Panton Discussions #4 and #5

Yesterday Laura Newman (OKF) and I met with Iain Hrynaszkiewicz of BiomedCentral and recorded a Panton discussion. Panton discussions are irregular discussions with figures in the Open world and have traditionally taken place in the Panton Arms in Cambridge, where the Panton Principles (http://pantonprinciples.org/ ) were announced.

The previous three discussions were with:

  • Richard Poynder
  • David Dobbs
  • Peter Murray-Rust (interviewed by Richard Grant, F1000)

Until recently discussions depended on my finding someone with a recorder and preferably video camera as well. Now I have permanent access to a camera and have learnt how to use it, so we don’t have to get people to Cambridge (though it’s nice to try). We’ve also got funding for Panton Fellowships (OSI) so that’s an extra resource and has enabled Laura and me to work together.

IainH has been a great advocate of Open data and this recording explores his ideas. I’m currently editing it but here is the most controversial part as a teaser – how does Iain pronounce his name?:

http://dl.dropbox.com/u/6280676/ih_prononunce.wmv

This clip is a test of whether blogging videos works in my environment.

When AnimalGarden found out we were going to BMC they insisted we had to have an interview with Gulliver Turtle – the Open Access Turtle. So here are a few snippets of their recording:

The current movie is in *.wmv –sorry if you can’t read it. I am getting a converter so the full interview

Should be in MP4

Ecology and Evolution – Issue 4 now published!

Cover image for Vol. 1 Issue 4

We are pleased to announce the publication of Issue 4 of Ecology and Evolution, completing our 2011 issues with a 16-paper, fourth installment. The journal continues to demonstrate high-quality scientific work under the broad scope umbrella; marine papers include Heide-Jørgensen and colleagues’ paper analyzing harbor porpoise behavior in the midst of climate change and Dixson and colleagues’ paper examining terrestrial chemical cues used by coral reef fish larvae. “Pristionchus uniformis, should I stay or should I go? Recent host range expansion in a European nematode”, by Sommer and D’Anna, examines host range expansion and host-switching of Pristionchus uniformis, a nematode atypically associated with two unrelated groups of beetles on two continents.

The issue includes two papers on invasion: Perkins and colleagues present a new, clean organizational framework for invasion, while Papadopoulos and colleagues discuss the demography and invasion potential in the economically-important, historically well-documented Mediterranean fruit fly. A beautiful image of the medfly from the Papadopoulous et. Al. paper graces the Issue 4 cover as we continue to collect author photographs for publication. Our 5th Issue will be published online in January 2012 and we look forward to posting more outstanding work. We would like to thank our authors, Editors, and Editorial Board Members for an outstanding start in 2011!

Priorities: Mandating, Providing and Defining Open Access (Gratis and Libre)

In “The Open Access Movement is disorganized; this must not continue,” Peter Murray-Rust [PM-R:] wrote:

PM-R: ?Stevan Harnad? argues inter alia that gratisOA (e.g. through Green, CC-restricted) rather than libreOA (e.g. through Gold, or CC-BY) should be adopted…?

Actually, I argue that Gratis Green OA rather than Libre OA should be mandated (by researchers? institutions and funders), because: 

(1) 100% OA is reachable only if we mandate it;

(2) only Green OA self-archiving (not Gold OA publishing) can be mandated; 

(3) all researchers want to provide Gratis OA (free online access); 

(4) not all researchers want to provide Libre OA (free online access plus remix and republication rights);

(5) all disciplines need Gratis OA;

(6) not all disciplines need Libre OA;

(7) Gratis OA is much more urgent than Libre OA;

(8) 100% Gratis OA is already reachable, 100% Libre OA is not;

(9) publisher restrictions are less of an obstacle for Gratis OA; 

(10) mandating Green Gratis OA is not only the fastest, surest and cheapest way to reach 100% Gratis OA but it is also the fastest, surest and cheapest way to reach Gold OA and Libre OA thereafter.

PM-R: ?If we restrict ourselves to STM publishing (where almost all of the funders? efforts are concentrated) there is not a shred of evidence that any author wishes to restrict the re-use of their publications through licenses.?

(a) OA is not just for STM articles: it?s for peer-reviewed research in all disciplines

(b) It is not just funders who are mandating OA but also institutions, for all research, funded and funded, in all disciplines

(c) Ask, and you will find more than a shred of evidence that not all authors (not even all STM authors) want to allow their verbatim texts to be re-mixed and re-published by anyone, without restriction.

(d) What all authors want re-used and re-mixed are their ideas and findings, not their verbatim texts.

(e) STM authors do want their figures and tables to be re-used and re-published, but with Green Gratis OA, that can be done; it is only their verbatim texts that they don?t want tampered with.

PM-R: ?Most scientists don?t care about Open Access. (Unfortunate, but we have to change that)?

Most still don?t know about it, and those who do are afraid to provide it, even though it has been demonstrated to be beneficial for them and their research (in terms of uptake, usage, applications, citations, impact, progress).

And that?s just why OA mandates are needed.

PM-R: ?Of the ones that care, almost none care aboutdetails. If they are told it is ?open Access? and fulfils the funders? requirements then they will agree to anything. If the publisher has a page labeled ?full Open Access ? CC-NC ? consistent with NIH funding? then they won?t think twice about what the license is.?

What they care about in such cases is not OA, but fulfilling their funders? (and institution?s) requirements.

That?s why OA needs to be mandated.

Most funders mandate only Gratis Green OA because it has fewer publisher constraints and fewer and shorter embargoes. But the advantage of mandating that the author?s version be made OA is that it makes it easier to give permission to re-use (the author?s version of) the figures and tables.

If consensus can be successfully reached on mandating Libre OA rather than just Gratis OA, all the better. But on no account should there be a delay in adopting a Gratis OA mandate in order to hold out for Libre OA.

Gold OA (whether Gratis or Libre) cannot be mandated, either by funders or institutions, and is hence not an issue. Funders and institutions cannot dictate researchers? choice of journal; nor can they dictate publishers? choice of cost-recovery model.

PM-R: ?Of the ones who care I have never met a case of a scientist ? and I want to restrict the discussion to STM ? who wishes to restrict the use of their material through licenses. No author says ?You can look at my graph, but I am going to sue you if you reproduce it? (although some publishers, such as Wiley did in the Shelley Batts affair, and presumably still do).?

The discussion of OA cannot be restricted to just STM, any more than it can be restricted to just Chemistry.

Authors, mostly ignorant of OA as well as of rights and licenses, mostly haven?t given any of them much thought.

But I can only repeat, even if they have not yet thought about it, many authors, including STP authors, would not relish giving everyone the right to publish mash-ups of their texts.

Graphs and figures are a different story; authors are happy to have those re-used and re-published in re-mixes by others (with attribution), and, as noted, the fact that the Green Gratis OA version is the author?s final draft rather than the publisher?s proprietary version of record makes this much simpler. (For the graphs in their version-of-record, some publishers might conceivably think of suing for this; but authors certainly would never do it, for their Green Gratis OA versions. So that?s another point in favor of Green Gratis OA.)

PM-R: ?the OA movement ? Cannot agree on what ?open access? means in practice?

They can agree, and they have agreed: http://www.earlham.edu/~peters/fos/newsletter/08-02-08.htm#gratis-libre

PM-R: ?the OA movement? Spends (directly or indirectly) large amounts of public money (certainly hundreds of millions of dollars in author-side fees) without changing the balance of the market

The OA movement spends no public money. Perhaps you mean Gold OA journal authors?

And the objective of the OA movement is not ?changing the balance of the market.? Its objective is OA ? Gratis, and, where needed, Libre.

PM-R: ?the OA movement? Has no clear intermediate or end-goals?

The OA movement?s end-goal is Gratis OA (free online access) and, where needed, Libre OA (free online access plus re-use, re-mix re-publish rights).

Where Libre OA is needed, Gratis OA is an intermediate goal.

PM-R: ?When I find an Open Source program, I know what I am getting. When I find an Open Access paper I haven?t a clue what I am getting?.

You can be almost 100% sure that what you are getting is the peer-reviewed, final, accepted draft.

And with that, researchers whose institution cannot afford access to the publisher?s version of record would be almost 100% better off than they are now.

And that?s why the first priority is mandating Green Gratis OA self-archiving.

(The disanalogies between Open Access and Open Source are too numerous to itemize.)

PM-R: ?When I publish my code as Open Source I can?t make up the rules. I must have a license and it must be approved by OSI?

But OA is about peer-reviewed research, and there it is the refereed and editor that must approve the article.

PM-R: ?the OS community cares about what Open Source is, how it is defined, how it is labelled and whether the practice conforms to the requirements?. By contrast the OA community does not care about these things?.

As stated earlier, the OA (advocacy) community knows what OA (Gratis and Libre, Green and Gold) and what their respective ?requirements? are.

It is not the OA advocates who don?t care enough about such things; it is, unfortunately, the researcher community: the ones who need to provide the OA content.

And what?s missing isn?t a definition of OA, but OA.

PM-R: ??Open Access? was defined in the Budapest and other declarations?.

And the definition ? not etched in stone but evolving  ? has been revised and updated: http://www.earlham.edu/~peters/fos/newsletter/08-02-08.htm#gratis-libre

PM-R: ?Everyone (including Stevan) would agree that this is now consistent with what is (belatedly) being labelled as OA-libre. Note that Stevan was a signatory to this definition of Open Access?.

I signed and helped draft the first OA definition, but at that time I was not yet aware of nuances whose importance has since become apparent, requiring a revision of the definition.

PM-R: ?My immediate concern is that unless we organize the definition, labelling and practice of Open Access we are simply giving OA-opponents or OA-doubters carte blanche to do whatever they like without being brought to account. We are throwing away hundreds of millions of dollars in a wasteful fashion. We are exposing people to legal action because the terms are undefined?.

I?m afraid I?m lost here: Who are ?we?? OA advocates? What money are we throwing away? Perhaps you means authors and their funders, spending money on Gold OA that is Gratis rather than Libre? Well, I agree that?s a waste of money, but not because the OA?s Gratis but because Green OA needs to mandated before it makes sense to pay for Gold OA.

PM-R: ?If you try to re-use non-libre material because it was labelled ?Open Access? you could still end up in court?.

Highly unlikely (especially if you?re re-using graphics from the author?s draft rather than the publisher?s version-of-record).

But if you have access to it at all, you?re already better off than those researchers who do not: And that?s the primary problem OA was defined and designed to fix.

PM-R: ?As a UK taxpayer I fund scientists to do medical research (through the MRC). The MRC has decided (rightly) that the results of scientific research should be made Open. But they are not Open according to the BOAI declaration?.

They are Gratis OA (after an embargo period). Once all research is Gratis OA (and immediately upon acceptance for publication), Libre OA?s day will come.

PM-R: ?Individuals such as Stevan, Peter Suber, Alma Swan, [have] relatively little coordination and no bargaining power?

True. But we did coordinate on the updating of the definition of OA. And EnablingOpenScholarship (EOS) will attempt to guide and coordinate the OA policy-making of universities and research instititions, worldwide.

But OA advocates, individually and collectively, are not the ones with the power to provide OA: the ones with the power to provide it are researchers themselves. And the ones with the power to mandate that they provide it are their institutions and funders.

PM-R: ?So my simple proposal is that we need an Open Access Institute

Let?s publish our papers in whatever is the best journal for them, but let?s concentrate on persuading institutions and funders to mandate that we make them Green OA.

I look forward to PM-R?s explanation of why he does not agree.

Victoria University, Australia, signs up for a Wiley Open Access Account

Victoria University in Australia is the latest organization to sign up for a Wiley Open Access Account and pay for its researchers to publish an open access article with Wiley.  Authors affiliated with Victoria University can publish research articles in Wiley Open Access journals and/or OnlineOpen, without directly paying any publication charges.  When Authors submit to a Wiley Open Access journal or opt for OnlineOpen they need to state their affiliation to Victoria University.

Victoria University joins a number of funders who have opened a Wiley Open Access Account since this was launched earlier this year. Browse our listing to see the institutions / funders who have an account or partnership with Wiley Open Access.

Wiley Annual Report 2011: costs down, profits up

The John Wiley and Sons 2011 Annual Report is now available. From the Overview, in brief, revenue from Wiley’s Scientific, Technical, Medical and Scholarly division (STMS) increased slightly to just under a billion U.S., while direct contribution to profit rose from 5 to 9% (for a direct contribution to profit of $425 million, or 42.5%) – from the Detailed Financials, p. 22.

From the Overview: Revenue growth and margin improvement due to outsourcing journal production were partially offset by higher operating costs from business growth.

Another way to express this: in 2011, John Wiley & Sons decreased their costs by outsourcing journal production. This decrease in costs was sufficient to pay for increase in growth (taking over more society journals) and to reduce their net debt, and still increase profit their profits by 5 to 9%.

Update December 21: note that the Wiley profit rate of 42.5% is an understatement of the total profit from Wiley journal subscription revenue. This is because close to half of Wiley journals are published on behalf of scholarly societies. These societies also make a profit from Wiley revenues, which is subtracted as a cost before calculating Wiley’s net contribution to profit from journal subscriptions. The actual percentage of Wiley revenue that goes to profit for both Wiley and the societies is somewhere between the 42.5% and the Wiley Gross Profit Rate of 73.1% (see page 22 of the Detailed Financials. That’s not a typo – this is a gross profit rate of seventy three point one percent).

Articulating the commons: a leaderful approach

Apologies for duplication – I think this belongs on both cc-licenses and the cc-community list. I expect that I will only write a very few messages where this makes sense.

Rather than having a few of us decide on what the commons is or should be, why not invite everyone to participate in the discussion (open source it), over at least the next few years? This would be a leaderful approach (acknowledging the inspiration of Occupy).

From a technical standpoint, what I mean is that the box that says “more permissions URL” should be expanded and renamed to something like “more detail”. Actively invite anyone who licenses material to tell more about what this act means to them – kind of like a will. Ideally, there needs to be a way to bring these comments together, perhaps through data mining, and occasionally sharing some of what people have come up with.

Some reasons to consider this approach:

1.    Opening the conversation in this way may open up new understandings about what sharing means, or could mean.  Some examples of things that people might want to say:
–    free for the 99%
–    free for anyone aiming for social and environmental justice
–    free to anyone not lobbying for restrictive copyright laws
–    free to anyone who has never sued a customer
–    free to use with respect

These kinds of things may or may not fit specific legal requirements, but I would suggest that building a commons is much more a cultural shift than a legal one.

My vision here is that Creative Commons is a great start towards a commons, but we all still have a great deal to learn. One reason is that before we settle on what the commons is, I think we (meaning all of humans around the world) need to consider other types of knowledge, such as traditional knowledges. The purpose this is  not just to respect the traditions (important though that is). We need to learn about these knowledges not just to respect traditional peoples, but to address a gap in our own knowledge. That there is a gap is our wisdom, I would submit, is substantiated by the fact that all of our science and technology has brought us to global financial crisis and impending environmental disaster through climate change. To address this, we need to consider different ways of thinking. One example is a traditional concept that knowledge / wisdom belongs to its environment, not to us. . In Western science, we may like to take things out of their environment and study them separately, but without the ecosystem, the lifeforms we study would not exist.

2.    It seems reasonable to assume that a commons that is collectively built and protected by the largest possible number of people will be much stronger than a smaller commons designed by a few experts. I think the best way to do this is a welcoming, inclusive approach. When we can commit things straight away to the public domain, that’s great! But let’s not forget that free reading onscreen with absolutely no either rights or privileges is still a lot better than no access at all, or no access with paying a lot of money.

3.    There are many different types of materials that can be shared through the Internet, and communities who interact with these materials in different ways. Even within scholarly communication, there are the scholarly journal articles that scholars have traditionally given away, books which cost much more to produce and generally earn royalties for the writer, creative works which for some academics generate real income, and research data. Data would be close to useful if shared but not for re-use, while derivatives of the writers of a top scholar would almost certainly be less valuable than the original. In other words, the best and most useful openness in scholarship might well be a strong imperative to allow derivatives in some cases, and ND in other cases.

To take a non-scholarly example, I understand that some of the CC legal cases have involved music in bars. Right now the options are to allow commercial uses, or not. I wonder if it might make sense to musicians and bar-owners to have another option, noncommercial – except in bars, under the condition that the bar-owner provides patrons with a way of purchasing the musician’s CDs – perhaps by distributing a flyer highlighting the night’s music with websites for the musicians featured? To figure out how to do things like this, we need to facilitate conversations. This is what I mean to propose, a leaderful approach to articulating the commons.

best,

Heather Morrison, MLIS
Doctoral Candidate, Simon Fraser University School of Communication
http://pages.cmns.sfu.ca/heather-morrison/
The Imaginary Journal of Poetic Economics
http://poeticeconomics.blogspot.com

Join the discussion! See the Creative Commons Version 4.0 discussion launch message, and join the cc-licenses list and/or the fairly high volume cc-community list. (or view the lists’ archives from these links).

Creative Commons and Noncommercial: CC Version 4.0 discussion

As posted to the cc-licenses list December 20, 2011

A few thoughts towards the version 4.0 discussions, focusing on noncommercial:

Noncommercial, to me, is NOT the most restrictive of the CC license elements, except in a technical sense. This is because noncommercial – the public sphere – is the very essence of the commons. As a long-term open access advocate, my considered opinion is that the strongest license for open access to scholarly works is CC-BY-NC-SA, as this is the license that most protects open access downstream.  As we move towards the development of a global commons, we need to keep in mind the society that we live in at present. The kind of license that may be ideal in the society many of us are striving for can be a danger to the commons in the interim. For that matter, in a society where sharing is the default, we should question whether licenses will still be necessary. Even at present, while CC licenses are most helpful in an open access context, I would argue that licensing should not be necessary; what is more important for the longer term is developing and articulating a culture of

 sharing. CC licenses is only one of many approaches.

I understand that there is some genuine confusion about what constitutes commercial use, and that this may differ by region. For this reason, it may be helpful to further refine the license terms, and perhaps include two different types of noncommercial. Some thoughts towards this end:

–    Is selling the actual conten the common element understood by anyone who uses noncommercial? If so, is this clearly spelled out in the NC license?

–    Education – learning and teaching – should not be considered commercial. Here is a post with my attempt to articulate this:
http://poeticeconomics.blogspot.com/2011/12/education-is-public-good-not-commercial.html

–    Providing commercial services that support education is a genuine gray area, and one where there may be good reason to have two different licenses. Organizations that rely to some extent on print-on-demand services should be able to say no to this, while many creators who have no interest in bothering with this might want to say sure, go ahead. I strongly advocate for understanding the need for creators to make a living, and including those who share as much as they can while reserving some rights so that they can make a living in the commons. For this reason, I do not support efforts to remove those who choose noncommercial from CC.

–    Advertising is another gray area. Here, I am wondering whether a key issue is not so much advertising per se, as the extent, and whether reciprocal services are offered. For example, an internet search service that leads users to CC licensed content and in the process uses very limited amounts of content is a very different situation from a commercial outfit creating a mirror site of a whole journal, publishers’ offerings, or scholar’s blog, and selling advertising on the mirror site, or a pharmaceutical company printing off thousands of reprints for their salespeople to take to doctors’ offices. In the former case, I wonder if there are fair use / fair dealing arguments, at least in some jurisdictions. If not, would this give the corporate sector reason to argue for fair use / fair dealing exemptions? In the latter case, I think many creators do actually wish to prevent such commercial use, which may impact the moral integrity of the creator as well as potential economic impact.

Many thanks to CC for great work advancing the commons over the past few years, and for the opportunity to participate in discussions towards the next round.

Heather Morrison, MLIS
Doctoral Candidate, Simon Fraser University School of Communication
http://pages.cmns.sfu.ca/heather-morrison/
The Imaginary Journal of Poetic Economics
http://poeticeconomics.blogspot.com

PLoS ONE: Five Years, Many Milestones

PLoS ONE is five years old today – warmest congratulations to everyone who makes this journal a success! On Friday, we celebrated our landmark anniversary with cake and champagne alongside the current and former staff and Academic Editors who have worked so hard to support PLoS ONE.
Birthday cake

The lovely cake that we shared at PLoS ONE's 5th birthday party on Dec. 16, 2011

As we look back over the the past five years and forwards to the next five, it’s interesting to review the original motivation for PLoS ONE as articulated by one of our co-founders, Mike Eisen:
Scientists are eager to apply the awesome power of the Internet revolution to scientific communication, but have been stymied by the conservative nature of scientific publishing. PLoS ONE redefines what a scientific journal should be – eliminating needless barriers between authors and their audience and transforming the published literature from a static series of articles into a dynamic, interconnected, and constantly evolving resource for scientists and the public.

Where Have We Come From?

The journal launched on 20th December 2006 and the occasion was marked by a minor earthquake in the vicinity of our offices. The tremors might have been a first clue to the seismic changes that would soon occur in the publishing landscape.

The journal was formally conceived by the PLoS Founders in May 2005 (although it had been anticipated by them several years earlier in PLoS’s history). At the time, it was named PLoS Reports but, in the months before launch, it was renamed PLoS ONE to reflect the journal’s concept as being the one potential home for all science.

PLoS ONE represented the biggest step to date in PLoS’s attempt to reinvent the prevailing system of science communication that had existed since the 17th century. The idea was simple: to reduce the time it takes to publish papers by providing a single location that would guarantee acceptance to any research that had been conducted and reported adequately (as determined by objective editorial criteria). The ‘impact’ of the paper would then be decided by the readers (after publication), not by editors and reviewers before publication. In doing so, the journal consciously sought to separate the act of deciding whether or not a paper should be published (a decision which clearly needs to be made ‘pre-publication’), from any evaluation of the significance or importance of that article (a determination which is best made ‘post-publication’).

The growth of the PLoS ONE exceeded even the most optimistic predictions. In the first full year of publication it published 1,230 articles (making it larger in volume than all but about 100 journals) and, within 4 years, it became the largest peer-reviewed journal in the world. To date, PLoS ONE has published more than 28,700 articles and in 2011 alone it will publish almost 14,000 articles (meaning that approximately 1 in 60 of all articles indexed by PubMed for 2011 will have been published in PLoS ONE).

Although simple, the approach was radical and innovative (as demonstrated by the awards it went on to receive from the ALPSP (pdf) and SPARC). According to Heather Joseph, Executive Director of SPARC, since it opened its door to submissions in August 2006, PLoS ONE has become a “game changer” in the publishing industry.

One particular innovation that helped define PLoS ONE has been the provision of ‘Article Level Metrics’ on every published manuscript (something which is actually provided on all PLoS articles). With ALMs, in addition to ‘traditional’ metrics such as citations, authors could now see detailed information about the total views and downloads of their paper, as well as information about blog coverage, social bookmarks and so on. This program was introduced in 2009 at least in part to represent an alternative means of measuring an article’s merits post-publication and it continues to be developed by us and by others.

In addition to wide readership and high citation rates, articles published by PLoS ONE have always generated significant media coverage, for example appearing in The New York Times Science section 6 weeks running and even inspiring a Google Doodle on one occasion. Research on antiviral therapeutics, a possible fourth domain of life, and a group of articles that shares an inventory of species distribution and diversity in key global ocean areas are just a few of the most recent examples of the cutting edge research that has been covered by media outlets from around the world.

To what can we attribute this success?  First of all, PLoS ONE came from the Public Library of Science – a well-established, not-for-profit publisher that had already proven itself as a trusted venue for high quality peer-reviewed publications (PLoS Biology, PLoS Medicine, and the PLoS Community Journals) – clearly PLoS ONE would not have been as successful without the support and brand recognition that those journals provided. Secondly, it seemed that Academics are increasingly realizing that the ‘game’ of submitting to a top journal and working down a ‘rejection ladder’ until a journal accepts the paper is a waste of everyone’s time and resources, and that PLoS ONE circumvents that process. And thirdly, it feels like an idea whose ‘time has come’ – as the movement towards Open Access to all journal content grows, it seems inevitable that a publishing model such as PLoS ONE will emerge as one of the most effective ways to publish scientific content.

Of course, none of the reasons listed above would have mattered at all, were it not for the many thousands of Academic Editors, peer reviewers and staff members who have provided their time and energy for the journal. In particular, the journal would not exist without our authors – a vital stakeholder group who have been supportive since day one. To date, we have published the work of over 100,000 authors and we regularly receive outstanding feedback from them via our Annual Author Surveys.

In the early days, some critics felt that the journal risked becoming a “vanity press”, and that any journal that aimed to publish “anything publishable” would naturally become a venue for poor quality papers. What we saw instead were carefully reviewed papers that only made it into press if they met our objective criteria for sound science and reporting. This came about with virtually no pressure from within – indeed, one might say that the secret to our success is that we have allowed our independent Academic Editors full autonomy to decide what is ‘good enough’ to be published, and they have done so by applying the standards and norms of academia to our unique publication criteria. By combining this approach with a series of strict checks and balances at the point of submission, and a separation of the financial from the editorial aspects of the journal, we have proven to the scientific community that we are serious about our goal of changing the status quo of scientific communication, and that we intend to do so in a high quality, transparent, and ethical manner.

Of course, our success has not gone unnoticed and, in the past year or so, a slew of PLoS ONE ‘clones’ have been launched by other publishers (some of whom had been quite skeptical of the PLoS ONE model in years gone past). Although we welcomed Nature Publishing Group to the party with a somewhat tongue in cheek post (and with a request to improve their copyright license), it is a fact that we genuinely welcome these new entrants. We believe that more PLoS ONE clones are a good thing that will accelerate the move towards full Open Access, and away from the current system whereby articles are reviewed by a chain of journals for the sole purpose of stratifying them according to their perceived ‘impact’. We expect that more clones will launch in the coming years and, provided they employ full ‘CC BY’ copyright licenses, we will continue to encourage them.

Where are we going?

What does the future hold for PLoS ONE? Well, firstly we will continue to develop our systems to accommodate the kind of growth we have seen so far. This includes a root to branch overhaul of our publication platform (which will take some time to realize, but which is already underway); an improved submission and peer review system; and increasing numbers of Academic Editors and reviewers. Secondly, we plan to improve our Article Level Metrics to a point where they will provide genuinely valuable context about individual articles and hopefully be more widely used and understood by decision makers such as tenure committees and funding bodies. Thirdly, we will be developing new and powerful ways to navigate our platform. And finally, we intend to continue experimenting and pushing the boundaries of academic publishing – PLoS ONE has already proven to be be a phenomenon in the Academic Publishing world, but we feel it has tremendous potential to further change the way that scientific research is communicated!

We would like to use the occasion of our 5th birthday to thank everyone who has believed in PLoS ONE and given their time and energy to make it the success that it is today.

This blog post was written by Peter Binfield (Publisher of PLoS ONE & the PLoS Community Journals), Damian Pattinson (Executive Editor of PLoS ONE) and Jackie Thai (Editorial Manager of PLoS ONE), with support from Jennifer Laloup (Publications Manager of PLoS ONE) Nick Ellinwood (Sr. Publications Assistant of PLoS ONE) and Stacy Konkiel (Marketing Associate of PLoS ONE). For further information about PLoS ONE, you can view a video of Pete Binfield presenting information about the journal to the COASP 2011 meeting; read the PLoS Biology Editorial published on 20 Dec 2011; or read this paper (PDF) which was presented at ELPUB 2009.

The Open Access Movement is disorganized; this must not continue

I am going to have to reply to an article by Stevan Harnad (http://openaccess.eprints.org/index.php?/archives/862-guid.html ) where he argues inter alia that gratisOA (e.g. through Green, CC-restricted) rather than libreOA (e.g. through Gold, or CC-BY) should be adopted because:

“Note that many peer-reviewed journal article authors may not want to allow others to make and publish re-mixes of their verbatim texts”

“It is not at all it clear, however, that researchers want and need the right to make and publish re-mixes of other researchers’ verbatim texts.”

“Nor is it clear that all or most researchers want to allow others to make and publish re-mixes of their verbatim texts. “

“Hence Gratis OA clearly fulfils an important, universal and longstanding universal need of research and researchers.

This is a new, specious and highly damaging assertion that I have to challenge. If we restrict ourselves to STM publishing (where almost all of the funders’ efforts are concentrated) there is not a shred of evidence that any author wishes to restrict the re-use of their publications through licences. My analysis is:

  • Most scientists don’t care about Open Access. (Unfortunate, but we have to change that)
  • Of the ones that care, almost none care about licence details. If they are told it is “open Access” and fulfils the funders’ requirements then they will agree to anything. If the publisher has a page labelled “full Open Access – CC-NC – consistent with NIH funding” then they won’t think twice about what the licence is.
  • Of the ones who care I have never met a case of a scientist – and I want to restrict the discussion to STM – who wishes to restrict the use of their material through licences. No author says “You can look at my graph, but I am going to sue you if you reproduce it” (although some publishers, such as Wiley did in the Shelley Batts affair, and presumably still do).

My larger point, however, is that the OA movement is disorganised and because of that is ineffective. The movement :

  • Cannot agree on what “open access” means in practice
  • Appears to be composed of factions which while they agree on some things disagree on enough others to make this a serious problem.
  • Does not sufficiently alert its followers to serious issues
  • Has no simple central resource for public analysis of the major issues.
  • Is composed of isolated individuals and groups rather than acting on a concerted strategy
  • Spends (directly or indirectly) large amounts of public money (certainly hundreds of millions of dollars in author-side fees) without changing the balance of the market
  • Has no clear intermediate or end-goals

I accept that all movements have differences of opinion. This happened in the Open Source movement. Richard Stallman proposed a model of [UPDATED] Free Software with a strong political/moral basis. Software should be free and should be a tool of liberation, and hence the viral GPL (similar to CC-BY-SA). Others see software as a public good where optimum values is obtained by requiring libre publication but not restricting downstream works to this model (similar to CC-BY). These coexist fairly well in two families – copyleft and copyright. There are adherents of both – my own approach is copyright where anyone can use my software downstream for whatever purpose save only crediting the authors (and with ArtisticLicence requiring forks to use a different name).

The point relevant to Open Access is that this market / movement is regulated. They have formed The Open Source Initiative (OSI, http://www.opensource.org/) which

“is a non-profit corporation with global scope formed to educate about and advocate for the benefits of open source and to build bridges among different constituencies in the open source community.”

“One of our most important activities is as a standards body, maintaining the Open Source Definition for the good of the community. The Open Source Initiative Approved License trademark and program creates a nexus of trust around which developers, users, corporations and governments can organize open source cooperation.”

This is critical.

When I find an Open Source program, I know what I am getting. When I find an Open Access paper I haven’t a clue what I am getting. When I publish my code as Open Source I can’t make up the rules. I must have a licence and it must be approved by OSI (they have a long list of conformant licences and discuss why some other licences are non-conformant.

The Open Source movement decided early on that the Non-Commercial clause in licences was inappropriate / incorrect / unworkable and NO OSI licences allow such restrictions. This is one of the great achievements of OpenSource

And it’s policed. When I published some GPL-licenced CML-generating code I added the constraint “if you alter this code you cannot claim the result is CML”. I was contacted by the FSF and told this was incompatible with the GPL. So I changed it.

In short the OS community cares about what Open Source is, how it is defined, how it is labelled and whether the practice conforms to the requirements.

By contrast the OA community does not care about these things.

That’s a harsh thing to say, and there are many individuals and organizations who do care. But as a whole there is no coherent place where the OA movement expresses its concern and where concerns can be raised.

The problem can be expressed simply. “Open Access” was defined in the Budapest and other declarations. Budapest (see http://www.earlham.edu/~peters/fos/boaifaq.htm ) says:

“By ‘open access’ to this literature, we mean its free availability on the public internet, permitting any users to read, download, copy, distribute, print, search, or link to the full texts of these articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose, without financial, legal, or technical barriers other than those inseparable from gaining access to the internet itself. The only constraint on reproduction and distribution, and the only role for copyright in this domain, should be to give authors control over the integrity of their work and the right to be properly acknowledged and cited.”

Everyone (including Stevan) would agree that this is now consistent with what is (belatedly) being labelled as OA-libre. Note that Stevan was a signatory to this definition of Open Access.

My immediate concern is that unless we organize the definition, labelling and practice of Open Access we are simply giving OA-opponents or OA-doubters carte blanche to do whatever they like without being brought to account. We are throwing away hundreds of millions of dollars in a wasteful fashion. We are exposing people to legal action because the terms are undefined.

In short “Open Access” is a legally meaningless term. And, whether you like it or not, the law matters. If you try to re-use non-libre material because it was labelled “Open Access” you could still end up in court.

As a UK taxpayer I fund scientists to do medical research (through the MRC). The MRC has decided (rightly) that the results of scientific research should be made Open. But they are not Open according to the BOAI declaration. Every paper costs taxpayers 3000 USD to publish and we do not get our money’s worth.

The fundamental problem is that this is an unregulated micro-monopoly market and no-one really cares. The BBC discuss today about how some bus operators had 70% of the market. That means they have an effective monopoly. They can run the services they want, not what we need. The only possible constraint is government regulation.

Scientific publishing is an unregulated pseudo-monopoly market where the publishers make the rules and make the prices. The bargaining (such as it is) comes from:

  • Libraries (who are fragmented, and who care only about price, not rights)
  • Funders (who are fragmented across disciplines and countries)
  • Small scholarly organisations such as SPARC. (BTW I thought SPARC was advocating for OA-libre but I can’t see much sign)
  • Individuals such as Stevan, Peter Suber, Alma Swan, with relatively little coordination and no bargaining power

These have been ineffectual in creating a coherent OA market. BMC and PLoS have been very useful in showing that OA is possible on several fronts – without them I think OA in STM would be effectively dead.

So the OA movement desperately needs coordination. Coordination of:

  • Terminology
  • labelling
  • Dissemination of information and coordinated search
  • Advocacy
  • Enforcement

It also needs to coordinate on price-bargaining in a more effective way than libraries do at the moment. We (our governments, our charities, our universities) provide the money but they don’t coordinate how it’s spent or what value they get.

So my simple proposal is that we need an Open Access Institute/initiative similar to the OSI for Open Source. It would cost a small fraction of what we already pay in unregulated Open Access fees (who for example challenges the 5000 USD that Nature charges for a hybrid paper). It costs more to run a car than to publish one hybrid paper per year in Nature.

Stevan’s response will be: “let’s concentrate on getting all papers published as Green before we worry about anything else”. I don’t agree with this and I will explain more later. The OAI will have to accommodate such differences of opinion and label the approaches properly rather than allowing everyone to redefine Open Access as they think best or trying to get everyone under a common ultra-fuzzy label.

[UPDATE: I typed “Open Source” instead of “Free Software” by mistake and apologize to RMS for the slip.]

 

Gratis Open Access Vs. Libre Open Access

The following commentary on Mike Carroll’s GOAL posting on Taylor & Francis’s press release is intended neither as an endorsement nor as a critique of T&F’s (or any publisher’s) gold OA offerings. It is just an attempt to clarify an important point about OA needs from the standpoint of researchers, who are both the providers and the primary intended users of peer-reviewed research articles:


MC: “[The T&F] press release is misleading and should be corrected. You say that T&F is now publishing ” fully Open Access journals”, but unless I’ve misread the licensing arrangements this simply is not the case.”

As far as I know, there is no such thing as “fully OA.”

There is Gratis OA and there is Libre OA:

T&F are selling Gratis OA. That means (1) immediate, permanent online access, free for all on the Web — to peer reviewed research journal articles.

(Note that along with free online access, the following also automatically comes with the territory:

(2) clicking,
(3) on-screen access,
(4) linking,
(5) downloading,
(6) local storage,
(7) local print-off of hard copy, and
(8) local data-mining by the user,

as well as global harvesting and search by engines like google.)

Mike Carroll is speaking about Libre OA, which means immediate, permanent online access, free for all on the Web (i.e., Gratis OA) plus certain further re-use, re-publication and re-mix rights.

(Note that many peer-reviewed journal article authors may not want to allow others to make and publish re-mixes of their verbatim texts. Journal article texts are not like music, videos, software or even research data, out of which creative modifications and remixes can be valuable. All scholars and scientists desire that their findings and ideas should be accessed, re-used, applied and built-upon, but not necessarily that their words should be re-mixed or even re-published — just accessible free for all online, immediately and permanently.)

Today, the only peer-reviewed research journal articles to which researchers have access are those to which their institutions can afford subscription/licensed access. That means research is losing the uptake and impact of all those potential users who are denied access to it.

All researchers want free online access to all research they may need to consult or use, not just the research to which their institutions can afford subscription access.

All researchers want their research to be accessible to all researchers who may need to consult or use it, not just to those whose institutions can afford subscription access.

It is not at all it clear, however, that researchers want and need the right to make and publish re-mixes of other researchers’ verbatim texts.

Nor is it clear that all or most researchers want to allow others to make and publish re-mixes of their verbatim texts.

Hence Gratis OA clearly fulfills an important, universal and longstanding universal need of research and researchers.

But it is not at all clear that this is true of Libre OA — at least not for the very special case of the peer-reviewed research journal article texts that are the primary, specific target content of the OA movement.

Hence it is not at all clear that there is anything T&F need to correct.

MC: “A fully open access journal is one that publishes on the web without delay and which gives readers the full set of reuse rights conditioned only on the requirement that users provide proper attribution.”

I believe that is not the definition of a fully OA journal but of a Libre OA journal.

MC: “T&F’s “Open” program and “Open Select” offer pseudo open access.”

Gratis OA is not pseudo open access. It is the difference between night and day for researchers who are denied access to the publisher’s version of record because their institutions cannot afford access.

And night is the current state of affairs for 80% of research, and has been for the past 20 years, even though the means to provide Gratis OA (fully) have been available for at least that long.

Gratis OA can be provided in two different ways:

Gold OA journals like the T&F journals offer Gratis Gold OA, for which the author — meaning the author’s institution or funder — must pay a publication fee. But most journals are not Gold OA journals, and hence the potential funds to pay for Gold OA are still locked up in institutional subscriptions to non-OA journals.

That means that not only can most research not be made OA by publishing it in Gold OA journals (since most journals are non-OA), but even for the Gold OA journals, the money to pay the publication fees (of those,like T&F, that charge a publication fee) is tied up in paying for non-OA subscription journals).

(This is equally true irrespective of whether the Gold OA journals offer Gratis OA or Libre OA.)

The second way to provide Gratis OA is through Green OA self-archiving (i.e., depositing the author’s peer-reviewed final draft in the author’s Institutional OA Repository immediately upon acceptance for publication).

Unlike Gold OA, Green OA does not require paying a publication fee. And Green OA can be provided for all articles, not just articles published in Gold OA journals.

And, most important, Green OA self-archiving can be mandated by researchers’ institutions and funders, whereas publishing in Gold OA journals cannot be mandated. (Publishers cannot be compelled to convert to Gold OA; reserchers cannot be told which journal to publish in; and the money to pay for Gold OA is locked into journal subscriptions, which cannot be cancelled until and unless the contents of those subscription journals are otherwise accessible.)

Most Green OA (and Green OA mandates) are Gratis Green OA — free online access.

But that is still the difference between night and day for researchers.

And Gratis Green OA self-archiving (but not Libre Green OA self-archiving) is already endorsed by over 60% of journals — including the top journals in most fields.

So please let us not belittle Gratis OA as not “fully” OA (and certainly not before we have it!). Let us provide it, and mandate providing it.

And let us not keep focusing on Gold OA: The fastest, surest and cheapest way to full OA is for institutions and funders to mandate Gratis Green OA self-archiving.

(And, as a bonus, that’s also the fastest, surest and cheapest way to Gold OA as well as Libre OA, thereafter.)

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.

Harnad, S. (2010) The Immediate Practical Implication of the Houghton Report: Provide Green Open Access Now. Prometheus 28 (1): 55-59.
ABSTRACT: Among the many important implications of Houghton et al?s (2009) timely and illuminating JISC analysis of the costs and benefits of providing free online access (?Open Access,? OA) to peer-reviewed scholarly and scientific journal articles one stands out as particularly compelling: It would yield a forty-fold benefit/cost ratio if the world?s peer-reviewed research were all self-archived by its authors so as to make it OA. There are many assumptions and estimates underlying Houghton et al?s modelling and analyses, but they are for the most part very reasonable and even conservative. This makes their strongest practical implication particularly striking: The 40-fold benefit/cost ratio of providing Green OA is an order of magnitude greater than all the other potential combinations of alternatives to the status quo analyzed and compared by Houghton et al. This outcome is all the more significant in light of the fact that self-archiving already rests entirely in the hands of the research community (researchers, their institutions and their funders), whereas OA publishing depends on the publishing community. Perhaps most remarkable is the fact that this outcome emerged from studies that approached the problem primarily from the standpoint of the economics of publication rather than the economics of research.

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.

MC: “Could you please explain why T&F needs to reserve substantial reuse rights after the author or her funder has paid for the costs of publication?”

This question is valid — but it is beside the point for the first and most important objective of the OA movement (still not reached in over a decade of trying), namely, immediate, permanent online access, free for all on the Web (i.e., Gratis OA).

T&F’s Gratis Gold OA would provide that; but even if T&F provided Libre Gold OA, that would not be the fastest, surest or cheapest way to reach full OA — by which I mean free online access to all 2.5 million articles published annually in the planet’s 25,000 peer-reviewed journals. See the growth curves in Richard Poynder’s “Open Access By Numbers.”

Free online access is what research and researchers need most. Mandating Gratis Green OA self-archiving will provide just that — and Gold OA, and as much Libre OA as researchers actually need and want — will be not far behind.

But not if we keep over-reaching for Libre OA or Gold OA instead of providing and mandating Gratis Green OA.

MC: “If your response is that the article processing charge does not represent the full cost of publication, what charge would? Why aren’t authors given the option to purchase full open access?”

Even the money to pay for Gratis Gold OA is still tied up in subscriptions, while subscriptions are still being paid for (and thereby paying for publication costs in full).

And mandating Gratis Green OA can provide free access at no extra cost, while subscriptions are still being paid for (and thereby paying for publication costs in full).

So why think about paying even more for Libre Gold OA today, when it’s not at all clear that researchers want or need it — whereas it’s certain that they want and need Gratis OA (and they don’t yet have it, even though it’s fully within reach)?

Stevan Harnad
EnablingOpenScholarship

American Scientist Open Access Forum Has Migrated to GOAL (Global Open Access List)

The straw poll on whether or not to continue the American Scientist Open Access (AmSci) Forum (and if so, who should be the new moderator) is complete (the full results are reproduced at the end of this message).

The vote is for (1) continuing the Forum, under (2) the moderatorship of Richard Poynder.

The AmSci list has now been migrated to http://mailman.ecs.soton.ac.uk/mailman/listinfo/goal where the BOAI list is also being hosted.

AmSci Forum members need not re-subscribe. All subscriptions have been automatically transferred to the new host site.

The name of the list has been changed to the Global Open Access List (GOAL) to reflect the fact that Open Access is no longer just an American or a Scientific matter. It has become a global movement.

The old AmSci Forum Archives (1998-2011) will stay up at the Sigma Xi site (indefinitely, I hope — though we do have copies of the entire archive).

The new GOAL archive is at: http://mailman.ecs.soton.ac.uk/pipermail/goal/

Stevan Harnad


Below are the complete results of Straw Poll on whether to continue the Forum, and on who should be the new moderator:

AGAINST CONTINUING AMSCI:

ARIF JINHA: I believe it would be better to have one forum, the BOAI. This forum has developed a doctrinal bias defined by the values and personality of its leadership. Though the leadership is to be commended for its credibility and vigour, it is not without its blind spots. It has not always OPEN to a diversity of perspectives. AMSCI is driven by assertive and competitive advocacy for mandates over Gold OA publishing. The rush to conclusion on the right path is premature and overly authoritative in its expression, therefore it is alienating. In truth, we have only really got started with the web in the last 10 years and authority is completely flattened by the learning curve. The BOAI is much wider in its representation of Open Access alternatives, it is therefore more neutral as well as having a wider reach for the promotion of Green OA. It means less duplication and less work devoted to instant communication, giving more time to develop a rigorous and scientific approach to meta-scholarship in the digital age.

FOR CONTINUING AMSCI:

DANA ROTH: I would disagree with Arif Jinha, in that it is the ‘assertive and competitive advocacy for mandates over Gold OA publishing’ that make AMSCI such an interesting listserv.

SUBBIAH ARUNACHALAM: First, I wish to express my grateful thanks to Stevan for all that he has done so far, and in particular for moderating this Forum for so long and so well. That he will continue to devote much of his time to promoting open access and institutional repositories gives me strength to do the same. Second, if Richard Poynder agrees (or if we could persuade him) to moderate this list, there is nothing like it. The baton would have moved to safe hands. Not only he has the stamina of a long distance runner, but he is also endowed with the qualities needed for a moderator. He is knowledgeable and levelheaded. Welcome Richard!

DOMINIQUE BABINI: Discussions and ideas in this forum are also inspiring for regional OA forums and lists, e.g., the Latin America and the Caribbean Open Access List (LLAAR, in Spanish). Thank you, Stevan, for your dedication as moderator all these years, and especially for your new OA initiatives and ideas. Thank you for your Skype contribution at the OA Experts Meeting last week in UNESCO headquarters, where we missed you [in person].  I also support Richard Poynder as [new] moderator for this Forum. 

MICHAEL E. SMITH: I am in favor of continuing the list, and either of the people you mentioned as potential moderators would be good choices.

PAOLA GARGIULO: I also agree that the list should continue. I’m in favour or Richard Poynder as moderator. Hope you will continue to contribute.

PETER SUBER: If Richard is willing to moderate, I vote for him.  I second Alma’s reasons why Richard would do well in this role.  I second Arthur’s best wishes to you, and I second (or third) Barbara and Hélène’s tribute to your work.  Finally, as the former moderator of SOAF and BOAI, I welcome you to civilian life.  It’s amazing what one can do when one has more time to do it.

BERNARD RENTIER: I vote for Richard Poynder. The excellence of his critical and fair papers speaks for his designation. If he is willing to do that, I am sure he will be an outstanding moderator. And that this will let Stevan be even more tirelessly to the point in every debate!

TOM COCHRANE: The value of the Forum cannot be overstated. It has provided a unique service in assessing the events and health of OA developments. It would be a regressive step in several ways if it were to fall over. It is not too much to claim that its way of charting developments, alerting readers to new issues, identifying useful research and work on OA, and in your hands, reminding its readership of the main issues ? all these have had a direct impact on practical developments. This has occurred to a degree that no single one of us ? from whatever part of the world –  can comprehensively take in. But believe me, it has played a vital role. But individual workloads need to be shared, and we at QUT understand your reasoning. We are happy with the Richard Poynder suggestion.

ELOY RODRIGUES: I also support Richard Poynder for moderator. I strongly support the continuation of the AmSci Forum, and I regret your decision of stepping down as moderator (even though I understand your reasons, and I do hope that it will turn out the right decision for you, and your efforts for OA progress). Thanks for your tireless work for Open Access! All the best (from Rio de Janeiro, where I was also archivangilizing for ID/OA mandates, at the Portuguese-Brazilian OA conference).

KEITH JEFFERY: I am sorry it has come to this; you know I support your point of view and moderation does require correction of misconceptions as well as just posting. I wish the Amsci list to continue and Richard is, of course, an excellent choice as future moderator.

ANDREW A ADAMS: I am in favour of the forum continuing to operate. I feel Richard would make an excellent new moderator.

PIPPA SMART: I am in favour of the forum continuing and would be very happy for Richard Poynder to moderate.

MARC COUTURE: I definitely wish the forum to continue. I may be only the occasional contributor, but I’ve always been a very steady reader. As to you not being the moderator anymore, I think it’s even a good thing, not because I share the opinion that a moderator should be neutral and discreet, but because it will spare you some precious time you could devote to useful purposes, OA-related or not. Note that I assume we will continue to benefit, in the forum, from the seemingly inexhaustible energy and the flawless, razor-sharp logic of our “weary” archivangelist.

BARRY MAHON: As a long time stirring stick in the OA (hard to know what word to use to describe it) world, and having crossed swords with both Stevan and Richard over the years, I have a heavy heart in accepting Stevan’s decision but an uplift that Richard has volunteered. It will, I wish, go on….and I’ll be there, or here, whichever is the more appropriate.

JEAN-CLAUDE GUÉDON: I also think this list should go on. And  having Richard or Thomas moderate is a good idea too.

BOB PARKS: Congratulations on stepping down. I hope it gives you more time to pursue OA!!! Either Krichel or Poynder would be a good moderator.  I fear that Krichel is over committed.

HEATHER MORRISON: Thanks very much for moderating the list all these years! I hope that the list will continue, and would support either Richard Poynder or Thomas Krichel as moderators.

SALLY MORRIS: The support for Richard as moderator of the continuing list seems clear. We really don’t need to see all the messages – I thought that was the point of keeping them off the list?

THOMAS KRICHEL: I think it should continue, as it appears to be the largest and most active forum.  I volunteer to do it?.  If Richard wants to do it, I’d be happy not to.

RICHARD POYNDER: Well I certainly vote for it to continue. I would even put my name down for the moderator’s hat if it was felt appropriate for a journalist to run such a forum, and people believed I could do the job adequately

ALMA SWAN: I am writing to nominate Richard Poynder as the new moderator for the AmSci Forum. I think he brings the right qualities – amongst them honesty, fairness, intellectual curiousness and efficiency – and is hugely respected as an independent, critical thinker on the issues that AmSci covers. I want the Forum to continue because it is a real discussion list rather than a bulletin board?

HELENE BOSC: In memory of the remarkable work done by Stevan Harnad for Open Access through this list, during 14 years, I wish it continues… Richard Poynder would be a perfect moderator!

BARBARA KIRSOP: If Stevan feels he can better operate in support of OA not as the moderator, then it would be great indeed if Richard Poynder would adopt the mantle. I think AMSCI should continue. I am somewhat in favour of a name change to highlight OA rather than the US – a name change could be a mini-re-launch perhaps and bring in new contributors – a fitting tribute to Stevan’s past efforts.

ARTHUR SALE: May I wish you the best as non-moderator. It is the right decision for you, I think. This may be a shock to you that I think that it is a plus, but I think we need to get new ideas into the OA transition, and you have done your bit and a lot more? and perhaps I can even convince you eventually that the Titanium Road is the way to go now! You will be bombarded with messages begging you to reconsider, but I do think it is the right decision. Then you can enjoy being yourself without constraint. No one person can bear the weight of the world, not even Atlas.

IRYNA KUCHMA: The AmSci Open Access Forum is an active discussion forum (SOAF and BOAI are more like the announcement lists) and my answer is (1) definitely to continue. It’s sad that you’ve decided to step down as a moderator. I wish I could help you with moderating it, but I am travelling a lot and sometimes not able to moderate the BOAI on time?. Hope you will find the ways to continue.

EUGENE GARFIELD: When I think about Stevan Harnad another information pioneer comes to mind. The Belgian documentalist Paul Otlet. His collaborator Henri LaFontaine,  received the Nobel Peace Prize. That’s the kind of recognition that Stevan deserves.

MICHAEL KURTZ: I liked that AMSCI reflected your point of view, I value that,
and expect I will always.  I hope I will always be able to discover
it, perhaps you will frequently post.

THIERRY CHANIER : First of all, I would like to deeply thank Stevan  for his  continuous work over these more than 10 years. This forum is a very important place where supporters of OA can find information, and share their actions. I would be happy if Richard Poynder becomes our moderator. As Barbara (Kirsop) put it : it may be time to change the name of our forum, forget the American qualifier in order  to reflect its international wider status.

TONY HEY: I think that Stevan must take some credit from the UK Government’s decision to insist on open access to publications and data … Well done Stevan and thanks for all your tireless proselytizing on behalf of open access!

New policy announced by David Willetts to make research freely available challenges business models of academic publishers

David Willetts, the science minister, said the government wants to move to open access while protecting peer review.
Science minister David Willetts David Willetts, the science minister, said the government wants to move to open access while protecting peer review. Photograph: Anna Gordon/Guardian
The government has signalled a revolution in scientific publishing by throwing its weight behind the idea that all publicly funded scientific research must be published in open-access journals.
The policy is in the government document Innovation and Research Strategy for Growth published on Monday, which also includes plans for a series of cash prizes for teams to solve specific scientific challenges and a new £75m fund for small businesses to develop their ideas into commercial products.
The commitment to making publicly funded research free to access is a direct challenge to the business models of the big academic publishing companies, which are the gatekeepers for the majority of high-quality scientific research. Previous attempts by open access publishers to break this stranglehold over the dissemination of scientific results have largely failed.
The strategy sums up the coalition’s work in the past 18 months on reshaping and developing the UK’s science base in the face of the economic crisis. It comes a few days after David Cameron made a speech calling for increased research collaboration between the NHS and the life sciences industry, which included a £180m “catalyst fund” for universities and companies to help develop projects until they attract outside investment.
“Our starting point is a commitment by the coalition to transparency and open access to publicly funded data,” said science minister David Willetts at a briefing to launch the government strategy. “Just writing my book, it was striking how you’d start researching a document and you’d soon hit a paywall and find that you had to subscribe when, sometimes, the work had come from research council projects.”
He added: “We set out very clearly in the document today our commitment to open access. We want to move to open access, but in a way that ensures that peer review and publishing continues as a function. It needs to be paid for somehow. One of the clear options is to shift to a system from which university libraries pay for journals to one in which the academics pay to publish. But then you need to shift the funding so that the academics could afford to pay to publish.”
He cited the example of the particle physics community in the US, which has switched from traditional scientific publishing to scientists paying to have their work appear in open-access journals. “They did that, I am told, as a switchover and the same amount of money was flowed through in a different way. It was clearly to retain the viability of learned journals in particle physics and, in turn, sustaining the whole system with peer review.”
Dame Janet Finch, a former vice chancellor of Keele University, has been asked by Willetts to investigate how a similar open-access scheme might work in the UK. “We have to let her, working with the publishing industry and the research councils, find a way forward,” said Willetts. “The publishing industry recognise the direction in which things are going and we have to work out a new model together.”
Finch is expected to report in the first half of 2012 but, meanwhile, Willetts said the UK research councils would be reminded that research papers from the work they fund should be as widely available as possible.
Finding new ways to solve pressing scientific challenges was another element of the science and engineering strategy. Willetts said that the government would invest up to £250,000 in a series of prizes that would be awarded to groups of people who could solve specific scientific problems outlined by organisations including the National Endowment for Science, Technology and the Arts (Nesta). “[Prizes] were used a lot in the 19th century and they rather fell out of favour,” he said. “They’ve been rejuvenated in the US and we’re keen to work with Nesta, which will set up a centre of expertise in this.”
In the 18th century, the British government offered a series of prizes to anyone who could develop a practical method of determining a ship’s longitude at sea. It led to a flurry of experiments and the development of the marine chronometer by John Harrison.
More recently, the Ansari X-Prize offered $10m to the first team to build a reusable manned spacecraft and was won in 2004 by Burt Rutan’s company Scaled Composites with its development of SpaceShipOne, subsequently the basis of the vehicles that will be used by Richard Branson’s Virgin Galactic. Unclaimed X-prizes are also available for building fuel-efficient cars and mass-sequencing genomes.
David Bott, director of innovation programmes at the Technology Strategy Board, which will work with Nesta to develop the prizes, said: “If you set the challenge in the right way, you unlock the creativity of the community rather than limiting it with our own lack of it.” He added that prizes could be used to drive people to work together, rather than in traditional silos.
The £75m fund for small and medium-sized businesses resurrects a similar scheme run by the now-defunct regional development agencies. It will offer companies money to engage in proof-of-concept R&D projects from which new products and services could emerge.
“If you look at the overall economic strategy of the government, it is about getting back to rebalancing the economy, stimulating growth,” said business secretary Vince Cable. “Much of that is going to come through from the SME [small and medium enterprise] sector, that’s where jobs are going to be created.”
Imran Khan, director of the Campaign for Science and Engineering, said the government strategy was “an important and comprehensive analysis of the UK innovation ecosystem”.
“We welcome the government’s emphasis on attracting innovative businesses to the UK, and initiatives such as the new innovation inducement prizes,” said Khan. “We call on the government to build on this start by setting aside serious funding to kickstart the sector and turn it into a game changer for UK economic growth – for instance, by setting aside the proceeds from the forthcoming 4G mobile spectrum auction to be reinvested in science, engineering, and innovation.”

New policy announced by David Willetts to make research freely available challenges business models of academic publishers

David Willetts, the science minister, said the government wants to move to open access while protecting peer review.
Science minister David Willetts David Willetts, the science minister, said the government wants to move to open access while protecting peer review. Photograph: Anna Gordon/Guardian
The government has signalled a revolution in scientific publishing by throwing its weight behind the idea that all publicly funded scientific research must be published in openaccess journals.
The policy is in the government document Innovation and Research Strategy for Growth published on Monday, which also includes plans for a series of cash prizes for teams to solve specific scientific challenges and a new £75m fund for small businesses to develop their ideas into commercial products.
The commitment to making publicly funded research free to access is a direct challenge to the business models of the big academic publishing companies, which are the gatekeepers for the majority of high-quality scientific research. Previous attempts by open access publishers to break this stranglehold over the dissemination of scientific results have largely failed.
The strategy sums up the coalition’s work in the past 18 months on reshaping and developing the UK’s science base in the face of the economic crisis. It comes a few days after David Cameron made a speech calling for increased research collaboration between the NHS and the life sciences industry, which included a £180m “catalyst fund” for universities and companies to help develop projects until they attract outside investment.
“Our starting point is a commitment by the coalition to transparency and open access to publicly funded data,” said science minister David Willetts at a briefing to launch the government strategy. “Just writing my book, it was striking how you’d start researching a document and you’d soon hit a paywall and find that you had to subscribe when, sometimes, the work had come from research council projects.”
He added: “We set out very clearly in the document today our commitment to open access. We want to move to open access, but in a way that ensures that peer review and publishing continues as a function. It needs to be paid for somehow. One of the clear options is to shift to a system from which university libraries pay for journals to one in which the academics pay to publish. But then you need to shift the funding so that the academics could afford to pay to publish.”
He cited the example of the particle physics community in the US, which has switched from traditional scientific publishing to scientists paying to have their work appear in openaccess journals. “They did that, I am told, as a switchover and the same amount of money was flowed through in a different way. It was clearly to retain the viability of learned journals in particle physics and, in turn, sustaining the whole system with peer review.”
Dame Janet Finch, a former vice chancellor of Keele University, has been asked by Willetts to investigate how a similar openaccess scheme might work in the UK. “We have to let her, working with the publishing industry and the research councils, find a way forward,” said Willetts. “The publishing industry recognise the direction in which things are going and we have to work out a new model together.”
Finch is expected to report in the first half of 2012 but, meanwhile, Willetts said the UK research councils would be reminded that research papers from the work they fund should be as widely available as possible.
Finding new ways to solve pressing scientific challenges was another element of the science and engineering strategy. Willetts said that the government would invest up to £250,000 in a series of prizes that would be awarded to groups of people who could solve specific scientific problems outlined by organisations including the National Endowment for Science, Technology and the Arts (Nesta). “[Prizes] were used a lot in the 19th century and they rather fell out of favour,” he said. “They’ve been rejuvenated in the US and we’re keen to work with Nesta, which will set up a centre of expertise in this.”
In the 18th century, the British government offered a series of prizes to anyone who could develop a practical method of determining a ship’s longitude at sea. It led to a flurry of experiments and the development of the marine chronometer by John Harrison.
More recently, the Ansari X-Prize offered $10m to the first team to build a reusable manned spacecraft and was won in 2004 by Burt Rutan’s company Scaled Composites with its development of SpaceShipOne, subsequently the basis of the vehicles that will be used by Richard Branson’s Virgin Galactic. Unclaimed X-prizes are also available for building fuel-efficient cars and mass-sequencing genomes.
David Bott, director of innovation programmes at the Technology Strategy Board, which will work with Nesta to develop the prizes, said: “If you set the challenge in the right way, you unlock the creativity of the community rather than limiting it with our own lack of it.” He added that prizes could be used to drive people to work together, rather than in traditional silos.
The £75m fund for small and medium-sized businesses resurrects a similar scheme run by the now-defunct regional development agencies. It will offer companies money to engage in proof-of-concept R&D projects from which new products and services could emerge.
“If you look at the overall economic strategy of the government, it is about getting back to rebalancing the economy, stimulating growth,” said business secretary Vince Cable. “Much of that is going to come through from the SME [small and medium enterprise] sector, that’s where jobs are going to be created.”
Imran Khan, director of the Campaign for Science and Engineering, said the government strategy was “an important and comprehensive analysis of the UK innovation ecosystem”.
“We welcome the government’s emphasis on attracting innovative businesses to the UK, and initiatives such as the new innovation inducement prizes,” said Khan. “We call on the government to build on this start by setting aside serious funding to kickstart the sector and turn it into a game changer for UK economic growth – for instance, by setting aside the proceeds from the forthcoming 4G mobile spectrum auction to be reinvested in science, engineering, and innovation.”

PLoS ONE News and Blog Round-Up

This month in PLoS ONE: Bathroom germs, yawn contagion and more!

The  specific locations and breeds of bacteria found in public restrooms was recently revealed when researchers at the University of Colorado took samples from public restrooms on campus, and used a genetic sequencing tool to identify 19 of the most common bacteria. This article was covered by CBS News, Scientific American and NPR.

Researchers from the University of Pisa explore possible causes associated with yawn contagion. The results indicate that yawns are most contagious between family members, followed by friends and then acquaintances.  The scientists attribute this phenomenon to emotional bonds, suggesting that we empathize and thus mimic, individuals we know better. The BBC, Fox News and International Business Times covered this article.

An archaeological excursion to Dhofar, Oman reveals artifacts dating back roughly 74,000 to 128,000 years. This new evidence suggests that the exodus from Africa may have occurred significantly earlier than previously estimated, and that early humans traveled inland, across valleys, rather than along the coast line. This article was covered by CBS News, ABC News and The Examiner . The image above comes from Figure 6 in the manuscript and shows Nubian Type 1 cores from Aybut Al Auwal.

Roughly 7,500 feet under the sea, a team of scientists capture video of the recently discovered ‘Yeti Crab’ (Kiwa puravida). The lack of sun at extreme ocean depths has forced many species to develop unique feeding methods. The Yeti Crab hosts nutrient-rich bacteria on its claws, and waves them near hydrothermal vents, that release hydrogen sulfide and methane. The bacteria ‘feed’ on these compounds, which the Yeti Crab then consumes. Wired, National Geographic and Scientific American covered this article.

For more in-depth coverage on news and blog articles about PLoS ONE papers, please visit our Media Tracking Project.

LBM2011 Singapore; a milestone in Text-mining and Natural Language Processing, OSCAR, OPSIN, ChemicalTagger

Yesterday I gave an invited plenary lecture at http://lbm2011.biopathway.org/The Fourth International Symposium
on Languages in Biology and Medicine (LBM 2011) Nanyang Technological University, Singapore .14th and 15th December, 2011

The meeting was on Natural Language Processing – using computational techniques to “understand” science in publications and get machines to help us with the often boring and error-prone part of extracting detailed meaning. It’s an exciting field and progress is steady.

The meeting itself was great. Very high standard of talks. I understood most of them both in their intent and their methodology. And a really great atmosphere – ca 30 people in a relaxed atmosphere and prepared to exchange ideas.

I realised the night before that this lecture represented a milestone in my NLP/TextMining career so I took considerable time to adjust it to the audience and the occasion. Normally in my lectures I don’t know what I am going to say (and choose from HTML slides). This time I wanted to pay tribute to all the people who have contributed so much over the years and have brought us to this milestone. So here’s the second slide of my talk:

(I’ve only included each person once). If there is anyone who is omitted let me know.

I’d like first to thank the people in the Centre I have had the chance to work with (including of course Jim Downing). They’ve been unusual in a good way in that they haven’t been obsessed with academic competition. They have worked as a team, creating joint products and they have also put a high premium of creating things that are useful and work. That’s not so common in academia and this group has traded H-indexes for software and systems that are out there and being used. If only academia gave credit for that they would be stars. That time will come.

I’m proud to say that they’ve all joined high-tech UK companies which have to be part of our future. Making digital things that people want to buy. Thermodynamics owes more to the steam engine than the steam engine to thermodynamics. We should be learning from the companies that this group has gone into. I’m proud of the software engineering that Jim introduced and that the group adopted without mandates or coercion but simply because it was so evidently right.

That pride has gone into the three products, OPSIN, OSCAR4 and ChemicalTagger.

In a real sense we can draw a line under them. They work, they are “out there” and they are used. We don’t know how much they are used because people are so secretive. I’d guess that there are probably 20-100 installations of OSCAR. We get little feedback because the software works. (We’ve got no formal feedback from OSCAR2 and we know that it’s widely used).

And I’m going to be unusually boastful, because it’s for them, not me:

OPSIN, OSCAR and ChemicalTagger are the best in their class that we know about. There may be private confidential programs that we don’t know about, but hey! Because they are Open Source people don’t try to compete and duplicate the functionality. They re-use it. So OSCAR is used in Bioclipse, used at EBI for their chemical databases and ontology. Open source doesn’t necessary make a program functionally better per se but it allows other people to work on it. More testers, more bugs discovered, more progress.

Why can we draw a line?

Because essentially we have done what we needed to. We’ve built them as frameworks and we are confident that the frameworks will work for some time before they need refactoring (everything needs refactoring). So if you think OSCAR4 has less functionality than OSCAR3, that’s because it’s modular. There is no point in US writing web interfaces that you need to put on your server. Instead we have written an API that is so simple and powerful it’s 2 lines of code in its basic form. Easy to understand, easy to test, easy to install, easy to customise.

There’s lost more to do, but it doesn’t involve rewriting the programs. OSCAR is designed to be extended through APIs. If you want to use a new corpus there’s and API. A new dictionary/lexicon? An API. A new machine-learning algorithm? Yes, an API. It should be hours, not years to reconfigure. Here’s how to do it:

ChemicalEntityRecogniser myRecogniser = new PatternRecogniser()

Oscar oscar= newOscar();

oscar.setRecogniser(myRecogniser);

oscar.setDictionaryRegistry(myDictionaryRegistry);

List<ResolvedNamedEntity> entities =

oscar.findResolvableEntities(text);

Five lines of code (of course someone has to write that recogniser and the dictionary but then you can plug and play them). So if you want OSCAR to use Conditional Random Fields, find an Open Source library (there are lots) and bolt it in as a Recogniser.

Yes, group, I am proud of you and yesterday was the day I said so publicly. I used your own (Powerpoint) slides!

So where does it leave us? What does the signpost point to?

I said yesterday that Language Processing research had two goals and I’ll prepend a third:

  1. LP research develops new approaches to LP. Our main contribution here has been to add chemistry and we’ve covered most of what’s involved. There is no reason why the technology shouldn’t be extended to different human languages, different corpora. We’ve not made any great Chomskian-like breakthroughs in understanding language itself. We haven’t been able to compare chemical corpora because we don’t have a collection of Open ones.
  2. LP uses discourse to give insights into the science itself. I’d hoped to do that in chemistry, but the universal refusal of chemistry publishers to provide Open corpora has meant that we have been restricted to patents. And patents, designed to conceal as well as to reveal, are not where new ideas in the fundamentals of chemistry come from. Contrast bioscience where language is a primary tool for understanding the discipline
  3. LP as a tool provides new useful knowledge to the whole world. Here again we are stymied by the publishers. As this blog has shown publishers are unwilling to make papers Openly available and for the extracted knowledge also to be Open. At a conservative estimate publishers have held back LP by a decade.

I then divided chemical LP into two areas:

  1. Chemical LP in chemical corpora. There’s nothing useful we can do here until the scientific literature is Opened. There are 10 million syntheses published a year, and even being pessimistic, PubCrawler and OSCAR could analyse 2 million of these (I think it’s higher). Richard Whitby in Dial-a-Molecule could use all this in his project for designing the molecules we will need in the future. But we are simply legally forbidden.

     

    So I am giving up LP in chemical documents. There is no point. Some commercial companies will possibly use OSCAR or OSCSAR-like tools to do a small bit of this – but necessarily inefficiently. We can forget the idea of a chemical Bingle. Chemistry remains stagnated

     

  2. Chemical LP in biological documents. Unlike the chemists, biologists really need and want LP/Textmining. They are also hampered by the restrictive practices, but they can probably work out the scope (so long as they don’t publish the extracted data – all our data are belong to the publishers). There’s areas such as metabolism (where Peter Corbett had some great and easily implantable ideas) which would yield massive results. Metabolism with why drugs work and why they don’t work. It matters. Lots of it is in the existing literature but technically and legally locked up, gathering dust.

So I am encouraging the bioscientists to use our software. I am happy to work with anyone – I am not slavishly tied to generate REF points. There is some valuable chemistry to discover by mining the bio-literature

And I intend to go more into the patient-oriented literature and to use LP to help the scholarly poor. Because it may help them to become scholarly richer in spite of everything. And I picked up quite a lot about medical LP at the meeting so I’m fired up.