasekhar (2013) Only the Open Access Movement can address the adverse impact of Western domination of the world of knowlege. Frontline (Oct 4 2913)

Interesting article, but I am afraid it misses the most important points:

1. As so often happens, the article takes “OA” to mean Gold OA journals, completely missing Green OA self-archiving and the importance and urgency of mandating it.

2. The article greatly underestimates the role of quality levels and quality control (peer review standards) in the perceived and actual importance and value of research findings, journal articles and journals — focusing instead on over-reliance and abuse of citation metrics (which does indeed occur, but is not the central problem behind disparities in (a) user access to journals to read, (b) author access to journals publish in, or (c) researcher access to funding to do research with).

Providing OA can completely remedy (a), which will in turn help mitigate (b) and that in turn may improve (c). (OA will also greatly enrich and strengthen the variety and validity of metrics.)

But not if we instead just tilt against impact factors and press for new forms of “branding.” Branding is simply the earned reputation of a journal based on its track-record for quality, and that means its peer review standards, as certified by the journal’s name (“brand”).

What is needed is neither new Gold OA journals, nor new forms of “branding.” What is needed is Open Access to the peer-reviewed journal literature, such as it is, free for all online: peer-reviewed research needs to be freed from access-denial, not from peer review.

And the way for India and China (and the rest of the world too) to reach that is for their research institutions and funders to mandate Green OA self-archiving of all their peer-reviewed research output.

That’s all there is to it. The rest is just ideological speculation, which can no more provide Open Access than it can feed the hungry, cure the sick, or protect from injustice. It simply distracts from the tried and tested practical path that needs to be taken to get the job done.

Stevan Harnad

Understanding the Science Behind the Marvel: Why is the Río Celeste so Blue?

Río _Celeste_Waterfall

Recently, PLOS ONE published the science behind the surprising coloration of the river in the photo above. The beautiful, cloudy cyan waters may look heavily photoshopped, but they’re quite real. This is the actual color of Río Celeste, one of Costa Rica’s more unusual natural wonders. While there are other known examples of waters in such striking hues, such as Japan’s Goshiki-numa lakes, the Río Celeste is the only known river whose color forms at the junction of two crystal-clear sources. And so the question asked for centuries is, what creates this sky-blue hue?

The photo below gives you a better idea of what happens when Quebrada Agria and Río Buenavista, the waterways that merge to form Río Celeste, meet. What you see here is called Teñidero, or ‘dye point’, where the transparent water suddenly turns to turquoise.


Río Celeste, similar to other examples of brilliantly colored waters, is located in a volcanic region. Hypotheses surrounding the origin of this milky blue hue include everything from thermal bacteria to the suspension of colorful minerals (such as copper) throughout the water.

Minerals suspended in water that do not dissolve are sometimes called colloidal particles, and are known for their ability to reflect and scatter light. Currently, these particles are one of the reasons for other examples of jewel-toned waters, such as Yu-gama Crater Lake in Japan. To see if they were also the cause of the sky-blue coloring in this case, researchers collected water and sediment samples from Río Celeste and the two rivers that merge to form it, and then tested the physical (size and distribution) and chemical (pH) properties of each.

The authors used a special separation technique, called ion exchange chromatography, to find out if colored metallic minerals such as copper, nickel, or cobalt were abundant enough to cause the Río Celeste’s turquoise coloration.

It turns out that there were only minute amounts of colored metals ores found in the samples—certainly not enough to cause a whole river to turn blue! However, what the researchers did find is that Río Buenavista has significant concentrations of silicon, as does Quebrada Agria, the latter of which additionally contains sulfate, chloride, and calcium.

Previous studies have shown that colloidal silica (silicon and oxygen) particles between 100- 450 nanometers (nm) in diameter could cause the blue coloration of the water because they reflect light in a particular way. In fact, if these particles are larger than 450 nm, they can create milky hues as well— the same colors and tones found in Río Celeste.

In the figure below parts a and b show a microscope image of the sediment found at the bottom of the Río Celeste; from this, researchers concluded that the pictured clusters were created by gradual buildup of smaller particles in the water. The spectrum below a and b indicates the makeup of this sediment is mostly aluminum, silicon and oxygen, with small amounts of sulfur and iron. Based on the light-scattering properties of colloidal silica, the authors hypothesized that the presence of aluminosilicate in the rivers could have a similar light scattering effect.


So where did these particles come from? It turns out Quebrada Agria’s waters contain aluminosilicate particles too small (< 10 nm) to have an effect. However, Río Buenavista contains aluminosilicates well distributed throughout, and while these are larger (184 nm), they are not concentrated enough to actually create a noticeable scattering of light.

They key to figuring out this puzzle was that, when testing the pH, researchers found that Quebrada Agria was fairly acidic (pH of 3.1, or about as acidic as an orange), and Río Buenavista was rather neutral with a pH of 6.8.

The researchers realized that when the acidic and neutral waters of the two rivers meet, their aluminosilicate particles clump together, resulting in enough particle concentration and size to scatter light and voilà  – the Río Celeste in all its turquoise glory!


Citation: Castellón E, Martínez M, Madrigal-Carballo S, Arias ML, Vargas WE, et al. (2013) Scattering of Light by Colloidal Aluminosilicate Particles Produces the Unusual Sky-Blue Color of Río Celeste (Tenorio Volcano Complex, Costa Rica). PLoS ONE 8(9): e75165. doi:10.1371/journal.pone.0075165

Images: Figure 1, 2 and 3 from the article.

Keywords: river, water, aluminosilicate, clay, light scattering, Mei scattering, Costa Rica, Río Celeste, Goshiki-numa lakes, Teñidero, Quebrada Agria, Río Buenavista, tourism, tourist sites, waterfall, lagoon, Yellowstone, thermal pools, colloidal particle, ion exchange chromatography, Yu-gama Crater Lake, thermal bacteria, silica

Openness Probe for the SSP Scholarly Scullery

Joseph Esposito:
“Stevan Harnad engaged Rick?s comment and asserted that such a policy was a very bad thing since it would set back the advance of Green OA. This is an interesting remark, as it reveals Professor Harnad?s conviction that librarians, indeed the whole world, should view the achievement of his idiosyncratic goal as their highest priority. As far as I know, it is not the mission of Rick?s institution or any other to put Green OA at the top of a list of desiderata. Most institutions put service to their own institutions first, as one would expect. Cancelling Green OA journals will indeed set back the advance of Green OA, but that?s beside the point.”
David Crotty (with 11 scholarly thumbs up from his co-cuisiniers):
“I find Dr. Harnad?s response here somewhat appalling. Progress in implementing Open Access will come from open discussion, analysis and experimentation, not from censorship, obfuscation and withholding information. When voices as disparate as Kent Anderson and Cameron Neylon are in agreement about OA reaching a new era of practical implementation, it should be a sign that Harnad is out of step here. It?s always valuable to have someone willing to point out the state of the Emperor?s clothing.”

Compliments to the chefs. Some suggested recipe upgrades:

1. No suggestion made that institutions cannot or should not cancel journals if their articles are all or almost all Green.

(No such journal in sight yet, however, since Green OA is still hovering around 20-30%, apart from some parts of Physics — but there it’s already been at or near 100% for over 20 years, and no cancellations in sight. For the rest, when Green OA — which grows anarchically, article by article, not systematically, journal by journal — prevails universally, because Green OA mandates prevail, all or most journal articles will be Green universally, so Green OA will not be a factor in deciding whether to cancel this journal rather than that one.)

2. The issue with Rick was not about the notion of canceling journals because their articles are all or almost all Green, but about cancelling journals (60%) because they do not have a policy of embargoing Green OA.

3. And such a perverse cancellation policy would not be a setback for Green OA but for OA.

I note in the SSP scullery discussion above that my suggestion that Rick shold post his OA-unfriendly cancellation strategy to library lists rather than to OA lists amounts to a call for censorship over open discussion. I note only that I am not the moderator of any list, hence have no say over their content. It was an open expression, on an open list, of my opinion (together with the reasons for it) that such discussion belongs on another open list. I do post this SK comment with some curiosity, as my own comments to SK have more than once failed to appear?

Stevan Harnad

Open Access in Europe: The Blind Men and the Elephant

Alas, the well-meaning Euroscientist article “Open access in Europe: the bear and the tortoise” is replete with the most common misunderstandings of open access (OA) — the very same misunderstandings that have kept OA from happening for so many years since it first came within reach.

Despite many hopeful announcements, no OA tipping point has yet been reached. (It isn’t even clear what “tipping point” means, if it doesn’t mean crossing a threshold as of which 100% OA is within sight and fast approaching.)

ERC “joining” Arxiv means providing partial payment to support the costs of a global repository that has been at the disposition of researchers worldwide since 1991. But it’s still only those researchers (mostly physicists and mathematicians) who have been depositing in Arxiv all along who continue to deposit in Arxiv. No tipping point in sight there, for the rest of the disciplines and the rest of the world.

If 62% of ERC-funded articles are OA it is because ERC has mandated OA (but the figure needs to distinguish OA itself, which needs to be immediate, from Delayed Access, which might be 6-12-24 months or even longer, after publication).

The EU Horizon 2020 Framework, too, must clarify and shore up its mandate on the question of the timing of the deposit as well as the timing of access.

Recommendations, Declarations, Statements, Invitations and Incentives to provide OA are very welcome, but alas they do not generate OA itself. Only effective OA mandates, adopted and implemented by research institutions, research funders and universities generate OA. And OA mandates are still few and (more to the point): far too weak (see ROARMAP).

No, the real problem it is not the possibility that publishers’ copyright agreements with authors can still embargo OA for 6-12-24 months or longer. The problem is that most OA mandates fail to mandate immediate deposit anyway, irrespective of how long they allow access to the immediate-deposit to be embargoed by the publisher. Once authors have done an immediate-deposit, the repositories have a Button that makes it possible to provide almost-immediate almost-OA during any allowable embargo period with one click from the would-user and one click from the author.

The UK, the worldwide OA leader since 2004, has not taken “significant steps” forward on OA recently, but significant steps backward. (The Finch Report and the new RCUK OA mandate “prefers” double-paying to publish in gold OA journals instead of letting UK authors continue to publish in their preferred journals and provide green OA by self-archiving in their institutional repositories). Other countries are in fact doing much better than the UK, most notably Belgium, with the Liège model OA green OA mandate — the one that all institutions and funders worldwide should be adopting. It requires immediate deposit in the institutional repository as the means of submitting work for research evaluation, and as a condition for research funding.

It is good that the Science Europe Statement favours OA, but as noted, the past decade has demonstrated unequivocally that statements are not enough: Effective green OA mandates (the Liège model) are needed (and the Science Europe Statement is not even a statement in favour of effective green OA mandates). Much more clarity, focus, and specificity are needed in order to get this job done.

And the first step is to stop saying and thinking that the difference between “gold OA” (publishing) and “green OA” self-archiving is that gold means instant OA whereas green means OA within 6 months: Gold OA requires authors to change journals and pay to publish. Green OA allows authors to continue to publish where they choose, at no cost, and to provide immediate Almost-OA regardless of whether and how long a publisher OA embargo is allowed. (And 60% of publishers do not embargo OA at all.)

Yes, developing countries could in principle outpace the EU and the US in providing OA to their own research output, but what both the developing countries and the EU and US need most is access to all of one another’s research output — and most urgently to the research output of EU and the US. Moreover, most developing countries are not yet outpacing the EU and the US in providing OA to their own research output.

The obstacles to OA have nothing to do with the (legitimate) need and desire of researchers to meet the quality standards of the top journals in their fields. And the solution is not just “incentives and support” (already tried many times, many places) but the universal adoption of an effective OA mandate, which is the Liège mandate — and green.

Physiological Reports Issue 1.4 Now Published

Physiological ReportsThe latest issue of Physiological Reports has now closed. This is the fourth issue of this new open access journal and submissions continue to be strong. We have now accepted 100 articles in the journal. Authors are encouraged to continue to submit their papers across all areas of physiology to this journal using the online submission site.

Below are the ‘editor’s choice’ articles for this issue:

Unique growth pattern of human mammary epithelial cells induced by polymeric nanoparticles
Rajaa Hussien, Bertrand H. Rihn, Housam Eidi, Carole Ronzani, Olivier Joubert, Luc Ferrari, Oscar Vazquez, Daniela Kaufer and George A. Brooks

phy227-toc-0001   Summary: We describe how nanoparticles can be used to draw serum growth factors to cell surfaces.







Obese melanocortin-4 receptor-deficient rats exhibit augmented angiogenic balance and vasorelaxation during pregnancy
Frank T. Spradley, Ana C. Palei and Joey P. Granger

phy281-toc-0001 Summary: Obese normal pregnant melanocortin-4-receptor (MC4R) deficient (+/?) rats compared to lean MC4R+/+ rats have similar placental levels of angiogenic (VEGF, A) and antiangiogenic (sFlt-1, B) factors and comparable angiogenic balance (C). However, white adipose tissue from obese normal pregnant rats have greater VEGF (D), sFlt-1 (E), and angiogenic balance (F). These data indicate that white adipose tissue is an important source of angiogenic factors in normal pregnant, obese animals.


Candidate genes for limiting cholestatic intestinal injury identified by gene expression profiling
Samuel M. Alaish, Jennifer Timmons, Alexis Smith, Marguerite S. Buzza, Ebony Murphy, Aiping Zhao, Yezhou Sun, Douglas J. Turner, Terez Shea-Donahue, Toni M. Antalis, Alan Cross and Susan G. Dorsey


Summary: Following cholestasis, failure of the intestinal barrier with decreased intestinal resistance, increased bacterial translocation, and increased episodes of sepsis has been well described; however, the exact mechanisms remain poorly understood. Anecdotal clinical evidence as well as our own animal data suggests a genetic predisposition to exaggerated cholestatic injury. In this study, a microarray analysis in two strains of inbred mice demonstrated changes in intestinal gene expression not only due to cholestasis but also due to the particular murine strain, implicating novel mechanisms involving the growth hormone pathway, the acute phase response, and the innate immune response.

Evidence for centrally induced cholinergic vasodilatation in skeletal muscle during voluntary one-legged cycling and motor imagery in humans
Kei Ishii, Kanji Matsukawa, Nan Liang, Kana Endo, Mitsuhiro Idesako, Hironobu Hamada, Kazumi Ueno and Tsuyoshi Kataoka


Summary: The aim of this study was to examine using near-infrared microscopy whether sympathetic cholinergic vasodilatation mediates the increases in blood flows of both noncontracting and contracting vastus lateralis (VL) muscles during voluntary one-legged exercise. Atropine (10 µg/kg iv) blunted the increases in concentration of oxygenated-hemoglobin in the bilateral VL at the start of one-legged cycling and during mental imagery of the exercise. Thus, it is likely that central command evokes cholinergic vasodilatation equally in bilateral VL muscles during voluntary one-legged cycling and motor imagery.

The RosettaCon 2012 Collection: Rosetta Developers Meet the Challenges in Macromodeling Head On

Rosetta2012 Collection ImageReproducibility continues to be one of the major challenges facing computational biologists today. Complicated experiments, massive data sets, scantily described protocols, and constantly evolving code can make experimental documentation and replication very difficult.  In addition, the need for specialized knowledge and access to large computational resources can create barriers when trying to design and model macromolecules.

Every year, the Rosetta developer community meets to discuss these challenges and advancements via Rosetta, a software suite that models and helps design macromolecules. In 2010, PLOS announced the RosettaCon2010 Collection, which made the latest research on protocols used to create macromolecular models available to all. Now, the PLOS ONE RosettaCon 2012 Collection continues to tackle issues related to use, reproducibility and documentation by highlighting new scientific developments within the Rosetta community.

The RosettaCon 2012 Collection comprises 14 articles detailing the scientific advancements made by developers that use Rosetta. In order to address reproducibility and documentation challenges, each article within this Collection includes an archive containing links to the exact version of the code used in the paper, all input data, links to external tools and example scripts.

This year’s Collection marks the tenth anniversary of RosettaCon and focuses on three long-term goals of the community: increase the usability of Rosetta, improve its current methods, and introduce completely new protocols.

Increasing the usability of Rosetta – Rosetta still requires specialized knowledge and large computational resources, but this collection features two articles describing advancements that make it easier for non-experts to use its applications. These articles introduce the Rosetta Online Server that Includes Everyone (ROSIE) workflow, which allows for rapid conversion of Rosetta applications into public web servers, and PyRosetta, a new graphical user interface (GUI) which allows users to run standard Rosetta design tasks.

Improving current prediction methods – Several articles describe improvements to Rosetta’s structure prediction capabilities and design methodologies. Some examples include improvements to loop conformational sampling, and a recently developed ray-casting (DARC) method for small molecule docking now enables virtual screening of large compound libraries.

Introducing new protocols – A number of articles featuring new procedures and applications that debuted at the conference are introduced in the Collection. Highlights include new methods for dealing with ligand docking, advancements to pre-refine scaffold proteins prior to computational design of functional sites, and new protocols to drive Rosetta de novo modeling.

The RosettaCon 2012 Collection continues to help serve the Rosetta community in an effort to ensure that newly developed protocols are as usable as more established workflows, are transparent, and are accurately documented even in an active development environment.

This post has been adapted from “The RosettaCon 2012 Special Collection: Code Writ on Water, Documentation Writ in Stone” which serves as a more in-depth overview of the new collection. To read all that this Collection has to offer, click here.

Speakers Announced for World Bank SPARC OA Week Kickoff

SPARC (The Scholarly Publishing and Academic Resources Coalition) and the World Bank are pleased to announce the following speakers for the Open Access Week 2013 kickoff event on Monday, October 21st starting at 3:00pm EDT in Washington, DC:

  • Dr. Stefano Bertuzzi, Executive Director of the American Society for Cell Biology (ASCB)
  • Brett Bobley, Chief Information Officer for the National Endowment for the Humanities 
  • Dr. Kathleen Fitzpatrick, Director of Scholarly Communication of the Modern Language Association
  • Dr. Cameron Neylon, Advocacy Director for Public Library of Science
  • Dr. Michael Stebbins, Assistant Director for Biotechnology in the Science Division of the White House Office of Science & Technology Policy

The kickoff event will take place at the World Bank. A LiveBlog and webcast of the panel discussion and ceremony will be available for those who cannot attend in person. The event will be recorded and be available to the community for use during and after local Open Access events. No registration is necessary for the webcast. Participants are encouraged to post their questions for the panel in advance and during the event at, and to stream the webcast to kick off their own Open Access Week events.

More information here.

Thisis the page to bookmark to watch the event live online.

MedOANet European Conference – Online Program and Information

The MedOANet European Conference will take place at the National Documentation Centre / National Hellenic Research Foundation in Athens, Greece, from 17 to 18 October 2013 during the International Open Access Conference.

The final conference of MedOANet will serve to present the results of the project, placing them in the wider European perspectives on Open Access policies, and providing a forum for the current debate on Open Access policy implementation practices within the EU. Specifically, the final conference will focus on best practices in policy implementation among research funders and research performing institutions, as well as a discussion regarding the role of open access within the European Research Area. Speakers include representatives of the European Commission and important stakeholders involved in the implementation of the European Research Area such as the European University Association, the League of European Research Universities and Science Europe.

The program of the International Open Access Conference @ EKT will include presentations by renowned experts and representatives from the areas of research and Open Access. The conference is of special interest for institutions that are involved in research policy and research performing institutions.

Máire Geoghegan-Quinn, Commissioner for Research, Innovation and Science will address a video taped opening message to the Conference.

The full program of the Conference can be found online here:

Elsevier Keeps Revising Its Double-Talk (But Remains Fully Green)

Alessandro Sarretta asked:

“In a blog post you said that ‘Elsevier is fully green Fully green means the refereed, revised, accepted final draft is openly accessible’

“This is correct reading this Elsevier web page that seems an old one._

“But reading the current Article Elsevier posting policy web page, it says:

Pre-print Definition: A preprint is an author?s own write-up of research results and analysis that has not been peer-reviewed, nor had any other value added to it by a publisher (such as formatting, copy editing, technical enhancement etc…).

Elsevier’s Policy: An author may use the preprint for personal use, internal institutional use and for permitted scholarly posting.

In general, Elsevier is permissive with respect to authors and electronic preprints. If an electronic preprint of an article is placed on a public server prior to its submission to an Elsevier journal or where a paper was originally authored as a thesis or dissertation, this is not generally viewed by Elsevier as ?prior publication? and therefore Elsevier will not require authors to remove electronic preprints of an article from public servers should the article be accepted for publication in an Elsevier journal.

“So the pre-print shall “not have been peer-reviewed”… Could you share your opinion on that?”

What matters is the postprint (the “Author’s Accepted Manuscript [AAM]”) not the unrefereed preprint.

Elsevier believes that individual authors should be able to distribute their AAMs [Accepted Author Manuscripts] for their personal voluntary needs and interests, e.g. posting to their websites or their institution?s repository, e-mailing to colleagues. However, our policies differ regarding the systematic aggregation or distribution of AAMs… Therefore, deposit in, or posting to, subject-oriented or centralized repositories (such as PubMed Central), or institutional repositories with systematic posting mandates is permitted only under specific agreements between Elsevier and the repository, agency or institution, and only consistent with the publisher?s policies concerning such repositories. Voluntary posting of AAMs in the arXiv subject repository is permitted.

Please see my prior analyses of this Elsevier double-talk about authors retaining the right to make their AAMs OA in their institutional repositories “voluntarily,” but not if their institutions mandate it “systematically”: Authors can always safely assert that whatever they do, they do “voluntarily,” including whenever they exercise the right to exercise a retained right, voluntarily.