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

Summary

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.

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…

Stevan

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.

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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/ 
                                                                                    (Or) 
As e-mail attachment to the Editorial Office :editor.jpb@omicsgroup.co 

We shall look forward to hear from you. 

Sincerely, 

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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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

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.

EV:
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.

EV:
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.

EV:
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

EV:
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.

EV:
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!

EV:
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”!)

EV:
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.

EV:
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.)

EV:
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.

EV:
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?

EV:
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.

EV:
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.

EV:
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.

EV:
?Stevan: Remember, I am an OA supporter?

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

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

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

EV:
?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…

EV:
?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.

EV:
?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.

EV:
?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.

EV:
?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.

EV:
?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

EV:
?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…)

EV:
?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.

EV:
?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?).

EV:
?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!

EV:
?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.

EV:
?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.

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

They are right.

EV:
?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.

EV:
?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? ;>)

EV:
?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)

#oss2011 @okfn

#oaweek

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