Pre-emptive cancellation costs far, far more than it saves

Bjorn Brembs: “What you’re saying here is that cancellations now are premature, because too few articles are actually available in green repositories? That libraries should hold off because otherwise we face access problems? If that is what you are saying here, then it may be worth spelling it out more clearly as for me that was not immediately obvious. Unintended consequences in publisher behavior (as you allude to above) aside, what is your opinion on using the funds of canceled subscriptions to improve repository functionality to improve green acess? This should only mean a brief interruption of service for much improved access shortly thereafter and a speeding up of the transition you envisage?”

1. Cancelling journals because their policies are Green — i.e., because they do not embargo Green OA self-archiving — is both absurd and destructive: It simply encourages journals to adopt embargoes.

2. Cancelling journals because (some of) their articles are Green is premature and self-defeating: Less than 20% of journal articles are unembargoed Green (i.e., immediate) OA today, and they are distributed randomly across all journals. Hence to cancel any particular journal because the proportion of its articles that is available Green today exceeds this global average is, again, just to penalize that journal, perversely (as well as jeopardizing the growth of Green OA itself, gratuitously).

The time to consider cancelling journals is once Green OA mandates and hence Green OA are at or near 100% globally, and hence the proportion of journal articles that are green OA is at or near 100%. At this point all journals will be at or near 100% and the global cancellation pressure will affect all of them, forcing them all to cut inessential costs, downsize, and convert to Fair Gold OA. (Then — and only then — is the time to redirect a fraction of each institution’s annual subscription cancellation windfall savings to pay the much-reduced Fair-Gold publication fees for the institution’s authors’ own annual article output, affordably and sustainably. Trying instead to start doing this now, pre-emptively — while percentage Green is still low, Green growth is still slow and unstable, subscriptions to core journals still have to be paid, and Fool’s Gold is still over-priced and double-paid (and double-dipped, if hybrid Fool’s-Gold) — would be a profound failure to think ahead.

In sum, to cancel journals now based on the percentage of their articles that are accessible as Green OA now would be as as short-sighted and futile as it would be counterproductive: Like the Finch Fiasco and , premature cancellation would only serve to delay the optimal and inevitable for yet another gratuitously lost decade.

(I begin to think that that might even serve as a fair punishment for all this seemingly endless readiness to run off in all directions but the right one, without troubling to think anything through even a few steps ahead!)

The Power of the Claw: Not Your Average “Soft” Material

Sep blog-tiger cropped

Earlier this month we gave you cuddling between affectionate lions. Lest we become overwhelmed by the desire to cuddle one of these (albeit adorable) feline predators ourselves, here is a look at exactly what one of their clawed paws could do to us, including to one of our toughest components: bone. In a PLOS ONE study published earlier this month, researchers tested the ability of claws to scratch the surface of bone. The effects of claw damage are often overlooked because claws are made of a material softer than bone. Contrary to expectations, however, these researchers found that claws produced recognizable bone damage.

The setup was simple: let a Kansas zoo tiger participating in their enrichment program spend an afternoon leisurely playing with carefully nested cow thigh bones, also called femora. To ensure that the cow femora were only accessible to tiger claws and not to tiger teeth, researchers bolted femora down into a log that was narrowly hollowed out—preventing the big cat from sticking his snout in.

Sep blog- cow femora

The result: impressively lacerated cow femora. Once tiger playtime was over, researchers removed the log, unbolted the femora, and microscopically examined the bone. Four scratches were clearly visible upon the bone’s surface. The scanning electron microscope (SEM) image below further highlights the depths of the tiger claw handiwork.

Sep blog-fomora scratches microscope

In this particular gouge, the main diagonal chasm in the image, the gulf made by the tiger’s claw penetrated the outer covering and subadjacent bone into the bony matrix. As we can see, tiger claws can do some damage.

Damage done to bone, however, is for the most part attributed to the effects of a predator’s teeth and not its claws, the reason being that measures of scratch resistance adhere to a so-called Mohs scale of mineral hardness. The Mohs scale is graded, with talc (1) as the softest material and diamond (10) as the hardest. On the scale, harder materials damage softer materials, but not vice versa. And in our case, bones are, in fact, harder than claws. Claws are made of the protein keratin—the same stuff is in hair, wool, nails, horns, and hooves—which scores a meager 2.5 on the Mohs scale. Bone, on the other hand, scores a much more formidable 5.0.

The current research, however, shows that we can expand our understanding of scratch resistance and mineral hardness to include the effects of softer materials striking harder materials, as long as we consider the kinetic energy involved, like the action of a tiger swatting or grabbing with its paw. In essence, more could be going on in the fossil record than previously thought.

Paleontologist and PLOS ONE Section Editor Andy Farke points out in the PLOS ONE blog The Integrative Paleontologist that fossils inevitably resurface as imperfect objects, which is, in part, what makes them so interesting: These fossils bear the visible marks in postpartum decay of a long and varied history. When studying bone narratives, paleontologists encounter everything from water damage to the bore marks of little critters. Including big-critter claw marks in the repertoire of possible bone modifications broadens this narrative and evidences, as the researchers themselves so aptly put it, the power of the claw.

For more information from the paleontologist perspective, check out blog posts on this article in The Integrative Paleontologist  by Dr. Farke and National Geographic.


Rothschild BM, Bryant B, Hubbard C, Tuxhorn K, Kilgore GP, et al. (2013) The Power of the Claw. PLoS ONE 8(9): e73811. doi:10.1371/journal.pone.0073811

Image 1: Tiger by Dave Stokes

Image 2: doi:10.1371/journal.pone.0073811

Image 3: doi:10.1371/journal.pone.0073811

@Jay_Naidoo @Okcon “use the tool that you have to fight for justice and ethics”

Listening to @Jay_Naidoo’s plenary on Wednesday at #okcon I had a revelation.

What matters is Justice.

Jay’s twitter describes him as  Chairman of the Global Alliance for Improved Nutrition(GAIN), former Minister in Mandela Cabinet, founding GS of COSATU and political and social activist. Jay gave  us 30 minutes of breathtaking passion about what we must do for the world. I tweeted it and have recaptured my tweets (below).  Jay urged us to action – at the end Andrew Stott (chair) asked

“what is most import thing for us to do in the next week?”

Jay:   “use the tool that YOU have to bring justice and ethics”

That has changed the rest of my life. The key word is JUSTICE. That’s what the OKF is about. That’s what my software is about. That’s what this blog is about. And it was the theme running through the whole of #okcon. We develop tools (blogs, protocols, Python, Java, CKAN, Open Spending, Panton Principles, etc.) to make the world a just society.

Jay articulated Nelson Mandela’s passion on stage – it was as if it was Mandela speaking. If you were not at the session is is the must-watch 30 minutes of #okcon – and watch it all.

Here are my tweets from Jay – the order doesn’t matter. Read them and then go out and fight for justice.

when you are poor the only food is junk food.

“one person one vote” => “one person one gigabyte” (of information)

we can now hold leaders to account. Citizenry must be informed and make power accountable

“we have liberated ourselves from the chains of secrecy”. Where is the money for the library and toilets?

when people know the truth and their rights they become unstoppable. Everyone of us is a journalist and whistleblower

give us (digital) tools for accountability.

SA has second most transparent budget in world. We have to make it understandable. Create a revolution

can we translate understanding of budget into local funding to deliver schools, etc.

SA delivered a political miracle .

old generation cannot tell young what they should do but must support them.

Andrew Stott asks  how do we make this happen.  we must give young people a voice . innovation to deliver a better society

Have to defeat language of denialism . We must be advocates of building society where we care about what happens to planet

money that belongs to our people (in S A) is stolen. Governance should be brought to ordinary people through Open Data

We must bring back ethics and accountability

How do we make our democracy work. How create livelihoods. S Africa now lags behind Kenya.

[telcoms in Africa]. Must design this (from bankrupt beginnings) to provide justice

technology has led to death of geography but not death of injustice

Live a life of truth. Undiluted truth. Then you will challenge injustice wherever it stands

how to we bring compassion into the cold steel of technology. Our technology is built from blood spilt in the Congo

[recalls Mandela] – “fighting poverty is not an act of charity, it is an act of justice”.

stand up and do something

Build a tsunami of hope and accountability – your job is to be accountable and serve society

“Overflowing of positive energy that makes us want to be better people”

tackle global malnutrition. Billion people will go to bed today without food

we have brought the world to its knees. What could we have done with the wasted financial millions. The problem remains

You must be brave like Steve Biko. Nothing to lose but your chains.



#okcon (first) thoughts (blog, hack)+ in Geneva Public Library

My blogging comes in fits and start. I sometimes used to feel upset if I didn’t blog each day. But now I two major imperatives – to blog and to hack Liberation Software. And for the last few weeks the software has been on top.

Also I have had technical problems. I have been using Word to author blogs since (a) I didn’t like WordPress interface (b) I can only use it online (unless you tell me different) and (c) I spent some time experimenting with Word’s voice recognition software (d) it was more convenient to use Word to create compound documents with included images. (c) no longer holds. (d) started to fail badly and doesn’t seem to have a cure. Word/Wordpress gave useless error messages, failed to upload, created multiple posts with same title, etc.

So I am coming back to using WordPress. I think it’s clunky but I have no alternative. It means I can only blog at certain times of the day and have to spend extra time uploading the images. But I have to do it.

Wow! I can copy. Maybe it’s not so bad. (BTW this is Chuff, the OKF okapi).  Animals are not allowed in libraries so he/she/it is sleeping in the hotel. I love public libraries – they have a sense of calm, quiet but also centuries of history of the struggle for freedom. See . They have free wifi. And there’s a student cafe in the next building.

My mind has been blown at #okcon. I need to blog on at least the following:

  • Mat Todd’s fantastic, world changing, session yesterday on Open Source Drug Discovery. The world has a crisis in dscovering new pharmaceuticals and, IMO, Open Knowledge and collaboration is a critical part. Without it we shall not defeat Neglected Tropical Diseases (NTD) or antibiotic resistance. We have to change the way we work.
  • Jay Naidoo’s completely inspirational talk yesterday. He is a colleagues of Mandela and brought the same massive message. (“South Africa was the political/democratic miracle of the twentieth century”). Jay brought me one word – JUSTICE – which is transforming the way I now see Open Knowledge. That is what we are about.
  • OKF itself. We are now a major resource for bettering the world. Some years ago I started telling people “Wikipedia is the digital triumph of the 2000′s. OKFN will be the triumph of the 2010s.” (I don’t think I ever wrote this). I now believe it.
  • Chuff. Down! Your time will come. In Berlin 2014. (This shows I can do strikethroughs).

But I also need to hack. Content-mining will be massive and I am making a contribution through PDF-hacking (#ami2). I’m now very close to nearly faultless conversion of BioMedCentral PDFs to semantic XML. Ross Mounce, Matt Wills and I will be starting on this in earnest next month for phylogenetic trees. It’s been desperately hard work and it’s really only because I don’t have a day-job I can give it the obsessiveness it needs. But #ami2 can do simple tables (nobody can do complex tables because there are no semantics describing them). #ami2 can do diagrams if the EPS strokes and characters are still there. I’ve done a complex phylo tree and am pleased with progress. (I’ll blog all this later).

So I’m going into blog-hack-blog-hack mode… (blog, hack)+ in regex-speak. The hacking takes precedence.

So maybe WordPress is now easier to use than it used to be – we’ll see. I might even try SVG later.


PLoS reaches 23% surplus. Time to lower those article processing fees?

Public Library of Science has released their 2012 financials. Kudos to PLoS for four years of not raising article open access processing fees. However, now that the PLoS surplus has reached 23%, isn’t it time to lower these fees?

Highlights from the PLoS financials:

The 2012 financial year represented a third consecutive year of sustainability for PLOS. Gross revenue grew 57% to $38.8 million (2011: $24.7 million), of which the increase in net assets was $7.15 million (2011: $3.95 million). PLOS’s expenses grew by 52% to $31.6 million (2011: $20.8 million), not least because of the increase in resources required to support the more than 26,000 articles published by the journals in 2012. This represents a 62% increase (2011: more than 16,000 articles); the total number of articles published by PLOS through 2012 was more than 68,000.

Hungarian Spectrum to be archive by Library of Congress

Bravo to Professor Eva Balogh, whose Hungarian Spectrum has been selected for archiving by the Library of Congress. Eva’s historic contribution — crucial and ongoing — to exposing and fighting back against the sinister downward forces holding Hungary in their thrall today eminently deserved this historic recognition (and I am sure there will be more): Eva, you have been a tireless critic and chronicler, drawing on your scholarly expertise as a historian, as well as personal experiance and an uncompromising ethical integrity. Végtelen hálával gratulálunk mindnyájan. — István

PLOS ONE’s New Look: Redesigned for Discovery

The PLOS Product and Development teams are constantly working to enhance the web experience for authors, editors, and readers. Today, we’re unveiling the latest update to PLOS ONE. Here’s an overview of what’s new:

Navigate Faster with Figures
The PLOS ONE home page now features a new way to discover and explore the latest research. Instead of seeing a list of articles, you’ll see a grid of articles each presented with a key figure. Hover over the figure for one-click access to the article’s abstract, figures, or full text.
home Subject Area Browsing
We’ve introduced a brand new way to navigate the research that PLOS ONE publishes across the entire spectrum of subject areas. Dive in by clicking “Subject Areas” at the top of every page. Once you find your preferred topic, click “View all articles” to get to one of our new subject-specific browse pages.
browseThese new pages feature a grid just like the home page, sortable by most recent or most popular allowing you to easily navigate all of PLOS ONE’s research articles. If you prefer, you can switch to a more traditional list of articles. If the subject area you’re browsing isn’t quite what you’re looking for, click the arrow to the left of the subject header to navigate one level up or down our taxonomy.
navIf you’ve found the right subject area for your research, you can click the mail icon to sign up for a weekly email alert for that subject area, or the RSS icon to subscribe to that feed.

As always, the article page gives you one-click access to the Article Level Metrics (ALMs), author information, comments, and related content.

More to Come
You can expect ongoing improvements to the PLOS ONE web experience. As always, we’ll be looking to the community for feedback and suggestions. Feel free to leave a us a comment below.

SPIE Open Access Publications

Have you checked out SPIE Journals? All of which include Open Access articles:

Optical Engineering
Journal of Biomedical Optics
Journal of Electronic Imaging
Journal of Micro/Nanolithography, MEMS, and MOEMS
Journal of Applied Remote Sensing
Journal of Nanophotonics
Journal of Photonics for Energy

Additional Open Access SPIE Publications include:

  • SPIE Reviews: virtual journals containing letters, review articles, and tutorials
  • SPIE Newsroom: researcher-authored technical articles organized by topical interest area
  • Fundamentals of Photonics: 10 tutorial modules written by experts
  • SPIE Professional, the Society’s quarterly member magazine: industry features and technology updates
  • Optipedia: encyclopedic articles, including text, equations, and graphs originally published in SPIE Press books.

Berlin 11 Satellite Conference


In conjunction with this year’s Berlin 11 Open Access meeting, the Max Planck Society and Right to Research Coalition will host the first-ever satellite conference to the Berlin conference series specifically for students and early stage researchers on November 18th in Berlin, Germany.  The meeting will feature presentations from leading voices of the Open Access community and will foster a discussion around the current state of Open Access, the unique challenges and opportunities students and early stage researchers face in the transition to Open Access, and how attendees can catalyze this transition.

This new satellite conference reflects the importance of students and early stage researchers as the next generation of scholars and the impact these groups are already having in opening up scholarly communication.  The agenda will be specifically tailored to the position of students and early stage researchers within the scholarly communication system.  It will address both the power these groups have to create change as well as the challenges early-career researchers face from a scholarly publishing system in transition.

Ecology and Evolution Publishes issue 3.9. Read the Highlights Here!

ECE 3 9The latest issue of Ecology and Evolution is now live! Over 30 excellent articles free to read, download and share. The cover image has been taken from the article ‘Different modes of evolution in males and females generate dichromatism in fairy-wrens (Maluridae)’ by Allison E. Johnson, J. J. Price, and S. Pruett-Jones. Below are some highlights from this issue:

purple_lock_open Different modes of evolution in males and females generate dichromatism in fairy-wrens (Maluridae) by Allison E. Johnson, J. Jordan Price, Stephen Pruett-Jones
Summary: Sexual dichromatism in birds is often attributed to selection for elaboration in males. However, evolutionary changes in either sex can result in plumage differences between them, and such changes can result in either gains or losses of dimorphism. We reconstructed the evolution of plumage colors in both males and females of species in Maluridae, a family comprising the fairy-wrens (Malurus, Clytomias, Sipodotus), emu-wrens (Stipiturus), and grasswrens (Amytornis). Our results show that, across species, males and females differ in their patterns of color evolution. Male plumage has diverged at relatively steady rates, whereas female coloration has changed dramatically in some lineages and little in others. Accordingly, in comparisons against evolutionary models, plumage changes in males best fit a Brownian motion (BM) model, whereas plumage changes in females fit an Ornstein Uhlenbeck (OU) multioptimum model, with different adaptive peaks corresponding to distributions in either Australia or New Guinea. Levels of dichromatism were significantly associated with latitude, with greater dichromatism in more southerly taxa. Our results suggest that current patterns of plumage diversity in fairy-wrens are a product of evolutionary changes in both sexes, driven in part by environmental differences across the distribution of the family.

purple_lock_open Tropical rain forest conservation and the twin challenges of diversity and rarity by Stephen P. Hubbell
Summary: Data from a global network of large, permanent plots in lowland tropical forests demonstrate (1) that the phenomenon of tropical tree rarity is real and (2) that almost all the species diversity in such forests is due to rare species. Theoretical and empirically based reasoning suggests that many of these rare species are not as geographically widespread as previously thought. These findings suggest that successful strategies for conserving global tree diversity in lowland tropical forests must pay much more attention to the biogeography of rarity, as well as to the impact of climate change on the distribution and abundance of rare species. Because the biogeography of many tropical tree species is poorly known, a high priority should be given to documenting the distribution and abundance of rare tropical tree species, particularly in Amazonia, the largest remaining tropical forested region in the world.

purple_lock_open Nonconsumptive effects in a multiple predator system reduce the foraging efficiency of a keystone predator by Jon M. Davenport, David R. Chalcraft
Summary: Many studies have demonstrated that the nonconsumptive effect (NCE) of predators on prey traits can alter prey demographics in ways that are just as strong as the consumptive effect (CE) of predators. Less well studied, however, is how the CE and NCE of multiple predator species can interact to influence the combined effect of multiple predators on prey mortality. We examined the extent to which the NCE of one predator altered the CE of another predator on a shared prey and evaluated whether we can better predict the combined impact of multiple predators on prey when accounting for this influence. We conducted a set of experiments with larval dragonflies, adult newts (a known keystone predator), and their tadpole prey. We quantified the CE and NCE of each predator, the extent to which NCEs from one predator alters the CE of the second predator, and the combined effect of both predators on prey mortality. We then compared the combined effect of both predators on prey mortality to four predictive models. Dragonflies caused more tadpoles to hide under leaf litter (a NCE), where newts spend less time foraging, which reduced the foraging success (CE) of newts. Newts altered tadpole behavior but not in a way that altered the foraging success of dragonflies. Our study suggests that we can better predict the combined effect of multiple predators on prey when we incorporate the influence of interactions between the CE and NCE of multiple predators into a predictive model. In our case, the threat of predation to prey by one predator reduced the foraging efficiency of a keystone predator. Consequently, the ability of a predator to fill a keystone role could be compromised by the presence of other predators.

purple_lock_open  Functional traits, the phylogeny of function, and ecosystem service vulnerability by Sandra Díaz, Andy Purvis, Johannes H. C. Cornelissen, Georgina M. Mace, Michael J. Donoghue, Robert M. Ewers, Pedro Jordano, William D. Pearse
Summary: People depend on benefits provided by ecological systems. Understanding how these ecosystem services – and the ecosystem properties underpinning them – respond to drivers of change is therefore an urgent priority. We address this challenge through developing a novel risk-assessment framework that integrates ecological and evolutionary perspectives on functional traits to determine species’ effects on ecosystems and their tolerance of environmental changes. We define Specific Effect Function (SEF) as the per-gram or per capita capacity of a species to affect an ecosystem property, and Specific Response Function (SRF) as the ability of a species to maintain or enhance its population as the environment changes. Our risk assessment is based on the idea that the security of ecosystem services depends on how effects (SEFs) and tolerances (SRFs) of organisms – which both depend on combinations of functional traits – correlate across species and how they are arranged on the species’ phylogeny. Four extreme situations are theoretically possible, from minimum concern when SEF and SRF are neither correlated nor show a phylogenetic signal, to maximum concern when they are negatively correlated (i.e., the most important species are the least tolerant) and phylogenetically patterned (lacking independent backup). We illustrate the assessment with five case studies, involving both plant and animal examples. However, the extent to which the frequency of the four plausible outcomes, or their intermediates, apply more widely in real-world ecological systems is an open question that needs empirical evidence, and suggests a research agenda at the interface of evolutionary biology and ecosystem ecology.

Read other top articles in this issue >

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