Monthly Archives: January 2013

Wiley signs Open Access Agreement with the University of Birmingham

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crest_biggerThe University of Birmingham has signed up for a Wiley Open Access Account and now pays for its researchers to publish an open access article with Wiley. Authors affiliated with The University of Birmingham can publish research articles in Wiley Open Access journals and/or OnlineOpen, without directly paying any publication charges. The University of Birmingham joins a number of funders who have opened a Wiley Open Access Account since this was launched.

Browse our listing to see the institutions / funders who have an account or partnership with Wiley Open Access.

More information about our open access options for funders and institutions can be found here.

No sense of direction? Consider consulting some carp

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The ability to navigate using the earth’s magnetic field is a skill that is not unique to humans.  Over the last few decades, scientists have discovered that numerous organisms have an ability to tell which way is north.  And the list is growing.

In one study, “Magnetic Alignment in Carps: Evidence from the Czech Christmas Fish Market,” Hart et al. reported that carp tend to align themselves along a north-south axis.  The authors photographed over 14,000 carp swimming in plastic tubs at pre-Christmas fish markets and found that, on average, the fish positioned themselves facing either the North Pole or the South Pole.

While the authors have not yet proven that carp can sense the geomagnetic field, they did rule out other possible orientation cues, including light, wind, temperature, and water flow. What benefit a common orientation may provide the fish remains unknown.  One possible explanation the authors present is that it may help the fish coordinate their movement when they swim in a school.

Some other organisms also have an ability to detect localized magnetic fields.  In a paper titled “Desert Ants Learn Vibration and Magnetic Landmarks,” Buehlmann et al. demonstrated that ants can sense a strong magnetic field created by two small magnets and use this as a landmark to find their nest.

In the absence of any other landmark (such as a vibrational, visual, or olfactory cue), ants who had been trained to associate the magnetic field with the nest entrance spent a lot more time near the magnetic field than ants who were naive to this landmark.  It is unclear how relevant this experiment is to ants in their natural environment, but the study nevertheless highlights the ants’ ability to sense a magnetic field.

While little is known about how carp align with the earth’s magnetic field or how ants sense a localized magnetic field, more is known about how some tiny organisms, aptly named magnetotactic bacteria, orient with a magnetic field.  These bacteria form straight chains of nano-size magnetic particles within the cells. The magnetic chains are attached to intracellular structures, thus allowing the bacteria to align passively with the earth’s magnetic field, like compass needles.

In a paper published earlier this month, Kalirai et al. showed that some magnetotactic bacteria form anomalous magnetic chains, with some sections of the chain oriented north and others south.  This finding contradicts scientists’ previous understanding that all the magnetic particles in a single chain would have the same alignment.  The study raises many questions: Would bacteria with anomalous magnetic chains have a competitive disadvantage in their natural environment?  Is there a single genetic mutation that leads to the anomalous magnetic chains?

All three of these studies raise intriguing questions, and we look forward to future discoveries from these scientists.

Image: Arrows indicate the orientation of carp swimming in a plastic tub (Hart et al. PLOS ONE 2012)

References:

Hart V, Kušta T, N?mec P, Bláhová V, Ježek M, et al. (2012) Magnetic Alignment in Carps: Evidence from the Czech Christmas Fish Market. PLoS ONE 7(12): e51100. doi:10.1371/journal.pone.0051100

Buehlmann C, Hansson BS, Knaden M (2012) Desert Ants Learn Vibration and Magnetic Landmarks. PLoS ONE 7(3): e33117. doi:10.1371/journal.pone.0033117

Kalirai SS, Bazylinski DA, Hitchcock AP (2013) Anomalous Magnetic Orientations of Magnetosome Chains in a Magnetotactic Bacterium: Magnetovibrio blakemorei Strain MV-1. PLoS ONE 8(1): e53368. doi:10.1371/journal.pone.0053368

RCUK & HEFCE CEOs Misinterpret Economist John Houghton’s Findings on Open Access Cost/Benefits

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In viewing their testimony before the House of Lords Select Committee on UK Open Access Policy, one is rather astonished to see just how misinformed are the three witnesses — Professor Rick Rylance, Chair of RCUK; Professor Douglas Kell, RCUK Information Champion; David Sweeney, Director (Research, Innovation and Skills), Higher Education Funding Council for England (HEFCE) — on a number of key points.

Professor Kell’s impression seems to be along the lines that “all the worldwide OA policies are like ours [the UK’s] regarding Gold, and the rest of the world is taking its lead from us.”

Unfortunately this is no longer the case at all.

And although the three witnesses extol the economist John Houghton‘s work as authoritative, they rather startlingly misunderstand his findings:

The witnesses cite Houghton’s work as (1) evidence that Green OA is more expensive than Gold and as (2) support for the UK’s new policy of paying for Gold OA in preference to providing Green OA.

Houghton’s findings support neither of these conclusions, as stated rather explicitly and unambiguously in Houghton & Swan’s most recent publication:

“The economic modelling work we have carried out over the past few years has been referred to and cited a number of times in the discussions of the Finch Report and subsequent policy developments in the UK. We are concerned that there may be some misinterpretation of this work… [our] main findings are that disseminating research results via OA would be more cost-effective than subscription publishing. If OA were adopted worldwide, the net benefits of Gold OA would exceed those of Green OA. However, we are not yet anywhere near having reached an OA world. At the institutional level, during a transitional period when subscriptions are maintained, the cost of unilaterally adopting Green OA is much lower than the cost of unilaterally adopting Gold OA ? with Green OA self-archiving costing average institutions sampled around one-fifth the amount that Gold OA might cost, and as little as one-tenth as much for the most research intensive university. Hence, we conclude that the most affordable and cost-effective means of moving towards OA is through Green OA, which can be adopted unilaterally at the funder, institutional, sectoral and national levels at relatively little cost.”

Houghton, J. & Swan, A. (2013) Planting the Green Seeds for a Golden Harvest: Comments and Clarifications on “Going for Gold” D-Lib Magazine Volume 19, Number 1/2

What Houghton and coworkers said and meant about Green as the transitional policy concerned an eventual transition from (1) today’s paid subscription access to (2) paid subscription access + Green OA to (3) post-Green Gold (with subscriptions no longer being paid).

Houghton was not at all referring to or supporting a transition from (I) the current RCUK policy in which Green is “allowed” (though grudgingly and non-preferentially) to (II) an RCUK policy where only Gold is allowed (but subscriptions still need to be paid)!

Quite the contrary. It is the added cost of subscriptions that makes pre-Green Gold so gratuitously expensive.

In the background, it’s clear exactly what subscription publishers are attempting to persuade the UK to do: Publishers know, better than anyone, now, that OA is absolutely inevitable. Hence they are quite aware that their only option is to try to delay the inevitable for as long as possible, on the pretext that it would destroy their business and hurt the UK economy to rush into OA without subsidizing subscription publishers by paying extra for Gold. And this self-interested alarmism is succeeding — in the UK.

Meanwhile, the policy-makers in the UK remain under the misapprehension that they are still the leaders, setting the direction and pace for worldwide OA — whereas in reality they are being rather successfully taken in by the publishing lobby (both subscription and Gold).

But it’s not just the publishing lobby: There are two other sources of misdirection:

(1) The Wellcome Trust, a private biomedical research-funding charity that believes it has understood it all with its slogan “Publishing is just another research cost, and a small one, 1.5%, so we simply have to be prepared to pay it, and in exchange we will have OA”:

What Wellcome does not reckon is that, unlike Wellcome, the UK government is not a private charity, with only two decisions to make: “What research shall I fund, and to whom shall I pay the 1.5% of it which is publication fees?”

The UK, unlike Wellcome, also has to pay for university journal subscriptions, university infrastructure, and a lot else. And the UK is already paying for 100% of all that today — which means 100% of UK publication costs. Any money to pay for Gold OA is over and above that.

Nor does Wellcome — a private funder who can dictate whatever it likes as a condition for receiving its research grants — seem to appreciate that the UK and RCUK are not in the same position as Wellcome: They cannot dictate UK researchers’ journal choice, nor can they tell UK researchers to spend money on Gold other than whatever money they give them.

Nor does Wellcome give a second thought to the fact that its ineffective OA mandate owes what little success it has had in nearly 10 years to publishers being paid to provide OA, not to fundees being mandated to do it.

Yet in almost every respect, the new RCUK policy is now simply a clone of the old Wellcome policy.

(2) The minority of fields and individuals that strongly advocate CC-BY licenses for all refereed research today have managed to give the impression that it is not free online access to refereed research that matters most, but the kinds of re-mix, text-mining, re-use, and re-publication that they need in their own small minority of fields.

To repeat, it is incontrovertibly true and highly relevant: CC-BY is only needed in a minority of fields — and in no field is CC-BY needed more, or more urgently, than free online access is needed in all fields.

Yet here too, it is this CC-BY minority that has managed to persuade Finch/RCUK (and themselves) that CC-BY is to the advantage of — indeed urgently needed by — all research and researchers, in all fields, as well as UK industry. Hence that it is preferable to use 1.5% of UK’s dwindling research funds to pay publishers still more for Gold CC-BY to UK research output (and pressure authors to choose journals that offer it) rather than just to mandate cost-free Green (and let authors choose journals on the basis of their quality standards and track-records, as before, rather on the basis of their licenses and cost-recovery models).

The obvious Achilles Heel in all this is unilaterality, as Houghton & Swan point out, clearly.

None of the benefits on which the UK OA policy is predicated will materialize if the UK does what it proposes to do unilaterally:

The Finch/RCUK policy will just purchase Gold CC-BY to the UK’s own 6% of worldwide research output by double-paying publishers (subscriptions + Gold OA fees).

In addition, the UK must continue paying the subscriptions to access the rest of the world’s 94%, while at the same time UK OA policy — by incentivizing publishers to offer hybrid Gold and increase their Green embargo lengths beyond RCUK’s allowable 6-12 in order to collect the UK Gold CC-BY bonus revenue — makes it needlessly harder for the rest of the world to mandate Green OA .

As long as the UK keeps imagining that it’s still leading on OA, and that the rest of the world will follow suit — funding and preferring Gold OA — the UK will remain confident in the illusion that what it is doing makes sense and things must get better.

But the reality will begin to catch up when the UK realizes that it is doing what it is doing unilaterally: It has chosen the losing strategy in a global Prisoner’s Dilemma.

Let us hope that UK policy-makers can still be made to see the light by inquiries like the Lords’ and BIS‘s, and will then promptly do the simple policy tweaks that it would take to put the UK back in the lead, and in the right.

(Some of the Lords in the above video seem to have been a good deal more sensible and better informed than the three witnesses were!)

Harnad, S (2012) United Kingdom’s Open Access Policy Urgently Needs a Tweak. D-Lib Magazine Volume 18, Number 9/10 September/October 2012

PLOS ONE News and Blog Roundup

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This January, PLOS ONE papers caught the media’s eye for research on shark embryos, trustworthy brown eyes, acts of kindness, and more! Here are some of the month’s highlights from our Media Tracking Project:

Researchers studying the brown-banded bamboo shark, or Chiloscyllium punctatum, have discovered that the baby sharks of this species can detect potential predators from inside their egg cases. Once detected, these sharks go very still and stop moving their gills to escape the predator’s notice. According to the researchers, similar ability to detect bioelectric stimuli is used by adult sharks to sense prey. If you would like to know more about this study check out the BBC, Discovery News, and the New York Times.

What makes a face look trustworthy? According to new research, eye color and face shape play important roles in the perceived trustworthiness of one’s face. Among their results, the researchers found that study participants perceived faces with brown eyes as more trustworthy than faces with blue eyes. Additionally, faces with a broad chin and mouth, large eyes, and closer-set eyebrows were perceived as more trustworthy than narrower faces with smaller eyes and more widely spaced eyebrows. For more about the study, visit the Huffington Post, Wired, and Scientific American.

Brrr! January can be quite chilly, but spring is on its way – and it might be coming earlier than anticipated. In a recent study, researchers used the historical records of Henry David Thoreau and Aldo Leopold, a noted conservationist, to trace the history of spring flowering times in the eastern United States. Beginning with records from 1852 and ending in 2012, researchers found that plants are flowering earlier now than in the past as spring temperatures continue to rise. According to their findings, there is a linear relationship between rising spring temperatures and flowering times. The researchers posit that as the climate continues to change, this relationship may be tested. To learn more about this study, read National Geographic, MSNBC, and NPR.

Being a kid can be rough sometimes, but according to this research, acts of kindness may increase happiness and lead to greater social acceptance from peers. In the study, participants aged nine to twelve were asked to perform three acts of kindness each week for four weeks. Participants who performed acts of kindness, or what the authors called “pro-social activities”, were happier and were selected by their peers as someone with whom they would like to work with at school. Read more about this study at the Washington Post, Wired, and the BBC.

Citations:

RM, Hart NS, Collin SP (2013) Survival of the Stillest: Predator Avoidance in Shark Embryos. PLoS ONE 8(1): e52551. doi:10.1371/journal.pone.0052551

Kleisner K, Priplatova L, Frost P, Flegr J (2013) Trustworthy-Looking Face Meets Brown Eyes. PLoS ONE 8(1): e53285. doi:10.1371/journal.pone.0053285

Ellwood ER, Temple SA, Primack RB, Bradley NL, Davis CC (2013) Record-Breaking Early Flowering in the Eastern United States. PLoS ONE 8(1): e53788. doi:10.1371/journal.pone.0053788

Layous K, Nelson SK, Oberle E, Schonert-Reichl KA, Lyubomirsky S (2012) Kindness Counts: Prompting Prosocial Behavior in Preadolescents Boosts Peer Acceptance and Well-Being. PLoS ONE 7(12): e51380. doi:10.1371/journal.pone.0051380

House of Lords Science and Technology Select Committee on Open Access

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Written evidence to House of Lords Science and Technology Select Committee on Open Access

Stevan Harnad

I. Overview of OA

1.   Open Access (OA) means free online access to peer-reviewed research journal articles. (There are about 28,000 such journals, in all fields and languages.)

2.   Most research journals recover their publication costs through institutional subscriptions.

3.   No institution can afford to subscribe to all or most or even many of the 28,000 journals, only to a small fraction of them, a fraction shrinking because of rising journal costs.

4.   As a result, all researchers today, at all institutions, are denied access to articles published in those journals whose subscriptions are unaffordable to their institutions.

5.   As a result, the research that is funded by public tax revenue, and conducted by researchers employed by publicly funded institutions (universities and research institutes) is not accessible to all of its primary intended users ? the researchers who can use, apply and build upon it, to the benefit of the public that funded it.

6.   The Internet and the Web have made it possible to remedy this access-denial problem, which had been a legacy of the Gutenberg era of print on paper, and its associated costs.

7.   Researchers can continue to publish their research in subscription journals, but they can self-archive their final, peer-reviewed drafts in their institutional repositories, free for all online, as a supplement, for all users whose institutions cannot afford subscription access to the journal in which the article was published (and, as an added bonus, free also for the tax-paying public that funded the research).

8.   Author self-archiving is called ?Green OA.?

9.   Sixty percent of journals (including most of the top journals in most fields) already endorse Green OA self-archiving by authors, immediately upon publication (no embargo).

10.   The remaining 40% of journals request an embargo or delay on providing OA for 6-12 months or more. (The publisher rationale for the embargo is that it protects journal subscription revenues that Green OA might otherwise make unsustainable.)

11.   There is as yet no evidence at all that immediate, un-embargoed Green OA self-archiving reduces subscriptions, even in fields, such as physics, where it has been practiced for over 20 years and has long reached close to 100%.

12.   The second way to provide OA is for the journal rather than the author to make all of its articles freely accessible online immediately upon publication.

13.   OA journal publishing is called ?Gold OA.?

14.   About 20% of the world?s 28,000 journals are Gold OA journals, but very few of them are among the top journals in each field.

15.   Most Gold OA journals continue to cover their costs from subscriptions (to the print edition) but the top Gold OA journals have no print edition and instead of charging the user-institution for access, through subscription fees, they charge the author-institution for publishing, through publication fees.

16.   There are also hybrid subscription/Gold journals, who publish non-OA articles and continue to charge institutional subscription fees, but offer authors the option of paying to make their individual article OA if they pay a Gold OA fee.

17.   Paying Gold OA fees is a problem for authors and their institutions because as long as most journals are still subscription journals, institutions have to continue subscribing to whatever journals they can afford that their users need.

18.   Hence paying for Gold OA today increases the financial burden on institutions at a time when subscription costs are already barely affordable.

19.   Paying for Gold OA while subscriptions still need to be paid is not only an extra financial burden, but it is also unnecessary, because Green OA can be provided for free while worldwide subscriptions are still paying the cost of publication.

20.   If and when Green OA becomes universal (i.e., at or near 100%, in all fields, worldwide), and if and when that, in turn, makes subscriptions unsustainable (with institutions cancelling subscriptions because the free Green OA versions are sufficient for their needs), then all journals can convert to Gold and institutions will have the money to pay the Gold OA costs out of their annual windfall subscription cancelation savings.

21.   There is every reason to believe that Gold OA costs after universal Green OA will be much lower than they are today: the print edition and its costs as well as the online edition will be gone, the worldwide network of Green OA Institutional Repositories will provide access and archiving, and journals will only need to manage peer review (all peers already review for free) and perhaps provide some copy-editing.

22.   It remains to explain how to achieve universal Green OA, so as (1) to provide universal OA, first and foremost, and then (2) to induce a transition to universal Gold OA at an affordable price if and when Green OA makes subscription publishing unsustainable, and (3) to release the institutional subscription funds in which the potential money to pay for Gold OA is currently locked.

23.   The way to achieve universal Green OA is for institutions (universities and research institutes) and research funders to mandate (require) that all research that they fund, and that they employ researchers to conduct, must not only be published, as now (?publish or perish?), but the peer-reviewed final drafts must also be deposited in the researcher?s institutional repository immediately upon acceptance for publication.

24.   Optimally, access to the deposit should be made OA immediately; in any case any OA embargo should be as short as possible.

25.   However, if necessary, an embargo of 6 months or even 12 months or longer can be tolerated in the case of the 40% of articles published in journals that do not yet endorse immediate Green OA.

26.   The repositories make it possible for authors to provide ?Almost-OA? to the deposits that are under OA embargo by automatically forwarding reprint requests from would-be users to the author, who can then decide, with one click, whether or not hey wish to email the deposited reprint to the requester.

27.   Researchers have been fulfilling reprint requests from fellow-researchers for over a half century, but in the online era this can be greatly facilitated and accelerated through universally mandated repository deposit.

II. UK OA Policy

28.   In 2004, the UK Parliamentary Select Committee recommended that UK universities and UK funding councils mandate Green OA self-archiving.

29.   With this, the UK became the world leader in OA and OA policy.

30.   Green OA self-archiving has since been mandated by both funding councils and universities in the EU, Canada, and Australia, including the National Institutes of Health, Harvard, and MIT in the US (over 250 Green OA mandates worldwide to date).

31.   Green OA mandates have been growing worldwide, guided by the UK model; to accelerate mandate adoption all that is needed is a few practical upgrades to the UK model (such as upgraded compliance mechanisms and fuller integration of institutional and funder mandates).

32.   But in 2012, instead of building on its 8-year success in worldwide OA leadership, the UK took an abrupt U-turn on OA, with the recommendations of the Finch Committee.

33.   The Finch Committee declared Green OA a failure, and recommended downgrading it to just preservation archiving.

34.   In place of mandating Green OA (which is almost cost-free, while publishing is still being paid for worldwide via institutional subscriptions) the Finch Committee recommended paying even more for publishing, by redirecting scarce UK research funds to paying for Gold OA, over and above what the UK is already paying for subscriptions.

35.   One can only conjecture as to the causes underlying this inexplicable about-face when Green OA mandates are growing worldwide:

36.   The cause may have been subscription-publisher lobbying of BIS against Green OA or Gold-OA-publisher lobbying for Gold OA.

37.   There was perhaps also some pressure from a vocal minority of OA advocates arguing that there is an urgent immediate need for something stronger than the free online access mandated by Green OA (the additional re-use rights conferred by a CC-BY license) for which this minority claimed that it is worth paying Gold OA fees.

38.   The outcome has been significantly to weaken instead of strengthen the RCUK OA policy:

39.   RCUK researchers may still choose between paying for Gold OA or providing cost-free Green OA, but RCUK expresses a preference for Gold and does not permit researchers to choose Green if their chosen journal?s OA embargo exceeds 6-12 months.

40.   This policy has the perverse consequence of giving subscription publishers a strong incentive (1) to add a hybrid Gold option just in order to collect the extra UK revenue, and (2) to adopt and extend Green OA embargoes beyond the UK?s allowable 6-12 months, to make sure that UK researchers must choose the paid Gold option rather than the cost-free Green one.

41.   The rest of the world cannot, need not, and will not follow suit with this profligate. perverse, and completely unnecessary UK policy change.

42.   In Europe, the Americas and Asia, low-cost Green OA mandates will continue to grow, while the UK loses its leadership role in worldwide OA, needlessly squandering increasingly scarce research funds, paying publishers even more in order to make UK research output (and UK research output alone — 6% of worldwide research output) OA, while the rest of the world makes its (94%) research output OA at next to no extra cost.

The Australian economist, John Houghton, has analyzed OA policy in country after country. The House of Lords Select Committee is urged to look at the outcome of those analyses, which is that it is far cheaper to mandate Green OA first, rather than to pay pre-emptively for Gold unilaterally. That not only provides OA, but it paves the way to affordable, sustainable Gold OA:

Houghton, J. & Swan, A. (2013) Planting the Green Seeds for a Golden Harvest: Comments and Clarifications on “Going for Gold” D-Lib Magazine Volume 19, Number 1/2

Conclusion: Instead of following the Finch Committee?s counterproductive recommendation to require and subsidise Gold OA, RCUK should adopt two important practical upgrades to strengthen the prior RCUK Green OA mandate: (1) integrate institutional and funder Green OA mandates so they can mutually reinforce one another and (2) implement an effective Green OA compliance mechanism, making institutions responsible for monitoring and ensuring compliance with both institutional and funder deposit mandates.

Appendix:

Comments on the Committee’s specific topics:

support for Universities in the form of funds to cover article processing charges, and the response of universities and other HEIs to these efforts

If there are UK funds to spare to subsidise Gold OA, fine, make them available — but mandate (require) Green OA self-archiving in all cases (ID/OA) and do not require researchers to choose a Gold OA journal unless they wish to.

embargo periods for articles published under the green model

The shorter the better, but always require immediate deposit (ID/OA) in the author?s institutional repository, even for embargoed articles, and implement the ?Almost OA? Button during the embargo.

engagement with publishers, universities, learned societies and other stakeholders in the development of research council open access policies and guidance

Publishers should endorse immediate Green OA, but ID/OA mandates are compatible with embargoes.

Universities should mandate Green OA too.

Funder and university mandates should be convergent, requiring deposit in the institutional repository, with the institution monitoring and ensuring compliance.

Deposits or their metadata can then be harvested to any desired central repositories.

Repository deposit should be designated the sole mechanism for submitting publications for institutional performance review or national research assessment.

Learned Society publishers, like all publishers, should endorse immediate Green OA, but ID/OA mandates are compatible with embargoes.

If and when universally mandated Green OA makes subscription publishing unsustainable, publishers can convert to Gold OA and institutions can pay for it out of the windfall subscription cancelation savings freed by the Green-OA-induced cancelations.

challenges and concerns raised by the scientific and publishing communities, and how these have been addressed.

The UK scientific community has rightly expressed considerable concern about (1) not being allowed to publish in their journals of choice, and about (2) having to pay for Gold OA.

The solution is to mandate Green OA and not to require Gold OA except if the author wishes it.

The UK subscription publishing community is being paid in full for publication, via worldwide subscriptions today.

If and when universally mandated Green OA makes subscription publishing unsustainable, publishers can convert to Gold OA and institutions can pay for it out of the windfall subscription cancelation savings freed by the Green-OA-induced cancelations.

international issues

The rest of the world need not, cannot, and will not follow the Finch Committee?s recommendation to pay pre-emptively for Gold instead of mandating Green OA.

It would be best if the UK returned to the direction it set in 2004; otherwise it is simply using UK research funds to provide (Gold) OA for the UK and the world at a much higher cost than necessary, and at the cost of inducing perverse effects in publishers (such as subscription publishers offering hybrid Gold in order to attract double payment for UK?s Gold subsidy, and adopting and increasing OA embargoes in order to ensure that UK researchers must pay extra for Gold OA).


Figure 1. The percentage of Green and Gold OA in the UK (2007-2011, Web of Science). Note that most OA is Green OA. From: Gargouri, Y, Lariviere, V, Gingras, Y, Carr, L and Harnad, S (2012b) Green and Gold Open Access percentages and growth, by discipline. In: 17th International Conference on Science and Technology Indicators (STI), Montreal, CA, 05 – 08 Sep 2012. 11pp.

Figure 2. The effect of Green OA mandates (comparing nonmandated vs mandated OA provision: 2002-2009). Data from Gargouri, Y, Lariviere, V, Gingras, Y, Brody, T, Carr, L and Harnad, S (2012a) Testing the Finch Hypothesis on Green OA Mandate Ineffectiveness. Presented: Open Access Week 2012

Counterattack: Hands Off Freedoms, Hands On Keyboards

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The dons are absolutely right that dictating where they may or may not publish, and coercing them to pay to publish is an assault on academic freedom:

“Open access plans are ‘attack on academic freedoms’” (Guardian Observer, & Telegraph, January 26)

But they are absolutely wrong that the fault lies with Open Access (OA), or with mandating OA.

The fault lies entirely with the way the UK government — RCUK, under the influence of the foolish and ill-informed recommendations of the Finch Committee — has proposed to mandate OA.

The Finch Committee has recommended weakening instead of strengthening the RCUK’s existing, 5-year-old OA mandate — which had allowed authors to continue publishing wherever they wished, and merely required them to make their final drafts OA within 12 months of publication by self-archiving them free for all online (“Green OA”).

Declaring the prior Green OA mandate a failure, the Finch Committee proposed instead to dictate to authors which journals they were permitted to publish in: only in journals that make their own published articles OA (“Gold OA”), with a CC-BY license, immediately upon publication, or in journals that formally endorse their authors providing Green OA within 6-12 months of publication. In addition, some scarce research money was to be diverted from research to pay publishers even more money, over and above what is already being spent on subscriptions, in exchange for Gold OA.

Authors naturally became incensed at the government dictating where they might or might not publish. (Nor did they appreciate money being diverted from dwindling research funds to pay publishers even more.)

Enough complaining. The error is easily corrected:

Let authors publish wherever they wish. Require them to deposit their peer-reviewed final drafts in their OA institutional repositories immediately upon publication.

Sixty percent of journals already endorse immediate Green OA. For the 40% that want OA embargoed, make the deposit Closed Access instead of OA during the embargo.

The repository has a Button for redirecting individual users’ reprint requests for Closed Access articles to the author, who can authorize the emailing of the reprint to the requester with one click if he wishes. This is not OA, but it is “Almost-OA” and is sufficient to tide over researchers’ access needs until embargoes die their inevitable and well-deserved natural deaths.

Meanwhile, 100% of articles are immediately deposited, 60% are immediately OA, 40% are Almost-OA, and authors retain their full right to choose their journals and not pay for Gold OA if they do not wish to.

They are strongly encouraged to make the deposit OA as soon as possible, but this is not a constraint on their freedom of choice of journals.

This is a strengthened version of RCUK’s prior Green OA mandate, without the Finch folly (nor the premature and unnecessary CC-BY requirement, which is not needed in most fields, not as urgent as free online access in any field, and only makes it gratuitously harder to mandate OA).

All this upgrade needs in order to make it optimal is:

(1) Funder mandates and institutional mandates should both stipulate convergent institutional deposit (not divergent, competitive deposit: institution-external repositories like EuPMC can harvest from the institutional ones).

(2) Institutions and funders should both stipulate that repository deposit is the only means of submitting publications for institutional performance review or national research assessment.

(3) Institutions should be designated to monitor and ensure that their researchers comply with both institutional and funder deposit mandates.

This optimized Green OA mandate is no more of an assault on academic freedom than the mandate to “Publish-or-Perish” is — in fact, it is merely a natural extension of P-or-P, for the online age.

Cervical Health Awareness Month

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Health risks can be frightening, but ignorance to these risks can be even more terrifying. In the past, we have discussed a range of women’s health issues, including obesity, cardiovascular disease and ovarian cancer.  To continue our commitment to health awareness, we would like to honor January as Cervical Health Awareness month.

PLOS ONE has published research tackling many aspects of cervical health, including cervical cancer and human papillomavirus.

Human papillomavirus, better known as HPV, is the most common sexually transmitted virus in the United States. According to the U.S. Center for Disease Control, at least 50% of sexually active people will contract the virus at some point in their lives.  There are more than 40 types of HPV, some of which may lead to cervical cancer. Cervical cancer is highly preventable with regular screening and vaccination to help prevent human papillomavirus.

To further expand our knowledge and understanding of cervical health, researchers from across the globe continue to explore HPV, the vaccine and its social effects.

For example, in a study published in PLOS ONE, authors in Tanzania explored the reasoning behind young girls receiving or not receiving the HPV vaccination. After interviewing both adults and students, researchers found that vaccine education and parental meetings were crucial for vaccine acceptance. Knowing women who had suffered from cervical cancer was also a factor in the decision-making.

The effectiveness of the vaccine is also a common concern. In another article, Canadian researchers developed a system to track the effectiveness of the HPV vaccination in preventing the virus.  The authors created a protocol for linking multiple data registries to allow for ongoing monitoring of the vaccines effectiveness, while also ensuring patient privacy was taken into account. This research aims to understand the long term effects of the vaccine and future vaccination tracking initiatives.

This study expands our knowledge on the vaccination results, but what about transmission of the virus? In a third PLOS ONE report, researchers explored the prevalence of HPV in the DNA of males with infected female sexual partners.  The authors found that HPV was prevalent in 86% of the male participants surveyed. These men had the same high risk viral type as the infected women, supporting the importance of awareness in men to protect themselves and their partners. This area of investigation is important in expanding our knowledge of transmission of the virus and the risk of cervical cancer development.

All these studies are aimed at improving our understanding of HPV risks and vaccination, and there are many more. As Cervical Health Awareness month draws to an end, explore more PLOS ONE research on the subject here.

 Citations:

Watson-Jones D, Tomlin K, Remes P, Baisley K, Ponsiano R, et al. (2012) Reasons for Receiving or Not Receiving HPV Vaccination in Primary Schoolgirls in Tanzania: A Case Control Study. PLoS ONE 7(10): e45231. doi:10.1371/journal.pone.0045231

El Emam K, Samet S, Hu J, Peyton L, Earle C, et al. (2012) A Protocol for the Secure Linking of Registries for HPV Surveillance. PLoS ONE 7(7): e39915. doi:10.1371/journal.pone.0039915

Rocha MGdL, Faria FL, Gonçalves L, Souza MdCM, Fernandes PÁ, et al. (2012) Prevalence of DNA-HPV in Male Sexual Partners of HPV-Infected Women and Concordance of Viral Types in Infected Couples. PLoS ONE 7(7): e40988. doi:10.1371/journal.pone.0040988

Image: Glass sculpture of human papillomavirus.  Photograph by Luke Jerram, “Papilloma 2011″


It’s late January; do you know where your resolutions are?

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New Year’s festivities have come and gone, and now, a few weeks into 2013, a few earnestly made resolutions may have fallen by the wayside. If you’re struggling with yours, two PLOS ONE studies could offer some hints for success.

The first report describes an investigation into three facets of goal attainment: keeping a goal active in your working memory; being aware of your current state, monitoring progress, and adjusting performance; and not behaving contrary to the goal.

The researchers used brain imaging during a simple task to explore interactions between these processes. They found that high demand for “goal maintenance” — keeping a goal active in your working memory — was correlated with lowered brain activity related to avoiding counterproductive behaviors, called “response inhibition.” In other words, if participants had to spend a lot of energy trying to remember their goals, they didn’t seem to have the brain energy to stop negative behaviors. The authors suggest that people might be able to counter this effect by increasing visual reminders of their goal, thereby decreasing the need for goal maintenance and freeing up resources for response inhibition.

Alternatively, you could try adding a financial bonus to the mix; results from a second study show that the promise of a monetary reward can immediately improve performance, even on an intermediate task not directly associated with the reward.

Participants in the study were presented with a simple aural task — identify whether two tones were high-pitched or low — and offered a financial reward for making a quick decision on the second note. The researchers found that this promised reward improved the participants’ performance for the entire task.

It isn’t clear, however, if the observed effect requires similarity between the intermediate task and the rewarded task. In this study, the two were identical, but the authors suggest that this may not need to be the case. They note that very different tasks may require similar preparation, and their results suggest that preparing for the future rewarded task is a key part of the observed effect.

So, if you’ve fallen off your resolution wagon and are looking for a way to get back on track, it’s not be too late — and you may even be able to make a little money out of the deal.

Citations:

Berkman ET, Falk EB, Lieberman MD (2012) Interactive Effects of Three Core Goal Pursuit Processes on Brain Control Systems: Goal Maintenance, Performance Monitoring, and Response Inhibition. PLoS ONE 7(6): e40334. doi:10.1371/journal.pone.0040334

Zedelius CM, Veling H, Bijleveld E, Aarts H (2012) Promising High Monetary Rewards for Future Task Performance Increases Intermediate Task Performance. PLoS ONE 7(8): e42547. doi:10.1371/journal.pone.0042547

Image: alykat on Flickr

Update: Travels, Semantic Computing for Science, Reproducibility, and Open Stuff

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I have been silent on this blog for too long (over 1 month) because I have been obsessively concentrating on two major software projects. This post is to keep you up to date and reassure those of like mind that I continue to be very active in trying to liberate knowledge.

Travels. I am off back to CSIRO Melbourne for a month where I’m helping Nico Adams with his Materials Summer School and Workshop. I think the semantic tools that we have all been developing are going to be valuable in creating better informatics and computational approaches to materials. I’m particularly interested in crystalline materials and computational processes.

I’m taking a week off to fly to Auckland, NZ for the tail of the Open Research meeting (Fabiana Kubke) and then Kiwi Foo. Very excited. I’m sorry I can’t spend more time with Fabiana but the Summer School overlaps.

In late Feb/March I have been invited to speak at the Columbia Research Data Symposium (http://conferences.cdrs.columbia.edu/rds/index.php/rds/rds ). This will be a very exciting meeting and I’m very grateful to Columbia. Originally I declined because I would have been sponsored by Elsevier and I have publicly stated that I am boycotting all Elsevier activities. Columbia’s sponsorship means I do not have to take an Elsevier-friendly line. I will blog this meeting before I go and outline some of the issues that the world has to decide on. In simple terms our academic digital freedom is at stake. Data presents a huge opportunity and doubtless large additional income. Academia and governments should act wisely and not outsource their decisions and ethics.

Then I’m off to Kitware , a scientific/consultancy company that makes money out of open Source, including VTK and Avogadro. I am really excited as I hope to bounce the Declaratron design off them. As always my software is not only Open but non-competitive. Anyone can join in the meritocracy.

AMI2 (http://bitbucket.org/petermr/pdf2svg ) is a project to turn PDFs into fully semantic computable, searchable, executable documents with human intervention. There are >2 million STM PDFs published each year in EuropePMC alone (more on that later). More and more are Open Access of some kind. We have developed a relatively comprehensive and high accuracy converter and tested it on some thousands of PDFs from several hundred publishers. (Don’t rush for your lawyers, publishers, I’m not going to publish your holy PDFs). The results of this are:

  • The technical standard of publishers’ PDFs is AWFUL. I don’t think I have found one that conforms to the PDF standard
  • We have learnt how to turn them into Unicode
  • The result is technically better than what the publishers produce.
  • The next stage, turning SVG into semantic form is doing well. I am particularly keen on extracting maths equations in semantic MathML form. Equations aren’t copyright are they? Perhaps they are – Pythagoras only died 2500 years ago, so maybe he is still in copyright somewhere. JSBach still is.

I’d love to hear from anyone interested in developing content mining

The Declaratron. This is a new declarative approach to reproducible semantic computing and directly addresses things like:

  • Can scientific computation be reproduced? The current answer is generally – only partially. To do so completely requires the complete semantic unification of all components – data, specification, computational engine and visualisation/publication.
  • Have we eliminated all syntactic error and as much semantic error as possible? For example are our units consistent? Are data linked to computable ontologies?
  • Can the algorithm be transported to a different environment without writing code?
  • Can we follow the progress of the computation?
  • Can we modify the algorithm, even in mid computation?
  • Can the machine document the complete course of the calculation at whatever granularity we desire?
  • Can the results be re-used in another context without human intervention?

… and a great deal more. I think the answer to all of these is yes and I’ll be showing how the Declaratron works.

Open Access/Knowledge. I shall try and blog something on Aaron Swartz. I didn’t know him, but I know people who did, and the wealth of tributes has been impressive in itself and also given me more insight into his passion for liberation. The smell of injustice is pervasive.

Content Mining. Hargreaves is going to turn its recommendations into law. No arguments. So in October 2013 I can legally mine anything I have access to and publish as CC-NC. Publishers will whinge scream lobby etc. But that will be UK law (it doesn’t require re-legislation and done through statutory instruments). There’s a lot of to-and-fro-ing. Neelie Kroes and colleagues are running something in Brussels in 2 weeks’ time – Ross is representing OKF. The publishers are running semi-closed lobbying shops. We all have to remain very vigilant as publishers have people who are paid to stop progress and we have to rely on volunteers, spare time, etc. That is why I am grateful to Wellcome and the RCUK for their very clear impetus and drive. They have shown passion where the Universities have been spineless or ultra-timid. I’ll write more on this before Columbia.

Chuff will be going to AU and NZ… and I’ll be meeting with OKF people there. Tweet or mail if you’re around Auckland/Warkworth 2013-02-07/12

 

Evolutionary biology steps up to the fight against cancer

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EVA 6 1Cancer organizations in developed nations predict that 2 in 5 people will be diagnosed with cancer during their lifetime.  Worldwide, the number of deaths due to cancer surpasses that of HIV, tuberculosis and malaria combined (American Cancer Society, 2011).  In response to these ominous statistics, the fight against cancer has spread into branches of science that are not traditionally associated with cancer research.   The field of evolutionary biology is a key example.

How can evolutionary biology help combat cancer?  The journal Evolutionary Applications has devoted the entire January 2013 issue to showcasing the many ways that evolutionary approaches can improve the understanding, treatment and prevention of a number of different types of cancer.  The multi-authored opening paper states: “an accurate evolutionary approach should unite and explain, rather than replace” the many avenues of cancer research (Thomas et al 2013).

This is the first compilation of its kind, and was spearheaded by international scientists affiliated with the Darwinian Evolution of Cancer Consortium in France and with the Center for Evolution and Cancer at the University of California, San Francisco. The issue is guest edited by Frederic Thomas, Michael Hochberg, Athena Aktipis, Carlo Maley and Ursula Hibner.

The general theme linking articles featured in the January issue of Evolutionary Applications is that improvements to our understanding of cancer can be gained by considering cancer as a complex ecosystem. Using the analogy of a forest, the fate of a forest depends both on the individual characteristics of trees, as well as the interactions of each tree with its biotic and abiotic environment.  Similarly, tumors can be comprised of cells that are genetically and physically distinct, and the fate of tumors depends both on cell-to-cell interactions within the tumor, as well as on the interactions of the whole tumor with the highly complicated environment of the human body.  

Evolutionary questions addressed in the issue include: Why do we get cancer?  How do evolutionary principles like natural selection, mutation, and genetic drift, work in a cancer ecosystem? How can we use evolutionary theory to minimize the rate of cancers worldwide?  Many novel results are reported in the published articles, including how blood vessels affect the internal environment of a tumor (Alfarouk et al. 2013), and how certain characteristics of tumors can help explain patterns of metastasis (Daoust et al. 2013).

Papers from the Evolution and Cancer Special Issue are all freely available on the Evolutionary Applications website: www.evolutionaryapplications.org. 

Michelle Tseng, Managing and Founding Editor

 References

 Alfarouk, K. O., Ibrahim, M. E., Gatenby, R. A. and Brown, J. S. (2012), Riparian ecosystems in human cancers. Evolutionary Applications. doi: 10.1111/eva.12015

American Cancer Society. Global Cancer Facts & Figures 2nd Edition. Atlanta: American Cancer Society 2011.

 Daoust, S. P., Fahrig, L., Martin, A. E. and Thomas, F. (2012), From forest and agro-ecosystems to the microecosystems of the human body: what can landscape ecology tell us about tumor growth, metastasis, and treatment options?. Evolutionary Applications. doi: 10.1111/eva.12031

 Thomas, F., Fisher, D., Fort, P., Marie, J.-P., Daoust, S., Roche, B., Grunau, C., Cosseau, C., Mitta, G., Baghdiguian, S., Rousset, F., Lassus, P., Assenat, E., Grégoire, D., Missé, D., Lorz, A., Billy, F., Vainchenker, W., Delhommeau, F., Koscielny, S., Itzykson, R., Tang, R., Fava, F., Ballesta, A., Lepoutre, T., Krasinska, L., Dulic, V., Raynaud, P., Blache, P., Quittau-Prevostel, C., Vignal, E., Trauchessec, H., Perthame, B., Clairambault, J., Volpert, V., Solary, E., Hibner, U. and Hochberg, M. E. (2012), Applying ecological and evolutionary theory to cancer: a long and winding road. Evolutionary Applications. doi: 10.1111/eva.12021

Set the default to open: my response to Canada’s Access to Information Act Consultation

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The Office of the Information Commissioner of Canada is conducting a public consultation into modernization of the Access to Information Act. Comments are due January 31. Following is my response.

Office of the Information Commissioner of Canada
Consultation on Access to Information Act
consultation@oic-ci.gc.ca
http://www.oic-ci.gc.ca/eng/modernization-atia_2012.aspx
January 21, 2013
Dear Suzanne Legault,
Re: Consultation on Access to Information Act
This is a response from an individual scholar and librarian who is active in the area of information policy and open access. Thank you very much for the opportunity to participate in this consultation. In brief, my recommendation is to set the default to open. Narrow the scope of limitations to open access to information to substantive matters of national security or personal privacy, with an empowered and sufficiently funded Office of the Information Commissioner of Canada to act as an effective monitor to ensure these limitations are respected. Expand the range of information that falls under the Act to include Cabinet confidences. Expand the entities covered under the Act to include companies that are contracted to undertake work on behalf of the federal government, and companies that receive contracts and or subsidies from the federal government.  Detailed responses to the General Questions follow.
Right of access
Question: In an environment of increasing globalization, should any person be able to obtain government held records, notwithstanding their physical presence or citizenship?
Response: yes, in an environment of increasing globalization, anyone should be able to obtain government held records, notwithstanding their physical presence or citizenship. In the spirit of open government, the default for government information should be open access to anyone, anywhere. Canadian benefit from access to information provided by other governments.
Coverage of the act
Question: Should all federal entities be subject to the Act as a matter of principle, or should some be exempt from the Act’s requirements? What criteria or principles should determine which entity is covered by the Act?
Response: the act should cover all federal entities, all entities undertaking work on behalf of the government, and all entities receiving funding of any kind from the government.  That is, when work is contracted by the federal government out to companies, the companies should also be covered by the act, exactly as if the work were being done by the government department. When a company is awarded a contract by the government, or is given a subsidy, any information relating to the contract or subsidy should be subject to Access to Information Requests and a general expectation of open access to this information.
Limitation on the right of access
Question: In what circumstances should a universal right of access be limited? Should federal institutions have the discretion to limit disclosure? If so, should they be required to demonstrate that a defined injury, harm or prejudice will probably result from disclosure? Should the public interest be considered in the decision to withhold records?
Response: Any limitations should apply to particular information, and then only for substantial reasons – information that is classified for security purposes or that cannot be released without compromising personal privacy. The default should always be open. It is essential that a watchdog such as the Office of the Information Commissioner be empowered and sufficiently funded to monitor and ensure that any limitations on access to information fall within this scope.
Cabinet confidences
Question: Should the Access to Information Act exclude records that directly inform Cabinet decisions? If the exclusion is permitted, on what should it be based? Should the Information Commissioner be able to review Cabinet confidences?
Response: Canada is part of the Open Government Partnership. It is timely to make a serious commitment to openness. Cabinet should conduct its work in the open. The criteria for keeping information confidential by Cabinet should be exactly the same for all other federal information – national security or personal privacy. This is important for the work of the government to be, and to appear to be, transparent.
Awareness and education
Question: What role can or should the Office of the Information Commissioner play in helping Canadians to become more aware of their rights under the Access to Information Act?
Response: The Office of the Information Commissioner should provide education and awareness through a variety of activities (website, information sessions both virtual and in-person), and should leverage opportunities to work with other organizations with education and awareness mandates such as schools and libraries [disclosure: I am a librarian].
Once again thanks for the opportunity to participate. I will post this response to my blog.
Heather Morrison, PhD
hgmorris at sfu dot ca
The Imaginary Journal of Poetic Economics
http://poeticeconomics.blogspot.com