If You Were Composing the Subversive Proposal Today…

Richard Poynder: “If you were composing the Subversive Proposal today how different would it be? Would it be different? If so, would you care to rephrase it to fit today?s environment? In other words, how would the Subversive Proposal look if written for a 2014 audience (in less than 500 words)?”

SH: Knowing now, in 2014, that researchers won?t do it of their own accord, I would have addressed the proposal instead to their institutions and funders, and in less than 200 words:

“To maximize the access, uptake, usage, progress, productivity, applications and impact of your publicly funded research output, mandate (require) that the refereed, revised, accepted final draft of all articles must be deposited in the author?s institutional repository immediately upon acceptance for publication as a condition for research evaluation and funding. If you allow a publisher embargo on making the deposit OA (freely accessible to all online), implement the automated almost-OA Button (and don?t let the embargo exceed 6-12 months at most). This is called ?Gratis Green OA.? Do not pay for Gold OA journal publication fees (?Fool?s Gold?) until global Green OA has made subscriptions unsustainable; then you can pay for Fair-Gold out of your subscription cancellation savings. Fair-Gold will also be Libre OA (with re-use rights such as data-mining, re-mixing and re-publishing). Ignore publishers? lobbying to the effect that Green OA will destroy peer-reviewed journal publishing: it will re-vitalize it and save the research community a lot of money while maximizing the access, uptake, usage, progress, productivity, applications and impact of their research.”

And this is how I should have written the original Proposal in 1994:


Abstract: We have heard many predictions about the demise of paper publishing, but life is short and the inevitable day still seems a long way off. This is a subversive proposal that could radically hasten that day. It is applicable only to refereed scientific and scholarly journal articles (but that is the lion’s share of the research corpus anyway), a body of work for which authors (researchers) do not and never have expected to SELL their words. They want only to PUBLISH them, that is, to reach the eyes of their peers, their fellow scientists and scholars the world over, so that they can build on one another’s work in that collaborative enterprise called learned inquiry.
      For centuries, it was only out of reluctant necessity that authors of research journal articles made the Faustian bargain to allow a price-tag to be erected as a barrier between their work and its intended readership because that was the only way to make their work public in the era when paper publication (and its substantial real expenses) were the only way to do so. But today there is another way, and that is by depositing it in the author’s institution’s online repository:
      If every research institution in the world this very day established a globally accessible online institutional repository for every piece of refereed research output from this day forward, and if all research institutions and research funders mandated (required) that the final, refereed drafts of all their research output must be deposited in the repository immediately upon acceptance for publication, the long-heralded transition to free online access would follow almost immediately.
      The only factor standing in the way of this transition at the moment is the fact that peer review happens to be implemented today almost exclusively by journal publishers. If all scholars’ refereed final drafts were universally available to all scholars online, institutions could cancel their journal subscriptions and refereed journal publishers would then have to restructure themselves, phasing out their obsolete print and online editions, access-provision and archiving and their costs, and downsizing to just implementing the peer review service, paid for by researchers’ institutions out of their subscription cancellation savings.
      The subversion will be complete, because the refereed research literature will have taken to the airwaves, where it always belonged, and those airwaves will be free (to the benefit of us all) because their true minimal expenses will be covered the optimal way for the unimpeded flow of research findings to all: In advance.

What’s in a Look? For Wolves, Maybe Everything


WolvesIt’s been said that the eyes are the windows to the soul. They allow us to communicate feelings across a room, direct the attention of others, and express emotion better than words ever could.  The importance of eye contact in non-human species is well known—we’ve all heard that you shouldn’t stare a bear or angry dog in the eyes—but we don’t know a whole lot about how gaze is used between individuals of the same species. Japanese researchers took on this topic in a recent PLOS ONE article, focusing specifically on how eye contact and communication is affected by eye visibility and facial patterning around the eyes of canids.

Their research observed 25 canid species, comparing variations in facial pattern and coloring to observations about their social behavior and evolutionary history. They found that canines may use facial markers to either highlight or de-emphasize their eyes. Species with more distinguishable eyes tended to live and hunt in groups, where gaze-communication facilitates the teamwork that is necessary to bring down large prey and stay safe. Those with camouflaged eyes were more likely to live alone or in pairs, where communication with other members of their species may not be needed in the same way.

facial area maps

Using photos of each species, the authors analyzed the contrast between five areas of the canine face: pupil, iris, eyelid margin, coat around the eyes, and facial area including the eyes, as shown in the figure above. They measured contrast assuming red-green colorblindness of the observer (fun fact: canids cannot see the full spectrum of color). Species were then grouped according to the visibility of their eyes, described in the figure below:

  • Group A contained species with easily visible pupils and eye placement
  • Group B contained species with camouflaged pupils but clearly defined eye placement
  • Group C contained species with fully camouflaged eyes and pupils

group types

The authors found the strongest correlation between eye visibility and living and hunting behavior. More species in Group A, like gray wolves, live and hunt in packs, whereas more species in Groups B and C, like the fennec fox and bush dog, live and hunt alone or in pairs. Species in Group A also spend significantly more time in “gazing postures,” with their sight and body directed at another animal, an action that accentuates their focused attention to other members of the group. The genetic similarity between species was not as useful in explaining these differences, with A-type faces found in 8 of 10 wolf-like species, and in 3 of 10 red fox-like species. The authors suggest that A-type markings developed independently once these groups had evolutionarily split.

Lighter iris coloring is thought to be an adaptation to ultraviolet light in many species, similar to variations in human skin pigmentation. To determine whether this adaptation could explain the variation seen in canid iris color, the researchers compared the eye coloring of three wolf subspecies from Group A originating from arctic, temperate, and subtropical regions, to see if any differences in their lighter coloring could be attributed to geographical origin. They found that iris color did not vary significantly between the subspecies, suggesting that it may have developed to facilitate communication and not as an adaptation to specific geographical locations.

When the authors reviewed social behaviors, they found a number of social species with B- and C-type faces, the groups normally found alone or in pairs. These species are known to use acoustic or other visual signals, like a howl or the flash of a white tail, to communicate with their comrades. This allows them to skirt one possible disadvantage of gaze-communication: when prey can also identify and follow a gaze, and realize they’ve been targeted.

Gaze communication may be an important tool for other canids, including our own companions, domestic dogs. Previous studies have shown that domestic dogs are more likely to make direct eye contact with humans than wolves raised in the same setting. This could mean that after thousands of years of cohabitation, dogs see us in socially useful ways that wolves never will. Luckily for us, that means we get to see this.

Citation: Ueda S, Kumagai G, Otaki Y, Yamaguchi S, Kohshima S (2014) A Comparison of Facial Color Pattern and Gazing Behavior in Canid Species Suggests Gaze Communication in Gray Wolves (Canis lupus). PLoS ONE 9(6): e98217. doi:10.1371/journal.pone.0098217

Images 2 and 3: Figures 1 and 2 from the article

The post What’s in a Look? For Wolves, Maybe Everything appeared first on EveryONE.

Marketing Manager, Open Research Marketing : London or New York : Naturejobs

“Macmillan Science and Education is seeking a Marketing Manager who will be for the planning and implementation of marketing to support a number of open access titles from the Nature Publishing Group and Palgrave Macmillan portfolio, including but not limited to Scientific Reports, Palgrave Communications, OA marketing for monographs, as well as wider support the companies open access initiatives….”

Toward a New Alexandria: Imagining the Future of Libraries (2010)

“Imagine a new Library of Alexandria. Imagine an archive that contains all the natural and social sciences of the West—our source-critical, referenced, peer-reviewed data—as well as the cultural and literary heritage of the world’s civilizations, and many of the world’s most significant archives and specialist collections. Imagine that this library is electronic and in the public domain: sustainable, stable, linked, and searchable through universal semantic catalogue standards. Imagine that it has open sourceware, allowing legacy digital resources and new digital knowledge to be integrated in real time. Imagine that its Second Web capabilities allowed universal researches of the bibliome. Well, why not imagine this library? Realizing such a dream is no longer a question of technology.”

Betting on Vetting

Over all, the issue is how to achieve open access for new research. For the article-driven fields, the discussion is already avidly under way, but few dare extend the principle to monographs. The web waits like a global petri dish, brimming with growth medium, but the spores are elsewhere. Why? Because tenure and promotion in the social sciences still require an increasingly pointless detour through paper and binding. Young scholars are effectively told: Drop your work into a black hole where it can be seen only by those who can afford the three-figure price of the average Routledge monograph or who enjoy lending privileges from a major research-university library. In our fields, publication is effectively privatization….[With a Review Institute] universities could now decide whom they want to hire and whom to promote without the slightest regard for what the publishers are up to. Publication and vetting will have parted ways. The new slogan for upward academic mobility would be “produce or perish.” That at least is not dependent on the vagaries of what the publishers think the book-buying public will absorb or how ruthlessly library budgets have been slashed….And that brings us to the best part of the proposal. Cutting the tie between publication and evaluation means that—thanks to the web’s practically limitless availability—every work, having passed through the Review Institute, can go straight to its intended audience, and anyone else in the world who is interested….”

Academic Knowledge, Open Access and Democracy (n.d.)

Synopsis: “This recommendation provides an evidence-based case for Open Access to address economic growth and social and commercial innovation through dissemination of academic knowledge in the digital age. It shows that Open Access (gold or green) could and should be properly mandated and monitored so that publicly-funded research is freely available to the tax-payer. This non-legislative measure will fulfill the government?s commitment to transparency and openness, ensure that British universities can compete in the changing European and global context, provide greater return on investment for the funding councils and enable fairer access to knowledge across society as a whole. Our recommendations are supported and undersigned here by many of the country?s leading creators, users and distributors of academic knowledge.”

Academic Movers 2014: In-Depth with Emily Drabinski

Q: You helped move the journal Radical Teacher, where you’re a board member, to open access. Talk about why you did that and what the process helped you learn? A: Radical Teacher had never had a librarian on the board before. I think that new perspective was helpful to them, having someone who understood the economics of publishing to help them make decisions about their future and survive as a publication. It reminded me that librarians know things. We’re a fundamentally helpful and self-effacing field, and that means it can be easy to forget what we know. Radical Teacher didn’t know why they were losing institutional subscriptions. As a librarian, I knew because I had cancelled them two or three times in the course of my career at that point….

Content Mining: we can now mine images (of phylogenetic trees and more)

The reason I use “content mining” and not “Text and Data Mining” is that science consists of more than text – images, audio video, code and much more.  Text is the best known and the most immediately tractable and many scientific disciplines have developed Natural Language Processing (NLP). In our group Lezan Hawizy, Peter Corbett, David Jessop, Daniel Lowe and others have developed ChemicalTagger, OSCAR, Patent Analysis, and OPSIN. (http://www-pmr.ch.cam.ac.uk/wiki/Main_Page ). So the contentmine.org is exactly that – an org that mines content.

But words are often a poor way of representing science and images are common. A general approach to processing all images is very hard and 2 years ago I though it was effectively impossible. However with hard work some subsets can be tractable. Here we show you some of the possibilities in phylogenetic trees (evolutionary trees). What is described below is simple to follow and simple to carry out, but it took me some months of exploration to find the best strategy. And I owe a great debt to Noureddin Sadawi who introduced me to thinning – I haven’t used his code but his experience was invaluable.

But you don’t need to worry. Here’s a typical tree. Its from PLoSONE, (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0036933 – “Adaptive Evolution of HIV at HLA Epitopes Is Associated with Ethnicity in Canada” .


The tree has been wrapped into a circle with the Root at the centre and the leaves/tips on the edge of the circle. To transcribe this manually would take hours – we show it being done in a second.

There isn’t always a standard way of doing things but for many diagrams we have to:

  • flatten (remove shades of gray)
  • separate colours (often by flattening them)
  • threshold (remove noise) and background)
  • thin (remove all pixels except the 1-pixel-think backbone)

and here is the thinned diagram:


You’ll see that the lines are all still there but exactly 1 pixel thick. (We’ve lost a few colours, but that’s irrelevant for this example). Now we are going to look at the tree (and ignore the labels):


This has been selected automatically on pixel count, but we can also use bounding boxes and many shape characteristics.

We now analyse the structure and break it into connected components – a topological tree – by standard traversal methods. We end up with nodes and edges – this is a snapshot of a SVG.


[The black lines are artifacts of Inkscape]. So we have identified every node and every edge. The next thing is to trace the edges – that’s easy if they are straight, but here they are curved. Ideally we plan to fit circles, but we’ll use segments for the time being:


The curves are actually straight-line segments, but… no matter.

It’s now a proper phylogenetic tree! And we can serialize it as Newick (or NexML if we wanted).


And here is an interactive tree by posting that string into http://www.trex.uqam.ca/ (try it yourself).


So – to summarize – we have taken a phylogenetic tree – that may have taken hundreds of hours to compute and extracting the key data. (Smart people will ask “what about the text labels?” – be patient, that’s coming).

… in a second.

That scales to over a million images per year on my single laptop! And the technology scales to many other disciplines and it’s completely Open Source (Apache2). So YOU can use it – as long as you give us the credit for writing it.




AAU-ARL Prospectus for an Institutionally Funded First-Book Subvention | Association of Research Libraries® | ARL®

“The Association of American Universities (AAU) and the Association of Research Libraries (ARL) are working together, through a Task Force on Scholarly Communication, to ensure a robust system of scholarly communication in the humanities and qualitative social sciences. The task force seeks to address the economic challenges facing scholarly monograph publishing and to exploit digital communication technologies to move the academy towards a sustainable, innovative, and open system for supporting humanistic research.

Specifically, the task force intends to address the inability of a market model to adequately support research monograph publication based primarily on scholarly merit. This prospectus describes a faculty title subvention designed to ensure the long-term economic viability of foundational scholarly monographic publishing, while promoting the emergence of innovative digital models….”

Alle skal have gratis adgang til forskningsresultater

From Google’s English: “A large part of the researchers’ scientific articles are now hidden behind pay walls, so it requires a subscription or a tax each time you want to read a research article. That education and research minister Sofie Carsten Nielsen now, do away with and will be a new national strategy to ensure free digital access to scholarly articles in the future….Sofie Carsten Nielsen has set up a national steering committee for Open Access, which will be responsible for coordinating the implementation of the strategy. The steering group comprises, among others, representatives of universities, libraries, and public and private foundations….”


Regeringen: Alle danske forskningsartikler skal være frit tilgængelige

From Google’s English:  “By 2022, all citizens have full and free access to all scientific papers describing the results of publicly financed research….Already in 2017, 80 percent of all scientific articles from Danish research institutions be free from digital online archives. From 2022, it should apply to all Danish research articles. That is the objective of a new national strategy for open access to education and research minister Sofie Carsten Nielsen (R) has just presented….Now a steering committee consisting of 16 representatives from universities, foundations and libraries so in the process of finding out how the objectives are met….The strategy provides for two different types of open access, which is called the golden and green model….”


Mining open data from home 15 year old wins Intel science prize. From…

From +Intel: “Because of his age, Nathan Han had difficulty finding a Boston area research lab willing to overlook liability issues and allow a fifteen-year-old to conduct research in its facility. But that didn’t stop the high school freshman from forging ahead on his own. Han was determined to study mutations of a gene linked to ovarian cancer, after learning that a family friend had been diagnosed with the disease. The upside for Han? The kind of research he wanted to conduct had far more to do with computer technology and data than traditional lab-ware such as test tubes and petri dishes. So, working from home, Han mined data from publicly available [i.e. open-access] databases and developed a machine learning software tool to study mutations of a gene linked to many kinds of cancer, including ovarian. The BRCA1 tumor suppressor gene has an important function as it is vital in protecting cells from developing cancer. Han detailed the characteristics of this gene and known mutations in order to “teach” his software to differentiate between mutations that cause disease and those that do not. In testing, Han’s device exhibited an 81 percent accuracy rate, demonstrating its potential as a breakthrough tool for accurately identifying cancer threats from BRCA1 gene mutations. Applications for Han’s research are vast, extending to research on other diseases, as well as to advancements in the developing fields of genomics, bioinformatics and big data. For this work, Han beat out nearly 1,800 other global finalists competing at the 2014 Intel International Science and Engineering Fair (Intel ISEF), a program of Society for Science and the Public, when he won the Gordon E. Moore Award, including a $75,000 scholarship.”
“Comment. I love this. First, it’s a beautiful example of initiative and ingenuity. Congratulations to Nathan Han. Second, it’s a compelling example of the benefits of open data. This kind of research by a 15 year old, working from home, without an affiliation at a well-endowed institution, would be impossible if the relevant data were locked behind paywalls. It would also be impossible for a 45 year old. For researchers affiliated with well-endowed institutions, the research would be impossible if the relevant data were sitting offline on a private hard drive. It reaffirms one of +Rufus Pollock’s arguments for open data: the best use of your data will be discovered by someone else. “