Halloween Highlight 2011: An Author Spotlight with David Hughes and Harry Evans

Zombie ant jack o' lantern

In the spirit of Halloween, we’ve asked Dr. David Hughes of Penn State University and  Dr. Harry Evans of  Federal University of Viçosa Brazil to share with us a bit about their manuscript, Hidden Diversity Behind the Zombie-Ant FungusOphiocordyceps unilateralis: Four New Species Described from Carpenter Ants in Minas Gerais, Brazil.   Both were kind enough to oblige and share with us their perspective via email.

The description of ants as zombies is not a pitch to popularity-even at Halloween-  but an orchestrated attempt to identify fungal-infected ants as very different from other ants in the society. Just because something looks, walks and quacks like a duck doesn’t mean it is actually a duck. The sinister thing about parasites which manipulate host behavior is that they can easily go unnoticed. The zombie ant moniker forces us to recall that we are looking at two organisms and the ant is not in the driving seat.

Our study in PLoS ONE, which used micromorphology together with spore function to delimit and describe new species, came about as it was obvious that the diversity of zombie ant fungi must be  higher than previously supposed because ant species diversity is high. We know that ants differ in many important behaviors which of course is due to brain differences. So, if your evolutionary gambit is brain control, then diverse brains will act as diverse selection environments leading to different species. Perhaps the most exciting thing is that we now recognize that these initial descriptions are just the tip of a very large iceberg and that many more zombie-inducing fungi await discovery, especially in tropical forests such as the Brazilian Atlantic rainforest in which we set our study.

In March, our editor wrote an overview of this paper.  To see last year’s Halloween post, click here.

Image by Roel Fleuren and pumpkin carving by Charissa de Bekker.

Save the date: Open Access Week 2011 wrap up

On November 15, at 1:00pm Eastern, SPARC will host another online discussion through the openaccessweek.org network, to gather participants and talk through this year’s milestones, experiences, and goals for 2012. Please save the date and watch for more post-OA week news from SPARC, the official organizer, later this week.



Open Access Week 2011 wrap up
Another free SPARC online event
Tuesday, November 15, 2011
1:00 – 2:00PM Eastern
Registration will open Nov. 2.


More information about Open Access Week is available at openaccessweek.org.


Best wishes,


Open Access Week Program Director 



Jennifer McLennan

Director of Programs & Operations



(202) 296-2296 x121

Fax: (202) 872-0884




Open Access Week 2011

October 24 – 30



The SPARC Open Access Meeting

March 11 – 13, 2012

Kansas City


Thesis chapter two: scholarly communication in crisis

An early draft of the second chapter of my thesis, Scholarly communication in crisis, is now available as part of my open thesis approach.


Scholarly communication at present is a complex system characterized by expansion of capitalism into scholarly publishing and a process of rationalization that at times leads to irrational results in conflict with the basic goals or values of scholars. The increasing enclosure of knowledge and information through the concept of intellectual property is key in the process of commodification of resources once considered a classical public good as nonrivalrous and nonexcludable. Alternatives identified to date include the commons, cooperative approaches, open access and emerging new publishers such as libraries.

Fool’s Gold Journal Spam

Dear colleagues,

They just keep coming, almost daily, pre-emptively spamming all the people we had been hoping to win over to Open Access.

Not only is it regrettable that OA is so unthinkingly identified in most people’s minds with gold OA publishing in general, but this growing spate of relentless fool’s-gold junk-OA spamming in particular is now coalescing with that misconception — and at the same time more and more universities and funders are reaching into their scarce funds to pay for this kind of thing, thinking this is the way to provide OA.

(Meanwhile, green OA mandates, the real solution, are still hovering at about 200 out of about 10,000 (2%!) — and mostly needlessly watered-down mandates. I wish I could figure out a way to turn this liability — fool’s-gold spam and scam — into an asset for spreading green mandates, but I’m afraid that even Richard Poynder’s critical articles are being perceived mostly as critical of OA itself rather than just of fool’s-gold OA.)

The real culprits are not the ones trying to make a buck out of this current spike in pay-to-publish-or-perish/gold-fever co-morbidity, but the researchers themselves, who can’t put 2+2 together and provide green OA on their own, cost-free; and their institutions and funders, who can’t put 2+2 together and mandate that they do it.

Instead of thinking, it’s easier to shell out for fool’s gold…

Richard’s exposés are helpful, but I think they are not enough to open people’s eyes.

So all we can do is hope that the spamming itself will become so blatant and intrusive that it will wake people up to the fact that this is not the way to provide OA…


PS Not only do I not work on anything faintly resembling “proteomics/bioinformatics” but I have no “relationship with OMICS Group” (except possibly prior complaints about spam)! These spam disclaimers are a lark. They seem to be using professional spam services that try to appear respectable.

From: “JPB”<editor.jpb@omicsgroup.co>
Date: October 28, 2011 4:29:28 AM EDT
To: “Stevan Harnad” 
Subject: Invitation for Special Issue: Journal of Proteomics & Bioinformatics
Reply-To: editor.jpb@omicsgroup.co

You are receiving this email because of your relationship with OMICS Group. Please reconfirm your interest in receiving email from us. If you do not wish to receive any more emails, you can unsubscribe here
Journal of Proteomics & Bioinformatics – Open Access

Dear Dr. Stevan Harnad, 

We are glad to announce the success of Journal of Proteomics & Bioinformatics  (JPB) an Open Access platform for proteomics, bioinformatics research and updates. 

To provide a rapid turn-around time regarding reviewing, publishing and to disseminate the articles freely for research, teaching and reference purposes we are releasing following special issues. 

Upcoming Special Issues Handling Editor(s)

Domain-Domain Interactions Dr. Chittibabu (Babu) Guda, University of Nebraska Medical Center, USA
Microarray Proteomics Dr. Qiangwei Xia, University of Wisconsin-Madison, USA
Canonical approach: Moleculomics Dr. Lifeng Peng, Victoria University, China
Shifts and deepens : Biomarkers Dr. Kazuyuki Nakamura, Yamaguchi University, Japan
Membrane Protein Transporters Dr. Mobeen Raja, University of Alberta, Canada
Structural and Functional Biology Dr. Viola Calabró, University of Naples “Federico II”, ITALY
HLA-based vaccines Dr. Mario Hugo Genero, Universidad Austral, Republica Argentina
Insulin Signaling & Insulin Resistance Dr. Zhengping Yi, Arizona State University, USA
Proteomics for Cancer chemoprevention Dr. Imtiaz Siddiqui, University of Wisconsin, USA
Membrane Proteomics Dr. Yurong Lai, Groton Laboratory, Pfizer, Inc, UK
We would like to request a contribution from you for any of these special issues or regular issues of the Journal to improve the Open Access motto in this field. 

For more details PS : http://www.omicsonline.com/SpecialissueJPB.php 

Why to submit and benefits : http://www.omicsonline.org/special-features.php 

Submit your article online at : http://www.editorialmanager.com/proteomics/ 
As e-mail attachment to the Editorial Office :editor.jpb@omicsgroup.co 

We shall look forward to hear from you. 


Editors, Journal of Proteomics & Bioinformatics 

Dr. Chittibabu (Babu) Guda, University of Nebraska Medical Center, USA 
Dr. Qiangwei Xia, University of Wisconsin-Madison, USA 
Dr. Lifeng Peng, Victoria University, China 
Dr. Kazuyuki Nakamura, Yamaguchi University, Japan 
Dr. Mobeen Raja, University of Alberta, Canada 
Dr. Viola Calabró, University of Naples “Federico II”, ITALY 
Dr. Mario Hugo Genero, Universidad Austral, Republica Argentina 
Dr. Zhengping Yi, Arizona State University, USA 
Dr. Imtiaz Siddiqui, University of Wisconsin, USA 
Dr. Yurong Lai, Groton Laboratory, Pfizer, Inc, UK 

Editorial office 
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My bike is (fairly) stable

An interlude. PNNL guest house provides its guest with low cost rented bicycles. I had a “free” day today (though I did some thinking) and cycled about 5+5miles through Richland to Bateman Island. But first, here is my bike:

Perceptive cyclists will notice that it has no brakes on the handlebars – in fact it has a backpedal brake. I haven’t ridden one of these before and didn’t find it very easy – if you backpedal then you stop, but if you put your foot down you keep going. I’m not sure what you do on steep hills. I think these bikes are popular in NL which doesn’t have many hills. I couldn’t go very fast, partly because the bike had only one gear, partly because it’s quite heavy and partly because of the air intake.

Zooming in we see:

All the bikes are named after elements. I got Technetium (http://en.wikipedia.org/wiki/Technetium ). The trouble is that all technetium isotopes are unstable/radioactive. The one I know (and is used in medicine) is technetium-99m with a half life of 6 hours. This means that after 6 hours half my bike would have disintegrated (actually it depends whether the bike represents a single atom – if so, then there was an evens chance that after 6 hours I would have no bike). I was even more worried about Tc-98 because this probably only lasts for milliseconds.

I needn’t have worried. The thoughtful PNNL bike people had chosen the isotope with a half-life of 4.2 million years. I had more chance of a car crash than spontaneous disintegration.

A beautiful day and Bateman island (http://en.wikipedia.org/wiki/Bateman_Island )was great (and isn’t Openstreetmap fantastic – it shows the cycleways unlike most other maps)– lots of birds on the river (which is quite wide here). I saw white pelicans, various grebes, ducks etc. which I’ll try to look up from memory:

And the causeway to the island

The Publication Paradox

This week is Open Access Week (follow #oaweek on Google+ and Twitter), and while I’ve shared a few links and talked to some of my officemates, I haven’t taken (or had, really) time to expand on my thoughts more fully. But I take Open Access very seriously, and I know the status quo (researchers signing over copyright to journals who lock away the research behind paywalls) won’t change unless more of us keep sharing openly to the widest audience possible. Because the antithesis of Open Access isn’t copyright — it is the unwillingness to share any ideas at all.


In the field of education, particularly in education policy, research is conducted and published in one of two ways: either by academics to submit to journals, or by think tanks and other groups who generally do non-university-based research. Academics will defend their system because their research is peer-reviewed, whereas much think tank research is not. In fact, in an effort to force a peer review process onto think tank research, the National Education Policy Center created the Think Tank Review Project, which includes reviews of think tank research and the annual Bunkum Awards. (Disclaimer: I know, work with, and take classes from various scholars at the NEPC.) If the academics are right, and their peer-reviewed research is superior, does that mean it is more influential? Hardly. According to this research by Holly Yettick (also affiliated with the NEPC), university-based education research is only cited about twice as often in major news outlets as research from think tanks, even though universities publish about 15 times more research (2009, emphasis mine). Yettick’s conclusions to this report include a recommendation to education reporters, urging them to consider more sources because “Unlike think tank employees, university professors generally lack the incentives and resources to conduct public relations campaigns involving outreach to journalists” (p. 15). My question is this: How does copyright and traditional publishing affect this incentive structure, and how can open access change it?


First, imagine you work at a think tank and you’re proposing research. Even before writing a word, you probably have an audience in mind that you’d like to reach with your work. Once your research is approved, you go about the research process and publish a report. Because the think tank does the researching and the publishing, no transfer of rights are necessary — the work was a work for hire and copyright belonged to the think tank from the very beginning. Now the think tank can set about trying to promote the results to the research to the media and other interested audiences. They have an incentive to promote because the research, the publication, and the promotion is carried out by the think tank, an organized unit that includes you in its shared ownership of the work. This gives the think tank a collective interest in spreading their ideas.


Now imagine you’re a researcher at a university. You too have an audience in mind that you’d like to reach, but when your research is finished you submit your report to a peer-reviewed journal. In order for the journal to publish (or sometimes, even to consider) your article, you must transfer to them your copyrights. The journal now owns the report, and this is where the incentive system starts to break down. The article might be read by your peers, and may help you receive tenure, but surely (I hope) your peers and tenure committee don’t comprise the true scope of your target audience. If you, the researcher, are still intent on making sure your work reaches the intended audience, how effectively can you promote something you no longer own? Most efforts to share your report will violate the publisher’s copyright. You could create derivative work, in the form of conference presentations, blog postings, or articles for magazines, but this actually requires extra effort to avoid a copyright violation, impedes future progress on other research, and often does not count towards tenure.


Instead of self-promotion, can you, a researcher, count on a journal to promote your work? Why would they? Do they know the scope of the audience you would like to reach? What incentives does the journal have to promote work they did not create? The journal wants subscribers, to be sure, but because they have no rights to your future research (or that of any scholar), their main incentive is to preserve a system that positions their journal as one of the few credible outlets for research. For example, the American Education Research Association has 25,000 members and publishes six peer-reviewed journals. If you’re an education researcher, you probably belong to AERA and you respect and read the scholarship in their journals. But in Holly Yettick’s dissertation research, searching through “nearly forty thousand articles in hundreds of publications” (2011, par. 14), she has yet to see a single AERA-published article mentioned anywhere. So while you might hear Brian Williams start a story on the NBC Nightly News with the phrase, “A new study published in the journal Science…,” you won’t hear an equivalent statement mentioning an AERA journal, despite education getting plenty of attention from NBC.


Think tanks have an advantage because the shared ownership of the creation and publication of research creates a common incentive for promotion. Even if the research is lower quality, the spread of the research to a wide audience gives the research power and influence. The traditional system of university-based researchers transferring rights to publishers in exchange for publication might produce higher-quality work, but leaves us with a publication paradox: how do creators promote something they don’t own, and how do owners promote something they did not create?


I see two options for improving the incentives to promote academic research: (a) publishers should own creation, or (b) creators should maintain ownership (or at least rights to open distribution). Option (a) essentially turns a publisher into a think tank, and would not fit with academia’s culture of academic freedom and independence. Some universities host their own journals, but they do not do so for the purpose of sponsoring and publishing their own work. Furthermore, most university researchers don’t want their work to be seen as “work for hire.” Option (b), which is not without its challenges, is the better option, and the growing Open Access movement is making it a more viable option every day. But for it to be successful, researchers are going to have to support change — not for selfish reasons, and not out of spite for publishers, but to ensure the best research is freely available to the audience for which it was intended.

(This post originally appeared on my blog at http://blog.mathed.net/2011/10/publication-paradox.html and is licensed CC BY-NC-SA.)



Yettick, H. (2009). The research that reaches the public: Who produces the educational research mentioned in the news media? (p. 37). Boulder and Tempe: Education and the Public Inerest Center & Education Policy Research Unit. Retrieved from http://nepc.colorado.edu/publication/research-that-reaches

Yettick, H. (2011, May). Media, think tanks, and educational research. Academe Online. Washington, D.C. Retrieved from http://www.aaup.org/AAUP/pubsres/academe/2011/MJ/Feat/Yett.htm

Open Access Doubts (and Reassurances)

In “
“>Open Access Doubts
” Eric F. Van de Velde lists some doubts about open access (OA).

There are very simple answers to each of Eric’s doubts. The doubts arise mostly from a library-based rather than a research-based perception of the OA problem and its solution.

There is only one doubt that is most definitely justified, though Eric has not expressed it: Researchers themselves — even though they and their research are the primary losers because of access-denial, and the primary beneficiaries of providing OA — are not providing OA in sufficient numbers until and unless it is mandated by their institutions and funders.

That does raise some doubts, but not about the feasibility or benefits of OA — only about the alertness of researchers to their own needs and the way to meet them.

Assessing the ongoing Open Access experiment, where are our doubts? I have three:

Is Affordable Better than Free?

Affordable is not better than free because even if journal subscriptions were sold at cost, with no profit margin at all, not all or even most institutions could afford to subscribe to all or even most peer-reviewed journals.

The purpose of OA is to provide online access to all would-be users, not just to those whose institutions can afford a subscription to the journal in which it was published.

Eric is conflating the journal affordability and the research accessibility problems.

A robust and user-friendly network of open scholarly systems seems farther away than ever because of inexpertly formatted content and bad, incomplete, and non-public (!) metadata.

No, researchers are not being denied access to peer-reviewed research because of “inexpertly formatted content and bad, incomplete, and non-public (!) metadata” but because of content to which (a) their institution cannot afford access and (b) that has not been made OA at all.

It is librarians who worry about formatting and metadata! Researchers worry about inaccessible content.

While there is always room for improvement, pay-walled journals provide professionally formatted and organized content with excellent metadata and robust services. The problem is cost. Unfortunately, we did nothing to reduce cost. We only negotiated prices.

Cost is not the OA problem: Access-denial is. Lowering cost is a library’s goal. Gaining access is the user’s need. And even lowering prices to cost-without-any-profit does not remedy access-denial

The root of the problem is site licenses… Site licenses are market-distorting products that preserve paper-era business processes of publishers, aggregators, and libraries.

No, the root of the problem is access-denial and the solution is access-provision. And the way to provide OA is for authors to self-archive their refereed final drafts (“green OA”). And the way to ensure that authors self-archive is to mandate it.

Universities can cut the Gordian knot right now by replacing site licenses with direct subsidies to researchers?Researchers, empowered to make individual price-value judgments, would become consumers in a suddenly competitive market for content and information services.

Instead of mandating green OA (cost-free), cancel all subscriptions and give the funds to researchers, and the market will take care of the rest?

Eric, when many of us are struggling to get something concrete and practical that has already been tried, tested, and proven effective — namely, green OA mandates — to be implemented by more institutions after 15 years of needlessly lost research access and impact, I don’t think this is the opportune time to try or even contemplate rather speculative hypotheses!

What are the Goals of Institutional Repositories?

Open Access advocates have articulated at least five goals for institutional repositories: (1) release hidden information, (2) rein in journal prices, (3) archive an institution?s scholarly record, (4) enable fast research communication, and (5) provide free access to author-formatted articles.

If “release hidden information” (1) means provide online access to refereed research to which access is currently denied to users at non-subscribing institutions, then this is the one and only fundamental rationale for OA, and has been ever since the online era made it feasible. (But I’m afraid this might not even be what Eric means by “release hidden information”!)

The other four goals are secondary ones: If all refereed research is (green) OA, whether or not it reins in journal prices (2) is secondary, since all users have access, whether or not their institutions can afford to buy access.

An institution’s scholarly record is already “archived” in the journals in which is was published (3) (all of them are now online and archived at the publisher’s toll-gated website). The trouble is that the institution itself has no record of its own research output. (Mandating green OA provides that.)

OA doesn’t just speed up research communication and progress (4), it maximizes research progress (by making it accessible to researchers who are otherwise denied access). That’s not just speed: it’s access and hence uptake, usage and impact.

And the purpose of OA is to provide free access for all would-be users, whether or not their institutions can afford paid access to the publisher’s version of record. Access to the author’s refereed final draft (5) may sound like less than perfect for a librarian, but it is the difference between night and day for an otherwise access-denied researcher.

Institutional repositories are ideal vehicles for releasing hidden information that, until recently, had no suitable distribution platform (1).

This is a profound error and misunderstanding: The fundamental reason for providing OA is to “release” published information that was only accessible to users at subscribing institutions rather than to all would-be users. It is not about information that had “no suitable distribution platform.” (Although pre-refereeing papers, other kinds of research content, and even the “grey” literature are all welcome in repositories too, OA’s first and foremost target content is refereed, published research.)

Institutional repositories fall short as a mechanism to rein in journal prices (2), because they are not a credible alternative for the current archival scholarly record.

Eric is conflating “gold” OA publishing with green OA self-archiving here: Green OA is a supplement, not a substitute, for refereed research journals. No “credible alternative intended”: just a remedy for access-denial.

And the goal of OA itself is not to “rein in journal prices” but to provide online access for all users, not just the ones whose institutions can afford the journal prices.

So Eric is again conflating the problem of journal affordability with the problem of research accessibility.

Without (2), goals (3), (4), and (5) are irrelevant. If we pay for journals anyway, we can achieve (3) by maintaining a database of links to the formal literature. Secure in the knowledge that their journals are not in jeopardy, publishers would be happy to provide (4) and (5).

Without lowering prices, access-denial to users whose institutions cannot afford subscriptions is irrelevant?

Keep paying their subscriptions and journals will provide access for those who can’t afford to pay for it?

Perhaps what Eric means is that if all subscribing institutions promised to keep paying the asking price in perpetuo, then journals would agree to make all their contents OA?

But who would (or could) make such a (foolish) promise?

A scenario consistent with this analysis is unfolding right now. The HEP community launched a rescue mission for HEP journals, which lost much of their role to arXiv.

The HEP community is the only one in the world that has already provided (green) OA for itself without the need for a mandate. Hence there is effectively no more access denial worldwide for the HEP subset of the journal literature. The HEP community has effectively solved its accessibility problem.

What the HEP community does as a follow-up, to address the affordability problem, is of far less concern and relevance to the rest of the scholarly and scientific community, which is still afflicted with access denial (and its resulting loss in research usage, progress and impact). What the non-HEP world needs is OA.

But it should be mentioned that the SCOAP3 project is effectively the one that I called into question above: No institution can or will guarantee that it will keep paying for subscriptions in perpetuo. So the jury is still out on whether such a scheme is sustainable. But we already know it is not scalable beyond HEP, because the non-HEP world has not yet even taken the first essential step, which is to provide green OA.

That’s why green OA mandates are needed.

Publishing reform will take care of itself after OA has (green) become universal — not before.

The SCOAP3 initiative pools funds currently spent on site-licensing HEP journals. This strikes me as a heavy-handed approach to protect existing revenue streams of established journals. On the other hand, SCOAP3 protects the quality of the HEP archival scholarly record and converts HEP journals to the openaccess model.

SCOAP3 is a consortial “membership” solution about whose sustainability and scalability there are, as noted, good reasons to have doubts.

But it is irrelevant. Because HEP already has (green) OA, unmandated, whereas the rest of the scholarly and scientific world does not.

Are Open-Access Journals a Form of Vanity Publishing?

If a journal?s scholarly discipline loses influence or if its editorial board lowers its standards, the journal?s standing diminishes and various quality assessments fall.

Harnad, S. (2010) No-Fault Peer Review Charges: The Price of Selectivity Need Not Be Access Denied or Delayed. D-Lib Magazine 16 (7/8).
ABSTRACT:Plans by universities and research funders to pay the costs of Open Access Publishing (“Gold OA”) are premature. Funds are short; 80% of journals (including virtually all the top journals) are still subscription-based, tying up the potential funds to pay for Gold OA; the asking price for Gold OA is still high; and there is concern that paying to publish may inflate acceptance rates and lower quality standards. What is needed now is for universities and funders to mandate OA self-archiving (of authors’ final peer-reviewed drafts, immediately upon acceptance for publication) (“Green OA”). That will provide immediate OA; and if and when universal Green OA should go on to make subscriptions unsustainable (because users are satisfied with just the Green OA versions) that will in turn induce journals to cut costs (print edition, online edition, access-provision, archiving), downsize to just providing the service of peer review, and convert to the Gold OA cost-recovery model; meanwhile, the subscription cancellations will have released the funds to pay these residual service costs. The natural way to charge for the service of peer review then will be on a “no-fault basis,” with the author’s institution or funder paying for each round of refereeing, regardless of outcome (acceptance, revision/re-refereeing, or rejection). This will minimize cost while protecting against inflated acceptance rates and decline in quality standards.

Harnad, S. (2011) Gold Open Access Publishing Must Not Be Allowed to Retard the Progress of Green Open Access Self-Archiving. Logos 21(3-4): 86-93
ABSTRACT:Universal Open Access (OA) is fully within the reach of the global research community: Research institutions and funders need merely mandate (green) OA self-archiving of the final, refereed drafts of all journal articles immediately upon acceptance for publication. The money to pay for gold OA publishing will only become available if universal green OA eventually makes subscriptions unsustainable. Paying for gold OA pre-emptively today, without first having mandated green OA not only squanders scarce money, but it delays the attainment of universal OA.

?Stevan: Remember, I am an OA supporter?

Eric, I know (and an old friend and comrade-at-arms!)…

?though I am getting discouraged about the slow progress.?

Me too (though I’ve been discouraged about that for about 15 years now…).

?You raise good points, but I think you are the one conflating issues. I will try to keep them separate. 1. Journal pricing: Independent of OA, it is important to take the cost of scholarly publishing down.?

Independent of OA. (So who’s conflating now? Your doubts were billed as being about OA, not about the cost of scholarly publishing…

?The argument I made in earlier blog posts is that site licenses are the root cause of the cost problem.?

The affordability problem: not the accessibility problem.

?It is time for libraries to get out of the banal role of middleman, and let researchers manage their own subscriptions. You call that a speculative hypothesis. I call it restoring a real free market…?

Speculative or non-speculative, it is not the research accessibility problem, and it does not solve it.

?I agree that Green Open Access would solve the access problem… provided everyone joins the initiative. The problem is, too few are joining?

The way to get everyone to join is for all institutions and funders to mandate it.

?and because of quality control issues too difficult to use.?

What is too difficult to use? I have no trouble using the OA content that’s there. The problem is that most of it (85%) isn’t there. That’s why the mandates are needed.

?The mandate movement is getting some traction, but most mandates come with loopholes.?

You’re right, so now EnablingOpenScholarship (EOS) is working to guide institutions on how to optimize those mandates by getting rid of their loopholes: http://bit.ly/EOSoaPolicy

?So, I am getting discouraged. I wonder when patience runs out.?

My patience ran out long ago! (For some perverse reason, I’m still plugging away at it…)

?We both agree that Green Open Access does not solve the cost problem of journals.?

And it is not intended to. It is intended to solve the access problem of researchers.

?You say that journal prices do not matter with Green OA in place. I say they do, because universities end up underwriting two overlapping systems… Admittedly, Green OA is the better bargain. But if Green OA is not reducing the cost of the other, it just adds to the total cost.?

1. Green OA’s cost per paper deposited is negligible. With 100% deposit (because of 100% mandates), even lower.

2. Green OA, if mandated, can provide 100% OA, solving 100% of the accessibility problem.

3. The journal affordability problem is not the same problem, and we’ve agreed not to conflate them (remember?).

?In the one example in which Green OA is near universal [SCPAP3], scholars are working hard to make sure their journals can maintain their current revenue stream.?

That’s their problem and their look-out (because we’ve agreed not to conflate, right?). I’ve many times cautioned that SCOAP3 is premature, unnecessary, unscalable and unsustainable. But I don’t care if I’m ignored: I’m too busy being ignored on how to solve the accessibility problem to worry about being ignored on how not to solve the affordability problem!

?There may be no explicit promise to maintain current subscriptions, but there certainly is an implicit one.?

An implicit promise there are strong reasons to expect that they cannot and will not keep, in the long term: http://bit.ly/ScoapCope But, again, that’s another problem, not my problem, not the accessibility problem.

?Current academics are scared to lose the formal scholarly record in its current form and the editorial boards that control the refereeing process.?

Academics (and research itself) both need peer review. Journals provide the peer review. (In the online era, they need no longer provide access and the archival record, but they do that too. Eventually they won’t have to.) But just as OA is not the journal affordability problem, it is not the problem of the future of publishing either. Green OA changes none of this: It just solves the accessibility problem.

?they are convinced that the journals in which they publish and on whose editorial boards they sit deserve to survive.?

They are right.

?It is the other journals, the ones in which they do not publish and on whose boards they do not sit, that are too costly and should disappear.?

This is a bit simplistic: Researchers want their quality journals, and they want the journals they read and publish in (all three are not always the same). Providing (and mandating) green OA does not change any of this (though it might eventually induce downsizing to peer review alone, and conversion to the gold OA model to recover peer review’s much lower costs):

Harnad, S. (2007) The Green Road to Open Access: A Leveraged Transition. In: The Culture of Periodicals from the Perspective of the Electronic Age, pp. 99-105, L’Harmattan.
ABSTRACT: What the research community needs, urgently, is free online access (Open Access, OA) to its own peer-reviewed research output. Researchers can provide that in two ways: by publishing their articles in OA journals (Gold OA) or by continuing to publish in non-OA journals and self-archiving their final peer-reviewed drafts in their own OA Institutional Repositories (Green OA). OA self-archiving, once it is mandated by research institutions and funders, can reliably generate 100% Green OA. Gold OA requires journals to convert to OA publishing (which is not in the hands of the research community) and it also requires the funds to cover the Gold OA publication costs. With 100% Green OA, the research community’s access and impact problems are already solved. If and when 100% Green OA should cause significant cancellation pressure (no one knows whether or when that will happen, because OA Green grows anarchically, article by article, not journal by journal) then the cancellation pressure will cause cost-cutting, downsizing and eventually a leveraged transition to OA (Gold) publishing on the part of journals. As subscription revenues shrink, institutional windfall savings from cancellations grow. If and when journal subscriptions become unsustainable, per-article publishing costs will be low enough, and institutional savings will be high enough to cover them, because publishing will have downsized to just peer-review service provision alone, offloading text-generation onto authors and access-provision and archiving onto the global network of OA Institutional Repositories. Green OA will have leveraged a transition to Gold OA.

?Free markets are set up to deal with exactly this kind of problem. The current system takes end users out of the price-value evaluation and has led to an unrestricted growth of the scholarly literature.?

How have you managed to draw me into a discussion of journal pricing and affordability, Eric, when we had agreed we were not going to conflate that with the OA problem? ;>)

?So, by all means, continue Green OA. However, also bring a real free market to the scholarly-journal business.?

But Eric, I’m also strongly in favor of putting an end to our unnecessary and cruel slaughter of animals in order to please our palates – but I don’t conflate that with OA either! Why must I speculate about the scholarly-journal business when all I want is that institutions and funders should mandate green OA self-archiving?

Stevan Harnad
EnablingOpenScholarship (EOS)

Update: Open Science conclusion; and PNNL NWChem/CML/Quixote update

#oss2011 @okfn


After my talk at OSS I published two posts on the value of Open Access – I used challenging language which has upset several people but seems to find a chord with others. The discussion has taken place on the Open Knowledge Foundation discussion list (http://lists.okfn.org/pipermail/open-science/2011-October/001032.html and about 25 more posts, culminating currently in a very long and researched post (http://lists.okfn.org/pipermail/open-science/2011-October/001053.html ) by Jenny Molloy, my co-presenter at OSS. Further discussion can take place on this list – it’s open to everyone.

For the next few days I am now devoting my energies to helping create the first fully Open Computational chemistry system. This is based on:

  • NWChem http://www.nwchem-sw.org/index.php/Main_Page which last year became fully Open Source. It’s the main Open program for atomistic calculations, and is complemented by Open plane-wave codes such as ABINIT, MPQC and Quantum Espresso (Please comment if I have missed any – I am also not aware of a list of Open Source computational chemistry – not the same as cheminformatics).
  • Chemical Markup Language and specializations in conventions such as CMLComp and compchem.
  • The JumboConverters framework
  • The Blue Obelisk (includes cclib, openbabel, Avogadro, Jmol, etc.) and other Open Source chemistry tools.
  • Chempound (a repository for semantic chemistry) built by Sam Adams.
  • The Quixote community http://quixote.wikispot.org/
  • The FoX library for XML and CML in Fortran

I have blogged about most of these before. At present what we are doing is:

  • Define a top level dictionary for compchem. Bert deJong at PNNL is optimistic that this is feasible in a reasonable time. It will be a community effort.
  • Define a revised convention for compchem (compchem1, say). Bert thinks there is a very clear infrastructure to almost all QC codes and that we can implement this.
  • Add CML output to NWChem. We are halfway there. I have compile FoX on windows and we are currently getting NWChem running on my machine

This will be supported by dictionary validation and document validation.

Anyone interested should post a comment or mail me or the Quixote list – see main page above


New Twitter Functionality on PLoS ONE

Recently, we added a nice new functionality to the PLoS ONE site. On the homepage, you will now see a ‘twitter’ widget in the right hand column (to the right of the “In the News” block). Whenever anyone issues a tweet with the words ‘PLoS ONE’ or ‘#PLoSONE’ in the text then their tweet will appear in the list here.

In addition, we also have the same functionality operating at the article level. The widget is able to display tweets about a particular article by looking for the article DOI appearing in an ‘unpacked’ URL. If there are no tweets for a particular article, it will not appear.

The paper, Inner Speech during Silent Reading Reflects the Reader’s Regional Accent, is a nice example of this widget in use.

We should point out that this handy widget has a few limitations.  For one, the widget isn’t able to store tweets for all eternity.  It will only be able to show recent tweets. Also, it isn’t connected to our Article Level Metrics …yet (we’re working on it though).

Otherwise, we think this widget will make a nice new addition to our site and will be a helpful way to see what our community is saying.

OA Repositories @ INDIA

Cross Archive Search Service for Indian Repositories (CASSIR)

This service is a part of the project “Development of OAI-Based Institutional Research Repository Services in India”, sponsored by Department of Scientific & Industrial Research, Ministry of Science & Technology, Government of India. This project is being carried out at National Centre for Science Information (NCSI), Indian Institute of Science (IISc), Bangalore. The service will harvest metadata as per the OAI-PMH protocol from the registered OA respositores in India. It also provides a web-based search/browse functionality over the harvested metadata.


Country Statistics for SHERPA/RoMEO

SHERPA Services is pleased to announce that it has added a ‘country’ field to its database of publishers’ copyright and self-archiving policies. This has enabled us to generate a statistical table of the number of RoMEO-listed publishers by country and continent:


‘Country’ has also been added to the Advanced Search options for publishers:


and as a query option for the Application Programmers’ Interface (API):


The apparent imbalance in the distribution of RoMEO-listed publishers by country reflects two things:

1. It reflects the focus of RoMEO on the journals with the highest impact, as indicated by Thomson Reuters’ ‘Web of Knowledge’, which are mostly published in the United States and Europe.

2. The proportionately higher numbers for some countries, notably Portugal and Norway, reflect the effort that our partners in these countries have put into adding their country’s publishers to RoMEO.

We hope that users will find this extra information useful.

Peter Millington & Jane Smith

DSpace Open Access repository development in Africa: Uganda, Zambia, Zimbabwe

Uganda, Zambia, Zimbabwe This is the fifth of a five-part series that looks at Open Access repository development in twelve African countries in celebration of Open Access Week Oct. 24-30, 2011. The first part (Botswana, Ethiopia and Ghana) may be found here: http://duraspace.org/dspace-africa-growing-openaccess-knowledge-and-culture. Parts two, three and four (Kenya, Malawi; Mozambique, Senegal; Sudan, South Africa) may be found here:


The series is co-authored by Iryna Kuchma, Open Access Programme manager, EIFL (http://www.eifl.net/) and EIFL-OA country coordinators: Netsanet Animut, Addis Ababa University and Chair of the Consortium of Ethiopian Academic and Research Libraries, Charles Banda, Copperbelt University, Zambia, Aissa Mitha Issak, Universidade Pedagógica, Mozambique, Gloria Kadyamatimba, Chinhoyi University of Technology Library, Zimbabwe, Richard B. Lamptey, Kwame Nkrumah University of Science and Technology, Ghana, Fredrick Kiwuwa Lugya, Makerere University Library, Uganda, Reason Baathuli Nfila, University of Botswana Library, Rosemary Otando, University Nairobi, Kenya, Kondwani Wella, Kamuzu College of Nursing, University of Malawi and Carol Minton Morris, DuraSpace.


African research output in the mainstream of world knowledge

Makerere University Library became the first library in Uganda to set up an institutional repository called Uganda Scholarly Digital Library (USDL, http://dspace.mak.ac.ug/). Launched as a science repository but later changed to cover other disciplines, USDL has a total of 1,600 full text articles, reports, posters, and other scholarly materials.
Through Open Access organizations and groups like Consortium of Uganda University Libraries (David Bukenya, dbukenya@ucu.ac.ug), EIFL-OA (Fredrick Kiwuwa Lugya, flugya@mulib.mak.ac.ug) and support from partners like INASP, EIFL, Sida Sarec, and Carnegie Corporation of New York, academic and research libraries in Uganda have started to show interest in having  institutional repositories.
The Open Access initiative has been further strengthened through partnerships such as the Irish African Partnership for Research Capacity Building and the Database of African Theses and Dissertations (DATAD). Through its Open Access repository, the Irish African Partnership for Research Capacity Building (IAP) brings together universities of Ireland, Malawi, Mozambique, Tanzania and Uganda in a unique, high-level partnership to develop a coordinated approach to research capacity building in order to make an effective contribution to the reduction of poverty. With the support of the Association of African Universities (AAU) DATAD aims at improving the management and access to African scholarly work (theses and dissertations) thus putting Africa’s research output onto the mainstream of world knowledge.


Building capacity for Open Access repositories

Zambia Library Consortium (ZALICO) promotes Open Access in the country and builds capacities among its member organizations to set up and maintain Open Access repositories.
In 2011 Zambia Library Consortium (ZALICO) has organized a national Open Access Repositories workshop funded by INASP to explore DSpace software for repository building. Participants from 12 institutions attended, including: National Assembly, National Institute for Industrial Scientific Research, National Technology Business Centre, The National Science and Technology Council, National Institute for Public Administration (NIPA), University of Zambia, Bank of Zambia, Zambia Environmental Management Agency (ZEMA) formerly Environmental Council of Zambia (ECZ), Zambia Agricultural Research Institute, Copperbelt University, Mulungushi University and Tropical Diseases Research Center (TDRC).
Open Access repositories are being developed by the following institutions: Copperbelt University Library, National Science Technology Center (NSTC), The University of Zambia and National Assembly of Zambia.


University libraries lead the way to Open Access repository development

In Zimbabwe OA initiatives have to a large extent been driven by university libraries through the Zimbabwe University Libraries Consortium (ZULC) with support from the International Availability of Scientific Publications (INASP) and EIFL.
All universities with the exception of the Catholic University, Great Zimbabwe University, Lupane State University and Solusi University have IRs at various stages of development. The major content of these repositories are journal articles, published conference papers, projects and dissertations, digital collections and past examination papers whose full texts are accessible on the universities’ local Intranets. Most collections are mounted on the Greenstone and/or DSpace platform. The University of Zimbabwe also provides book chapters, working papers, research reports and seminar papers. The repository is listed in the Directory of OA Repositories (OpenDOAR) and it is accessible on the internet.
University of Zimbabwe( UZ): The institutional repository (http://ir.uz.ac.zw/jspui/) was established in 2005 using DSpace software. It contains past exam papers, conference papers, staff publications, DATAD: abstracts of theses and dissertations, EDT–db: full text of electronic theses, book chapters, working papers, research reports and seminar papers. It is available through the internet. The UZ has the most successful institutional repository. It is well populated and it is accessible on the web. This is due to a number of factors. The UZ is the mother of all universities with a well documented research culture which attracts funding from donor organizations. It has a publishing house with a decent output. The UZ library personnel were the first to receive institutional repository training which they are now cascading to other libraries. It has a bandwidth of 27mb which is the envy of other universities. Its long history and location in the capital city makes it a favourite destination for the best librarians. The above factors have created a conducive environment for the implementation of a successful institutional repository at the UZ.
The University of Zimbabwe (UZ) library with financial support from EIFL has embarked on a campus wide Open Access (OA) Advocacy Campaign which will target the UZ management and administrative personnel and Deans of Faculties. The ultimate purpose is to advocate for the adoption of a campus wide OA policy. During OA week a one day workshop will be held for 20 UZ management staff (Executives i.e. Vice Chancellor, Pro Vice Chancellor, Registrar, and Deans of Faculties) in an endeavour to achieve management buy in on the concept of OA, with the hope of advocating for OA policy formulation and implementation in the near future. A series of workshops and presentations targeting teaching staff (chairpersons of departments and lectures) in all 10 faculties will be held by faculty librarians with the sole purpose of marketing and publicising of both the concept of OA and OA resources relevant to individual faculties. An advocacy video will be documented which will contain testimonies of local academics who have so far benefited from exposure on IR platform and other success stories. Overall the library is looking forward to the adoption of a University OA Policy, which will enable access to knowledge in support of teaching, learning and research at the UZ, and as such this prospective advocacy campaign will be a conducive platform to this vision.
Only the UZ’s IR is listed in the OpenDOAR. The rest are only available on Intranets for a number of reasons. Firstly, institutions are reluctant to mount their IRs on the Internet due to very limited bandwidth which limits connectivity. Secondly institutions are afraid of infringing intellectual property rights on some of the works in their IRs. At some institutions submission to the IR is done through the Research and Scholarship Committee to ensure compliance with intellectual property rights and to enhance submission.
Zimbabwean institutions are at an advanced stage of developing IRs. Most institutions have IRs running on their Intranets. Uploading IRs onto the net is only a matter of time for most institutions. The major constraint is fear of copyright infringement and lack of IR policies. Further training in these aspects would ensure expedited uploading onto the web and availability of Zimbabwean research to a wider global audience.

R2RC Launches New Open Publishing Guide for Students

The Right to Research Coalition has announced a new student guide to publishing openly, entitled “Optimize Your Publishing, Maximize Your Impact.”  This new resource presents students with the ways in which they can make their research openly available for the widest possible readership and lays out the benefits of doing so – both as authors and as readers.  How do you know where to submit your manuscript?  What are the factors that go into deciding the most appropriate publication outlet?  Which journal will give your article the widest audience? Where to publish is too important of a decision to put off until the end of the research process.

In addition to information on openaccess journals, repositories, and authors’ rights, the guide includes a publishing choices decision tree outlining the different opportunities to make an article openly available throughout the publication process.  The publication process can be complicated, and an article can still be made openly available even if it’s published in a subscription-based journal.  The decision tree lays out all of the options, so students understand the flexibility they have when deciding to make their work openly accessible.

While there are many general, how-to resources for open publishing, this guide is specifically tailored to address students’ concerns when it comes to publishing an article and launching their research career.  From how to approach a research advisor about Open Access to the dividends the open access citation advantage can pay when launching a career, students are in a unique position when it comes to deciding to publish openly.

The new resource is also designed to be flexible. Not only can students use it to educate themselves and their peers about open publishing choices, but faculty can also use it to start the conversation with their students.  And, librarians can integrate it into their scholarly communication programs, especially during library orientation for new students.  There is also space on the final page for the guide to be localized to a particular institution and include information on a campus’ institutional repository or openaccess policy.

Today’s students are tomorrow researchers, and this guide will help students make informed decisions about how and where to publish their work for maximum impact.

The Right to Research Coalition’s open publishing guide was produced with generous support from the Open Society Foundations.



Cross-posted from our blog at: http://www.righttoresearch.org/blog/r2rc-launches-new-open-publishing-guide-for-studen.shtml