FRPAA in the Spotlight: Public Access Bill featured in Congressional Briefing, Two Dozen Bipartisan Co-sponsors add their Support.

Fresh on the heels of yesterday’s well-attended Congressional briefing on the issue of public access to the results of taxpayer funded research, 24 new bipartisan co-sponsors have officially been added to the roster of supporters for H.R. 4004, The Federal Research Public Access Act. 

Estimating the True Costs of Gold Open Access Publishing

Many estimates have been made of the true costs of Gold Open Access (OA) publishing (e.g., by Claudio Aspesi, in the discussion of Richard Poynder’s recent article), but the estimates are rather arbitrary and unrealistic if the other causal factors that could raise or lower them are not taken into account.

The two most important causal factors are (1) Green OA and (2) institutions’ subscription budgets.

Institutions cannot cancel essential journals if their contents are not otherwise accessible to their users.

If Green OA is universally mandated, then authors’ final, peer-reviewed drafts of all journal articles are deposited in institutional repositories and freely accessible to all users whose institutions cannot afford subscriptions to the journals in which they appeared.

This makes it possible for institutions to cancel subscriptions, eventually making the subscription model unsustainable as the means of covering the costs of publication.

Subscription cancelations force journals to cut inessential costs.

With the refereed final drafts of all articles accessible to all through Green OA, journals no longer need to (1) provide the print edition, (2) provide the online edition or (3) provide access or archiving: The distributed network of Green OA repositories provides all that is needed. The rest are all obsolete products and services in the universally mandated Green OA era.

When the costs of (1), (2), and (3) are unbundled from publication products and services made obsolete by universal Green OA, the only essential cost remaining is that of implementing peer review.

Peers review for free, so the cost of peer review is just the cost of managing the peer review process, including the editorial expertise and judgment in choosing referees, adjudicating referee reports, and adjudicating revised drafts.

If peer review is provided as a “no fault” service to the author’s institution, per submitted draft, regardless of whether the outcome is rejection, revision, or acceptance, the cost of rejected articles can be unbundled from the cost of accepted articles; this not only lowers and distributes the cost of peer review, but it removes the risk of lowered peer review standards and over-acceptance for the sake of making more money through Gold OA.

This much lower cost of post-Green OA no-fault Gold OA — my guess is that it would be between $200 and $500 per submitted draft — would not only be incomparably more affordable than today’s pre-Green OA fees for Gold OA, but the money to pay for it would be available, many times over, from a fraction of institutions’ permanent annual windfall subscription savings released by the cancelations made possible by universally mandated Green OA.

The only essential element for having Gold OA at this much more realistic and affordable price is one cost-free act on the part of the universal providers of all research output: Institutional Green OA mandates (reinforced by research funder Green OA mandates).

Without taking these costs and causal factors into account, estimates of the costs of OA are arbitrary and the wait for universal OA will continue to be long.

Harnad, S. (2007) The Green Road to Open Access: A Leveraged Transition. In: Anna Gacs. The Culture of Periodicals from the Perspective of the Electronic Age. L’Harmattan. 99-106.

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).

Harnad, S. (2010) The Immediate Practical Implication of the Houghton Report: Provide Green Open Access Now. Prometheus 28 (1). pp. 55-59.

Harnad, S. (2011) Open Access to Research: Changing Researcher Behavior Through University and Funder Mandates. JEDEM Journal of Democracy and Open Government 3 (1): 33-41.

Understanding of Open Access

Dear colleagues,

The moment has come when all the thoughts, ideas, the initiatives and the best experiences concerning Open Access to find a streamlined expression capable to set in motion a vector for actions in Romania.
To this purpose, The Understanding of Open Access has been launched. It is a document with a double significance: “understanding” as a consensual agreement among the signatories and “understanding” meaning a good apprehension of the concepts behind it.

What sparked this document?
Kosson community members shown a great interest and involvement for the valorisation of the electronic information resources in Open Access regime since 2005. From that moment on, a long path was followed in translating, studying and promoting the concepts and the models for the Open Access. In the year 2010, the Romanian Library Association adopted a Motion on Open Access during the national conference.
This important moment needed to be elevated in order to project concrete actions in the future and this led to this programatic and pragmatic document expressing the will and understanding of the Romanian stakeholders.

Why it needs your support and where to promote it?
The first answer springs out of the need to clearly state the fact it is not only necessary to have some knowledge about Open Access, but to understand what this means. This difference in semantics it is needed now more than ever when many things seems to dilute and apparently are being mangled in many other matters of concern.
Another answer is the need for more clarity in all it needs to be done in the future. To this purpose the document points to concrete objectives.

What is the purpose of the understanding?
It will lead to a better consolidation of the members actions around the community goals and offers solid guidelines to the knowledge gains and further development opportunities.
It offers a clear fixed mark for the future of the Open Access in Romania and Europe at large.
It constitutes the base for future actions and activities tightly linked to Open Access advocacy in Romania.
It will be the measure for future calibration of our performances as the objectives will be counted in solid facts for the Romanian society and for the world.

What can I do?
1. Read, understand and sign the document at
2. Advertise and advocate among your fellow colleagues the existence of this document, what it means and what are the objectives.
3. Discuss among your friends and colleagues about the ways you could involve your institution in advocating Open Access to information.
4. Acquire deeper and useful knowledge about this paradigm because your institution will be affected in the future directly or by influence by the Open Access implementations.
5. Initiate debate, write useful materials and involve all the stuff working in your institution.
6. Take the document with you and convey its meanings and objectives further to the management level, and raise the awareness to the final goal of achieving an Open Access mandate and an institutional endorsement for the Understanding.

Let us dedicate some time to understand Open Access, together, for our better knowledge and for those whom we serve.

This is not a document addressed only to Romanian stakeholders. It has a wider scope as it reflects our efforts to integrate our actions on global level. You all are welcome and invited to endorse it! Thank you!

ACS Fall meeting Skolnik Symposium “Molecular Science and the Semantic Web”: Invitation to submit abstracts

As recipients of the Skolnik award Henry Rzepa and I are organizing the symposium at the ACS Fall meeting in Philadelphia (Aug 19-23). Depending on how many abstracts we receive this will last between 1 and 3 days, most likely 1.5-2. The theme of our symposium is

“Molecular Science and the Semantic Web”

Many readers will already be aware of the symposium and we have already received some abstracts (deadline March 25, i.e. this week and it is strict). However some may have held back as some symposia in the past have been invitation-only. This is not the case here – anyone may submit an abstract and Henry and I will be the primary judges of their suitability. The abstracts should address the title above and should ideally have a strong basis in modern Semantic Web thinking and practice (for example “Web 3.0″ but not limited to that). Abstracts are short (150 words) and all abstracts are indexed by Chemical Abstracts and some other indexing agencies

The “Semantic Web” theme honours the ideas of TimBL and can cover things like tools, linked open data, and Open communities. We are aware that some disciplines may be ahead of chemical practice in the Semantic Web. A small number of presentations might be from “outside chemistry” if the authors can convince us that their work can have a direct bearing on future progress in chemistry.

Product placements of tools and data are unlikely to be acceptable.

A very small number of presentations may be remote (with Henry or me managing the real-time process). These are completely at our discretion and likely to be limited to people we know and we can guarantee will provide compelling input.

Please note that the ACS does not provide expenses for speakers.

Is the purpose of scholarship private profits?

This post is a reply to a post David Prosser wrote on the GOAL list in response to my post on the RCUK consultation.

On 18-Mar-12, at 5:07 AM, David Prosser wrote:

Say I wanted to data mine 10,000 articles.  I’m at a university, but I am co-funded by a pharmaceutical company and there is a possibility that the research that I’m doing may result in a new drug discovery, which that company will want to take to market.  The 10,000 articles are all ‘open access’, but they are under CC-BY-NC-SA licenses.  What mechanism is there by which I can contact all 10,000 authors and gain permission for my research?


Many thanks for raising this question, David, which brings up a number of interesting points. There is one that I would like to highlight first off as a basic underlying assumption that from my perspective should be challenged. That is the assumption that the increasing corporate involvement in universities is desirable. I argue that it is not. Co-funding of university research by pharmaceutical companies is problematic. What I would recommend instead is reversal of the corporate and high income earner tax breaks brought in, in many countries, over the past few decades as part of the neoliberal ideology*. That way, the public will have enough resources so that universities can be funded by the public to conduct research in the public interest. This would likely need to happen at a global level – an appropriate role for international bodies, from my perspective – to avoid the current risk of capital flight (companies pick up and move to wherever tax rates, employment and environmental standards are lowest to achieve the highest profits) which is undermining western democracy as a whole.

To illustrate why I say that funding of university research by the corporate sector is problematic, here are just a few examples:

1.    Why would pharmaceutical companies want to fund research that might challenge the claims of their successful drugs?
2.    What incentive would a pharmaceutical company have to find a cheap or free alternative to their expensive drugs? For example, if a pharmaceutical company is making a lot of profit from selling drugs to combat colon cancer, why would it fund research on public campaigns to encourage preventive measures such as eating vegetables? In the U.K., my understanding is that recent cuts have hit the social sciences and humanities hard. This means universities need to rely more on funding sources such as pharmaceutical companies while at the same time there is less support for this kind of basic, public-oriented research.
3.    Should research on the environment be conducted by and for the public interest – or report to the companies responsible for pollution?

*  Note on neoliberal ideology: think Thatcherism / Reaganism, the idea that the invisible hand of the market will take care of everything, if only we give it free reign. The “invisible hand of the market” comes from  a superficial skim of Adam Smith’s The Wealth of Nations (superficial because proponents do not speak to Smith’s simultaneous call for the strong hand of the state, or the basic underlying assumption of continuous growth, which many would argue is impossible given the real limits of our ecosphere). For more on neoliberalism, I recommend David Harvey’s brief and highly readable “A brief history of neoliberalism”. We’ve been giving this a try for four decades, and what are the results? The global financial crisis of 2008, the debt crisis in Greece (and other countries), the Citizens United decision in the U.S. giving corporate money a right to free speech – a significant blow to democracy. It is timely to question this basic assumption, not continue on our current  path.

This message is posted here rather than to the GOAL list because this discussion is not permitted on the GOAL list. Further discussion is welcome from my perspective through many venues, however please note that I am no longer subscribing to GOAL

Update; and a semantic amusement for you

I’ve extremely busy so this is just to let anyone know I am still working on a number of threads.

  • Chem4Word. We had a really valuable discussion yesterday (sic) in Microsoft Research Cambridge with Alex Wade, Joe Townsend, Clyde Davies and me. We went over the code for Clyde’s benefit as he is writing it up (a) for further C4W work and (b) for #semphyssci publication. Even though I was PI of the project and heavily involved there are swathes of code I didn’t even know existed. It’s a VERY impressive piece of work and Joe Townsend and several others can take great pride. A major part of the next phase is with Nico Adams whom I shall be visiting soon.
  • Panton Fellowships. We are delighted in the very high quality response to the PFs and Laura Newman (OKF) has been doing a great job servicing the applications for us to make decisions on who to interview (skype).
  • Hargreaves. Jenny Molloy, Diane Cabell and I are putting together a response to IPO/Hargreaves. (I’ve got responses from 6 publishers I wrote to – thanks! – and will summarise and postb them to this blog, probably in a day or two.
  • Semantic Physical Science. I am really excited. We have now developed a completely declarative approach to forcefields such that it should be possible to define the complete problem on the fly using MathML and CML (MathCML). Given that a forcefield (misnamed) evaluates the energy as a function of molecular geometry, atom types and a parameterised forcefield it will be possible to code this in a page or two of declarative code supported by standard libraries. The forcefield can be manipulated (e.g. to calculate derivatives) so it should be possible to both optimise geometry and elaborate trajectories in a declarative manner. With Mark Williamson, Andrew Walker, Martin Dove and Jens Thomas.

And so a semantic amusement.

A cup contains 200 ml of water and an apple (4 cm radius) is placed on top.

From reading this description what can be deduced by:

  • A 10 year-old Anglophone child
  • A first year undergraduate scientist
  • A logician
  • “Shallow thought” – the accumulation of current “AI” – e.g. Wolfram Alpha, True Knowledge, Cyc, Google, Wikipedia and any other engines you think would be relevant (the problem is given to them cold – they are not trained in this domain).

(I’m interested because I want to develop “Shallow thought” for chemistry – more on that later).

Drosophila Research Captures our Hearts, and Attention

The American Heart Association Council on Functional Genomics and Translational Biology recently released their list of “Top Advances in Functional Genomics and Translational Biology for 2011” and we are pleased to announce that PLoS ONE article “A mighty small heart: the cardiac proteome of adult Drosophila melanogaster”(1) is one of 10 featured publications!  All 10 articles were summarized in a paper published in Circulation: Cardiovascular Genetics, published by the American Heart Association(2).  The finalists were selected from hundreds of papers in the literature, with input from the Early Career Committee of the Council on Functional Genomics and Translational Biology.

In this article, Cammarato and colleagues describe the full complement of proteins that exist in the adult Drosophila heart.  The insect heart, also referred to as the dorsal vessel, is a simple pulsing tube that maintains the flow of haemolymph (ie. bug blood) through its open circulatory system (lower image and inset, shown with nearby abdominal muscle).  The haemolymph is not restricted to vessels — there are no veins and arteries — but instead bathes the tissues in one big internal cavity.  Unlike our circulatory systems, the insect system has no role in delivering oxygen to tissues and cells, so the haemolymph contains no red blood cells.  Similarly to our system, it does carry various immune cells and nutrients necessary for the health and function of the animal.  Despite any differences, we have long known that many of the genes involved in making a fly heart are the same as those needed to make a mammalian heart.

The authors of the PLoS ONE study carry out a comprehensive survey of proteins that make up the adult Drosophila heart.  Importantly, they compared their results to those found by researchers that have examined adult mouse hearts, and the similarities they identified are astonishing.  Essentially, the authors have paved the way for new studies that will use Drosophila in research of heart disease and its treatment.

For decades, research in Drosophila has provided insight into various complex biomedical problems, and now we can turn to this model to fight the number one cause of death worldwide (3).  We offer our heartfelt congratulations to Cammarato and colleagues, and we ask that you forgive the pun.

  1. Cammarato A, Ahrens CH, Alayari NN, Qeli E, Rucker J, et al. (2011) PLoS ONE 6(4): e18497. doi:10.1371/journal.pone.0018497
  2. Circulation: Cardiovascular Genetics. 2012; 5: 143-145 doi: 10.1161/?CIRCGENETICS.111.962621

Images by André Karwath, used under CC-BY-SA license and from