Publisher Embargoes, Immediate-Deposit Mandates, and the Request-a-Copy Button

On Thu, Nov 28, 2013 Bo-Christer Björk wrote in GOAL: The idea that publishers would tolerate large scale mandate driven green OA (say 50-60 %) of articles with no embargoes or counteractions is pretty naive. Elsevier has shown the way with rules stipulating that Green OA is OK, unless its mandated, in which case they require special deals with the the institutions in question. And many publishers who previously had no embargo periods are starting to define such.”

Björk’s comment, unfortunately completely misses the point.

Yes, publishers can and will try to impose embargoes on Green OA, especially encouraged by the perverse effects of the UK’s Finch/RCUK preference and subsidy for Gold.

That is not being denied, it was being affirmed: “Joint ‘Re-Engineering’ Plan of UK Government and UK Publisher Lobby for ‘Nudging’ UK Researchers Toward Gold Open Access

But the immediate-deposit (HEFCE/Liege) mandates are immune to these publisher embargoes. They are the compromise mandate that fits all funders and institutions, regardless of how long a maximal publisher embargo they allow.

(Green OA after one a one-year embargo has been pretty much conceded by all publishers, whether or not they admit it, so that’s the worst case scenario; one year of access-denial is now the figure to beat: The HEFCE/Liege mandates get everything deposited in institutional repositories immediately upon acceptance for publication, whether or not it is made OA immediately. And that means that access to everything immediately becomes at most 2 keystrokes away, one from the requestor, one from the author, thanks to the repositories’ automated “Almost-OA” Button: see more below.)

As to Elsevier’s “special deals” for mandating institutions: sensible institutions will politely inform Elsevier that they are, as always, quite prepared to negotiate with publishers about subscription pricing (“Big Deals”) — but definitely not about university internal record-keeping and archiving policy, which is none of publishers’ business.

As to Elsevier authors (who — not their universities! — are the ones negotiating rights agreements with their publishers): They can rest assured that Elsevier is still completely on the Side of the Angels in its explicit, formal recognition of their authors’ right to provide immediate, unembargoed (Green, Gratis) OA to their final drafts, by self-archiving them online, accessible free for all, in their institutional repositories — a right that Elsevier has formally recognized ever since 2004.

Let me repeat that very clearly: All Elsevier authors today retain the right to make their papers OA immediately upon publication — no embargo — by depositing their final refereed drafts in their institutional repositories and setting access to them as OA immediately.

The recently added Elsevier double-talk about “voluntariness” and “systematicity” has absolutely no legal force or meaning. As it stands, it is just vacuous, pseudo-legal FUD and can and should be safely ignored by authors.

And if and when Elsevier (putting at further risk its already rather unhappy public image) ever does decide to bite the bullet and changes its rights agreements from what they state currently to state instead that, as of today, Elsevier authors no longer retain the right to make their papers (Green, Gratis) OA unembargoed, then the institutional repositories’ automated request-a-copy Button will tide over researcher needs during the embargo with one click from the user to request a copy and one click by the author to provide one. This is not OA, but it’s “Almost-OA.”

Once the immediate-deposit mandate, the Button, and X% Immediate-OA + (100-X)% Almost-OA prevail worldwide, it won’t be much longer till embargoes die their inevitable and well-deserved deaths under the overwhelming worldwide pressure for OA, which by then will already all be only one keystroke away.

Meanwhile, X% Immediate-OA + (100-X)% Almost-OA will already be incomparably more access than all non-subscribing would-be users have (or have ever had) till now.

It is rather hard to say on whose side Björk is on, and why! It’s one thing to objectively measure the level and growth rate of Green and Gold OA, Immediate and Delayed, across disciplines and time, as Björk does, valuably. It’s a rather different thing to advocate for Gold OA.

Now, I am myself an unambiguous and unambivalent advocate for Green OA, whether when I am objectively measuring its growth rates or designing tools and policies to facilitate and accelerate mandating it. And my reasons (likewise no secrets) are the many reasons that Green OA can be facilitated and accelerated by mandating it.

Gold OA, in contrast, costs extra money (over and above uncancellable subscriptions) and can only grow on publishers’ terms, and publishers’ timetable.

I know of no reason to believe that OA can or will grow faster via the paid Gold route than the mandated Green route: The reason Björk gives above (publisher embargoes) certainly does not entail that conclusion at all. Immediate-deposit mandates are immune to publisher embargoes and will accelerate the demand and supply of OA unstoppably as they are adopted more and more widely.

That suggests a new parameter whose growth rate Björk and others might now find it interesting to measure: The growth rates of various kinds of mandates, keeping a special eye on the most powerful and effective one: The HEFCE/Liege model. Because that’s where most of the action in the next few years will be taking place…

Stevan Harnad

Winter Service Update


As we head into winter and as the holiday festivities begin, we wanted to let our authors know in advance that they may experience a slight delay in the peer review process of their manuscript if they submit anytime between now and the end of the year. This is because many of our academic editors and external referees will be out of the office at some point during the holiday season.

Despite many people being on vacation, the work of the journal continues and so we will endeavor to ensure that all manuscripts submitted to PLOS ONE are evaluated as quickly as possible, but please accept our advance apologies for any delays you experience.

In the meantime, we encourage you to visit the following links for information and answers to some of our common questions. For anything not covered here, please contact us at and we will respond as quickly as possible.

Image: Emily’s Snowman Cookies by Ralph Daily

I’ll Have What He’s Having: Dogs Eavesdrop on Human Interactions


In the spirit of Thanksgiving and sharing a warm meal with loved ones, we’d like to take a moment to give some social credit to our loving, faithful, and clever furry friends. Researchers have been investigating the question of whether animals can eavesdrop—or listen in on third-party interactions—for some time, and evidence of potential eavesdropping has been identified in dogs and other mammals, fish, and birds.

Dogs are especially good candidates for studying eavesdropping because they are social animals and have been domesticated, so they are accustomed to interacting with humans day-in and day-out. Most dog owners know how well their dogs can “read” them, and some might argue that their dogs can do this better than other people they know. Researchers have also confirmed that dogs can recognize human emotions, facial expressions, and friendliness versus hostility, the latter even in strangers.

In a more nuanced form of social interaction, dogs have been shown to prefer certain people over others depending on the outcome of third-party interactions. To further investigate how dogs respond to interactions among people, the authors of this recently published PLOS ONE article asked whether dogs can develop a preference for or against givers, or “donors,” in a “begging” interaction between people.


The study recruited 72 dogs of various breeds and sizes and put them in a testing environment that either resembled a home or a dog care facility. While the dog watched from across the room, two human assistants acted as “donors” (females, pictured above) who offered food to a “beggar” (male, above), and the beggar either reacted positively or negatively to the offered food. The extent of the reaction was controlled to try to determine which social cues the dog was picking up on: gesture + verbal (GV), gesture only (G), or verbal (V) only.

In the GV group positive scenario, the beggar received a yummy corn flake, ate it, and said “So tasty!”; in the negative scenario, the beggar said “So ugly!” gave the corn flake back, and then turned his back. The G and V groups differed in that they isolated the gesture and verbal components, respectively. After the beggar left, the dog was released and had 10 seconds to decide between the donors, who did not signal the dog in any way. Dogs that did not make a choice were removed from the analysis.

As the results below show, dogs were more likely to choose the donor who received a positive reaction; the authors also noted that the dogs tended to watch or gaze at the donor who received a positive reaction longer than the donor who received a negative reaction. However, the authors state that both gesture and verbal cues (the GV group) were required to show a reliable difference among the groups.


Although these results alone are not conclusive, as it is difficult to control for all the variables affecting these scenarios (e.g., the authors note that dogs chose randomly if the donors switched places), the authors suggest that the dogs may have attributed a “reputation” to the donor based on the beggar’s reaction, where both gesture and verbal cues were required for the dog to make this association.

While not the same as a scientific experiment, it might be fun to “test” your dog in various eavesdropping scenarios, especially in relation to available food* on the Thanksgiving table.

Happy Thanksgiving from PLOS ONE!

Citation: Freidin E, Putrino N, D’Orazio M, Bentosela M (2013) Dogs’ Eavesdropping from People’s Reactions in Third Party Interactions. PLoS ONE 8(11): e79198. doi:10.1371/journal.pone.0079198

Image Credits: Figure 1 by carterse, Figures 2 and 3 from the article

*food safe for pets to eat, of course!

Critique of UK Government’s Response to BIS Recommendations on UK Open Access Policy

Critique of excerpts from UK Government Response to BIS Committee

Joint “Re-Engineering” Plan
of UK Government and UK Publisher Lobby
for “Nudging” UK Researchers
Toward Gold Open Access

UKGOV: “…in the long term the most effective form of OA will be Gold OA?. there is no distinction to be made between the Government’s and BISCOM’s direction of travel for OA. The envisaged final destination is likely to be what the Finch Group termed a ‘mixed economy’ of Gold and Green OA, the proportions of which the decisions of researchers and behaviour in the market will decide?”

Throughout its response to BIS, it is evident that the UK Government is not perceiving OA primarily as a means of maximizing UK research uptake and impact — for the benefit of the UK tax-payers that fund the research, and for the progress and productivity of research, in the UK and world-wide — but as a means of sustaining the current revenue streams of peer-reviewed journal publishers, come what may.

That is why the Government’s “travel” plans tend to be framed far less in terms of the real needs of UK research and researchers and far more in terms of “business models,” “market,” a “mixed economy,” and how these can be “re-engineered” to keep them congruent with publishers’ terms and timetable.

There seems to be little room in the UK Government’s vision for even considering the following contingencies:

— that 100% OA is not only already fully feasible today, thanks to the online medium, but also urgent for research and researchers, indeed already overdue;

— that the online era has already made a lot of the traditional products and services of journal publishers (and their costs) obsolete;

— that publishers’ current revenue streams are greatly and needlessly inflated;

— and that the embargoes and other retardants that publishers are themselves placing in the path of OA are not, in reality, necessities, to sustain the essential functions of peer-reviewed journal publishing, as publishers claim; they are merely contrived to prop up the expensive and obsolescent functions of publishers in order to sustain publishers’ current highly inflated levels of income at all costs, come what may.

What is keeping the economy “mixed” and slow to provide OA, in other words, is that publishers are holding OA hostage to their current revenue streams, by embargoing Green, and transitioning to Gold only on terms and on a timetable that lock in those revenue streams.

The UK Government’s “re-engineering” plans are designed to make sure any transition stays on that track and timetable.

UKGOV: “…Government’s approach, therefore, amounts to a subtle re-engineering of the present market. By ‘nudging’ the flow of revenue for the publishing industry towards it becoming income from Article Publication Charges (APCs) for Gold OA?”

This “subtle re-engineering of the present market” consists of sustaining current publisher income streams (and modera operandi) by only providing OA on condition that current subscription revenue levels per article are sustained, and continue to be collectable in the form of Gold APCs in place of subscriptions.

There is no thought given to the distinct possibility that with all peer-reviewed final drafts deposited in institutional Green OA repositories, there will no longer be any need or demand for a print edition, online edition, access-provision or archiving (and their associated costs) from the peer-reviewed journal publisher: only the need for peer review (which is only a fraction of the cost of subscription publishing today).

And no thought of the real “market” that could indeed decide whether in a 100% Green OA world there will be any real demand left for anything else that peer-reviewed journal publishers offer, forcibly co-bundled with the peer review.

UK publicly funded research is being conceived by the UK Government as if it were primarily an investment in the journal publishing industry rather than in research productivity, applications and progress.

Some “nudge”! Some notion!

UKGOV: “…96% of journals have an embargo period of 24 months or less; 64% of journals have an embargo period of 12 months or less? This illustrates the extent to which the Government’s policy already is being complied with?”

Hardly. The effect of the UK policy has been precisely the opposite. More and longer embargoes have been adopted by publishers since the new UK policy was announced and began to be implemented.

Yet despite this perverse effect, the percentage of publishers that endorse immediate, unembargoed Green OA remains over 60% according to SHERPA Romeo data (much as it was before the Finch/RCUK policy). (This figure is camouflaged in the Government’s composite category of 64% with “an embargo period of 12 months or less .”)

(And aren’t the ones who are supposed to comply with a funder mandate the fundees, rather than publishers? Are we mixing up our constituencies here — or simply giving a hint of who’s really calling the shots?)

UKGOV: “…The Government, through HEFCE and the Research Councils, will continue to encourage Jisc, the Open Access Implementation Group (OAIG) and others to promote standardisation and compliance across subject and institutional repositories?”

Far more important for the UK Government to promote would be the institutional adoption of a mechanism for verifying compliance with its OA policy — in particular, its Green option (rather than just focusing on how the Gold is spent). HEFCE has provided a potential mechanism, in requiring immediate deposit (whether or not OA to the deposit is embargoed) for REF eligibility.

Institutions (ever eager to ensure compliance with funders’ conditions) will thereby be recruited and strongly motivated to monitor and ensure timely compliance. (Funding that would be a constructive use for unspent RCUK Gold OA funding.)

UKGOV: “…RCUK have balanced the objective of timely OA to all users with the need to respect, through a mutually acceptable embargo period, sustainable business models?”

Translation: RCUK has collaborated with publishers in embargoing OA to make sure that OA is only provided on publishers’ terms and timetable. (This is the UK/publishing-industry “re-engineering” plan.)

Fortunately, there is a remedy for this, and that is the HEFCE immediate-deposit mandate, plus the institutional repositories’ automated request-a-copy Button, which allows users to request and authors to provide (with one click each) a copy for research or educational purposes during any embargo (i.e., the Liege-model mandate, which is the one the UK should adopt.)

UKGOV: “…A re-engineering of the research publications market entails a journey not an event. Necessarily it requires a period of transition for the process of change. Longer embargo periods, as illustrated below, play an important part under some circumstances during the transition process?”

Translation: RCUK has collaborated with publishers in embargoing OA to make sure that OA is only provided on publishers’ terms and timetable.

This “journey” to “re-engineer the research publications market” is actually a government-funded business trip to guarantee publishers’ current income at UK tax-payers’ expense (and at the cost of lost research usage and impact). Not a happy “event” for UK research and researchers — or for global OA.

UKGOV: “…Government believes that the first signs of the impact of its OA policy on embargo periods have been beneficial?”

Beneficial for publishers, perhaps, but certainly not for researchers, nor for OA, since the policy’s perverse effect has been to encourage publishers to adopt and extend embargoes, not to shorten or drop them. (Nevertheless, over 60% of journals still do not embargo Green OA, despite the UK OA policy.)

UKGOV: “…as stated in David Willetts’ letter of 20 June 2013, UK policy already is leading to shorter embargo periods for Green OA?”

It is very hard to imagine what David Willetts is imagining here: The adoption of a Green OA embargo that is within Finch/RCUK’s current allowable limits is hardly a triumph for OA if the publisher formerly did not embargo Green OA at all (or had not yet formulated a policy).

Moreover, an embargo of a year or longer is no boon at all for OA. It is unspoken, but I think it’s fairly clear that most publishers are by now resigned to one-year embargoes on Green, along with a mandated push toward hybrid Gold. They know that most of the revenue in question comes from that first year.

So a “deal” to let publishers hold OA hostage to that one-year embargo (or else pay Gold) is not good news for research and research progress in an era where immediate 100% Green OA is fully within reach, technically and practically speaking, and where the costs of peer-reviewed journal publishing could be radically reduced if freed from the grip of publisher Green OA embargoes.

But again, there is a remedy for this, and that remedy is the HEFCE immediate-deposit mandate, plus the institutional repositories’ automated request-a-copy Button, which allows users to request and authors to provide (with one click each) a copy for research or educational purposes during any embargo. (This is again the Liege-model mandate, which is the one the UK should adopt.)

UKGOV: “…Publication of the results of publicly funded research is an integral part of the research process?”

This re-statement of the Wellcome Trust mantra continues to ignore the fact that the UK (but not Wellcome) also has to pay the costs of journal subscriptions. Hence the Gold APC costs are over and above subscription costs (which are likewise “a legitimate part of the cost of undertaking research”).

That means Gold OA APCs today are needless double-payments, over and above uncancellable subscriptions: “Fool’s Gold.” The only way they can turn into “Fair Gold” is if mandatory Green OA first prevails, eventually allowing subscriptions to be cancelled (and driving down publication costs by offloading access-provision and archiving onto Green OA repositories).

Then the price of Gold will drop to a fair, affordable, sustainable level, single-paid out of the institutional subscription cancellation savings, instead of double-paid, needlessly, as now, out of scarce UK research funds — needless because while subscriptions are still being paid (fully and fulsomely), Green OA can provide the OA.

UKGOV: “…HEFCE and other Funding Councils have agreed that QR funding may be used [to pay for Gold] at the discretion of the HEIs. Hence, HEIs have access to the necessary public funds to cover the cost of implementing the Government’s and RCUK’s OA policy?”

For UK researchers and institutions who deplore wasting scarce research funds to pay publishers even more money, it is hardly solace to tell them that if their UK Gold allotment runs out, they can squander their research money from other sources on fool’s gold too.

(But fortunately, be the Government ever so grudging about it, freedom of author choice between Green and Gold is now restored by RCUK, so the best protection against wasting UK research funds on Gold is to provide Green instead, via immediate-deposit, irrespective of embargo-length.)

UKGOV: “…The Government is aware of the reluctance of some HEIs to promote the Government’s preference for Gold OA, on the grounds that it represents a reduction in funding available for research, but the cost of the Government’s funded OA policy is estimated to be? approximately one per cent of the science budget? This is a marginal cost expected to be outweighed by the benefits to the economy arising from direct innovation and spill over benefits?”

(1) As noted, the UK’s designated funding for outgoing UK Gold is far from being the whole of the UK’s publication funding: The UK continues to pay for essential incoming journal subscriptions. And it is that level of spending that the UK is collaborating with publishers to “re-engineer” so as to sustain it whether it’s paid in the form of subscriptions or in the form of Gold APCs.

(2) So the extra marginal costs of the UK Gold subsidy (a further 1% of the UK’s research spend) are over and above the existing UK publication spend.

(3) Researchers cannot be expected to welcome the loss of yet another 1% of their already sparse research funding — and especially not when it is lost just for the purpose of propping up publishers’ already inflated revenue levels, come what may, in exchange for an OA that researchers could have at no further expense (beyond the existing UK subscription spend) via Green OA — if it were not for the publisher embargo on it — an embargo that the UK government is reinforcing, with its joint “re-engineering” plans to “nudge” researchers toward Gold OA.

Fortunately, there is a remedy for this, and that is the HEFCE immediate-deposit mandate — plus the institutional repositories’ automated request-a-copy Button, which allows users to request and authors to provide (with one click each) a copy for research or educational purposes during any publisher embargo (i.e., the Liege-model mandate, which is the one the UK should adopt.)

Because RCUK has restored authors’ freedom of choice of journal, and because HEFCE proposes requiring immediate-deposit for REF eligibility, UK researchers can choose to publish in any journal and can fulfill the RCUK mandate through immediate deposit in their institutional repository, whether or not OA to the deposit is embargoed. It is this immediate deposit that can — with the help of the repository’s automated request-a-copy Button during any embargo period — “re-engineer” publishing to Fair Gold (after 100% Green OA has prevailed, and made it possible for publishers to downsize to an affordable, sustainable price for peer review alone) instead of the Fool’s Gold toward which the UK government has set the “direction” for the UK’s “journey” toward OA.

BISCOM: “The Government and RCUK should clarify that Gold open access is the ultimate goal of, rather than the primary route to, their open access policies. We recommend that the Government and RCUK reconsider their preference for Gold open access during the five year transition period, and give due regard to the evidence of the vital role that Green open access and repositories have to play as the UK moves towards full open access. (Paragraph 70)”

UKGOV: “…Gold OA, at 12 per cent, is now proving to be the dominant form of OA.

Gold OA the dominant form of OA? Far from the truth.

Spontaneous, unmandated Green OA is already twice that figure, and if effectively mandated (on the HEFCE/Liege model) Green OA is over 10 times that figure, with the majority of deposits being done even before the date of publication.

UKGOV: “…the Government and RCUK would maintain that the merits of Gold OA (immediate, final published version, compatibility with data mining, unrestricted access and re-use, with attribution) mean that it is preferred to Green OA.

Preferred by whom? Finch/RCUK or UK researchers (and the rest of the world)?

(1) Much of today’s Green OA is immediate; some of today’s Gold OA is delayed. The embargoes are a result of publisher preference to sustain their current revenue levels come what may.

(2) To researchers who are denied access to unaffordable publishers’ versions, toll-free online access to the author’s Green OA final draft is the difference between night and day, insofar as research applications and progress are concerned.

(3) While access itself is restricted (both by publishers’ subscription access tolls and by publishers’ OA embargoes) freeing access is incomparably more important and urgent than paying publishers still more for further re-use rights.

(4) The fastest, fairest and surest way to reach Fair Gold OA and all the re-use rights users need and authors want to provide is to first mandate that authors provide Green OA — rather than to require pre-emptive double-payment, over and above uncancellable subscriptions, out of scarce research funds, for Fool’s Gold OA, at arbitrarily inflated prices, on the pretext of needing to sustain publishers’ current revenue streams (otherwise peer-reviewed publishing will perish).

UKGOV: “…The use of repositories is a feature of both Gold and Green OA. In terms of the sustainability of long term access to published research and data?”

Before institutional repositories can preserve access they must first provide it. To provide it they must have effective deposit mandates.

(There are no publisher embargoes holding up data-archiving, so it is a red herring to mention data in this context.)

The remedy is again obvious (to all but the UK Government: the publishing lobby is certainly fully aware of it, because it is fighting it tooth and nail):

Mandate immediate-deposit of all articles, whether published in a subscription journal or a Gold OA journal, whether OA is embargoed or immediate, whether the OA is Gratis (toll-free online access) or Libre (toll-free online access plus various re-use rights such as text-mining, re-mixing and re-publication).

That, with the help of the Button, will ensure that 100% Green Gratis OA — and eventually Fair Libre Gold OA — will come to pass as quickly as possible: affordably, scalably and sustainably.

UKGOV: “…the UK OA Decision Tree sets out clearly the direction of travel. This is not incompatible with researchers having a free choice as to whether or not to follow the preferred path. Government and RCUK hope they will choose to do so. Government welcomes RCUK retaining this decision tree. It has been agreed by all affected parties, and does not simply reflect the publishers’ position, but the consensus position arrived at by members of the Finch Group?”

I suppose it’s enough that the Government agrees that UK researchers and institutions are free not to follow the preferred path, hence can ignore the decision tree.

But it would have been more forthright and sensible to abandon the decision tree altogether, rather than leave it as a misleading sign-post.

It is indeed true that the UK-Government/Publishing-Lobby joint “re-engineering” plan for “nudging” UK researchers toward (Fool’s) Gold Open Access “does not simply reflect the publishers’ position, but the consensus position arrived at by members of the Finch Group.”

But what is patently false is that it has “been agreed by all affected parties.”

UKGOV: “…Government believes that by [funding hybrid Gold] the rate of adoption of Gold OA by publishers and researchers alike will accelerate?”

No doubt it will. But the goal of UK research, researchers, their institutions and the UK tax-payers who are funding the research is not to accelerate the UK rate of adoption of Gold OA but to accelerate the rate of provision of OA — in the UK and worldwide.

UKGOV: “…Evidence quoted above from the Publishers Association suggests that this is already proving to be the case. Researchers would be disappointed to have publication in their favoured journals denied to them if they opt for Gold OA and publishers would not want the inefficiencies, or brand dilution effects, of always putting publication of Gold OA material in to a new and separate journal?”

This ludicrous and embarassing piece of self-promotional spin is so obviously a page borrowed from the publishers’ agenda that it does not deserve a reply. It is shameful that the Government of the United Kingdom is echoing this tendentious sales pitch as its own.

UKGOV: “…Government does not consider it appropriate for publishers to rely on retrospectively amortising their APC revenue to discount global subscription rates, as some now do. This may address ‘double-dipping’ in one sense, (no increase in total revenue to the publisher) but it does nothing to address the concerns of research intensive individual institutions, wherever they are located around the world. Such institutions paying APCs for Gold OA publication in particular journals should see some related and proportional discount in their total subscription fees, with the same publisher, to avoid them disproportionately funding the translation to Gold OA?”

This pious homily is actually masking a piece of uncritical, unreflective and unrealistic nonsense:

If the Government agrees that a UK subscription rebate of only 6% of a UK Gold OA 6% overspend (i.e., 6% of 6%), over and above the UK’s 100% subscription spend, is not an “appropriate” way for publishers to refrain from double-dipping, what on earth does the UK imagine publishers will do instead? Because if publishers simply deduct the fee for UK hybrid Gold OA directly from UK subscription fees, that’s just tantamount to declaring the UK can have all the hybrid Gold OA it wants for free.

That would be just fine (since subscription fees are already paying the costs of publication in full): UK authors would automatically be free of embargoes and would automatically retain all desired re-use rights for the hybrid Gold journals in question.

But free hybrid Gold for subscribers is not at all what publishers have in mind, given how anxious they are to embargo Green (so I suggest that the UK re-discuss their joint “re-engineering” plans in this regard).

Here’s a hint: Publishers are only interested in a transition scenario that guarantees their current income streams, regardless of where they come from. They are just as averse to immediate-Gold OA as to immediate-Green OA, because it is the sustainability of their current revenue levels that is at risk. So unless the hybrid Gold fees are real and sustainable — which they are not, if they are merely funny-money, available to every subscribing institution as a free bonus — publishers will not budge on the UK Government’s plaintive nudge for a “proportional discount in their total subscription fees.”

Stevan Harnad

Content Mining; #ami develops her commandline and meets Ducktyping

Sleepless the bear and #ami2 the kangaroo meet Duck.

S: Hello Duck. What are you doing?

D: I’m helping #ami2 create her commandline parser. We’re going to use ducktyping.

S: what’s a commandline? [*]

Chuff: it’s one of the greatest inventions in computing. (…_Was_the_Command_Line) You type commands that you and the machine both understand. It’s better than GUIs. It interfaces with UNIX tools. #animalgarden will use commandlines for #ami2.

S: so what’s Ducktyping?

D: Let’s look in Wikipedia ( ). “the duck test, attributed to James Whitcomb Riley (see history below), which may be phrased as follows:

When I see a bird that walks like a duck and swims like a duck and quacks like a duck, I call that bird a duck.[1]

I walk like a duck and I quack like a duck so I am a duck.

A: The test is a rule. I can implement rules. Is there more?


In duck typing, one is concerned with just those aspects of an object that are used, rather than with the type of the object itself. For example, in a non-duck-typed language, one can create a function that takes an object of type Duck and calls that object’s walk and quack methods. In a duck-typed language, the equivalent function would take an object of any type and call that object’s walk and quack methods. If the object does not have the methods that are called then the function signals a run-time error. If the object does have the methods, then they are executed no matter the type of the object, evoking the quotation and hence the name of this form of typing.

Duck typing is aided by habitually not testing for the type of arguments in method and function bodies, relying on documentation, clear code and testing to ensure correct use.

S: So why are we using it?

D: Humans don’t like complicated commandlines, so we’ll make it very simple for them. The commandline has to work out what they want?

S: You mean guess?

A: No. I am not allowed to guess. I have to have precise rules.

D: Exactly. So here’s the problem. #ami2 can run over many different types of object. If we had commandline options for all of them the humans would forget them and muddle them. We’ll do the hard work. First the command itself. #ami has lots of things it can do, but if we write something like:

java –jar org.xmlcml.xhtml2stm.species.SpeciesVisitor

the humans will mistype it or get bored and never even try. So we’ll replace this with a script:


S: Isn’t that a lot of work for PMR and #ami2?

A: No. Mark Williamson showed us how to use maven to do it automatically. It’s already in the POM file.

D: Now we come to the ducktyping. Let’s say we ask a human to type:

species –-input ducks.html –-inputFormat HTML

half of them will mistype it, half will forget the “–inputFormat” and half will get bored. (The numbers add up since some humans will make TWO mistakes). So we use ducktyping to work out what they want.

species –i ducks.html

S: “-i”??

D: Some humans don’t like long words so we give them two options (–input and –i). It’s hardly any more work for PMR.

Chuff: So how do we know it’s an HTML file?

D: we use . We assume that the suffix “.html” means it’s an HTML file.

S: Suppose it isn’t?

D: Then the job fails.

Tasmanian Devil: Serves them right. Devil will drag them off to hell.

S: No, we like to think humans can learn gradually. We’ll try to fail gracefully. We can ask the file what type it thinks it is.

D: Many good file formats have a magic number that tells you what they are. XML files should know what namespace(s) they have. For example I could say “this XML file contains Chemistry (CML) and Maths (MathML) embedded in XHTML.

S: Wow. And are you implementing this, #ami?

A: PMR said he might. At present there are the following input types:

  • HTML (from the publisher’s site)
  • HTML from #ami2
  • PDF
  • XML from publisher
  • XML from PubMed (NLM)
  • SVG (from #ami)
  • Text
  • DOI

And lists or directories of all the above

S: Wow! What a lot to have to manage. Can it go wrong?

D: Yes. If a human points #ami2 at a list of holiday photos we won’t get much sense out.

Chuff: If we want people to use it we have to assume they will goof up whenever they can. We have to do almost all the work.

D: But when it’s working, then it’s easy for all of us.

S: So are there any optional options?

D: Yes. For example where we have a directory with many files in, we might want to filter those we want. For example:

species –i ducks/ –inputFormat xml htm html

will look for files of the form

    ducks/*.xml ducks/*.htm ducks/*.html

S: So presumably the bored ones can just type “-if”?    

D: Yes.

OWL: What happens if the directory contains other directories?

D: What a smart question!

OWL: I am the semantic OWL after all.

D: We have an option for recursion through the directories.

S: “Recursion”??

D: One of the most powerful and beautiful concepts in software ( ). You ask the method to invoke itself (either directly or implicitly).

S: Won’t that go on for ever.

D: If someone’s made a mistake, yes. Then you get a Stack Overflow …

Devil: Or I cart you off to hell.

D: … but good programs trap this. #ami will use the (–r –recursive) flag. If present it will go through all directories.

S: So I can write:

species –i notebook/ -r –if html pdf

D: exactly. The “/” tells us it has to be a directory. And if you type:

species –i / -r –if html pdf

it will traverse all your disk…

Devil: Unless I carry you off before that.

S: OK. What about output.

Duck: we need you to specify it. If you omit it it would either have to use the same place each time (overwriting) or use the input as a template. We might do that later. But at present we write:

species –i ducks/ html –o my/results/species.xml

and the results go to a named file.

S: Isn’t it too complicated for humans to work out where to put their results?

D: We try to make it easy for them. But at some stage a scientist has to work out what they are doing…

Devil … because if they don’t, I’ll cart them off…


















[*] I was asked this question by an informatics student [no names or places] halfway through their PhD. People just assume button pressing will solve everything.

Critique of RCUK’s Response to BIS Recommendations on UK Open Access Policy

Critique of excerpts from

Research Councils UK Response to BIS Committee

RCUK: compliance targets for the numbers of papers made available Open Access will be increased year-on-year, as will the funding we make available to support Article Processing Charges (APCs).

This is a publishing industry timetable and terms.

The RCUK compliance target should be for OA (Green + Gold), not just for Gold payments; and the annual OA target should be 100%.

Funding-based annual targets slow OA growth whilst making it much more costly to provide OA.

What is needed is a mechanism for monitoring and ensuring timely compliance. That’s what institutions (recruited by HEFCE‘s immediate-deposit mandate for REF2020 eligibility) will provide.

RCUK: During the transition period, we are allowing authors to use journals with embargo periods longer than the headline figure in the policy, but in line with those agreed by the Government, for publicly funded research where no funds are available to cover the payment of APCs.

This is unclear. Relaxing the enforcement of embargo limits on Green is good, because it preserves author freedom of choice of journal. But if it is only for when there’s no money to pay for Gold, it again incentivizes publishers to offer over-priced, double-paid hybrid Gold and to adopt or lengthen Green embargoes so as to collect as much extra UK Gold revenue as available.

RCUK: We are not convinced that institutional repositories are always the best way of providing [OA], and that solutions such as ‘request a copy’ button or emailing the researcher for a copy of the paper are not scalable to a wider constituency of users.

RCUK has misunderstood the repositories’ request-a-copy Button. It only requires a key press by the requestor and a key press by the author; the emailing is then automatic, by the repository software.

It is not clear what RCUK means by “not scalable”: Any requestor with email access can request a copy, for either research or educational purposes.

The purpose of the Button is

(1) to make immediate-deposit mandates adoptable and scaleable to all institutions and funders;

(2) to provide Almost-OA during any embargo period;

(3)to immunize against publisher embargoes on Green OA;

(4) to make sure authors only need to deposit once, institutionally (from there, deposits can be exported or harvested);

(5) to recruit institutions to monitor and ensure compliance with OA mandates;

(6) to make sure all articles are deposited;

(7) to document the demand for OA;

(8) to increase global demand and pressure for immediate OA;

(9) to hasten the transition from Almost-OA to OA.

RCUK: the headline figure quoted in the report that 60% of journals already allow immediate un-embargoed self-archiving of the peer-reviewed version of the article does not reflect the reality for Research Council funded authors. A comparable figure for journals used by Research Council funded authors is between 17% and 20% .

Sixty percent continues to be the worldwide estimate of the proportion of subscription journals that do not embargo Green OA. It is not clear where or how RCUK draws its UK-specific estimates, but it is likely that they are factoring the perverse effects of the Finch/RCUK policy itself, which has induced major publishers like Elsevier — which does not embargo Green OA — to adopt embargoes for UK content (if UK authors seek the re-use rights RCUK prefers) unless hybrid Gold fees are paid, as well as to add pseudo-legal hedges about “voluntariness” and “systematicity” to its formerly unhedged policy on Green OA.

RCUK is confusing cause and effect in its assessment of embargoes: The UK’s explicit funding and preference for CC-BY Gold and downgrading of Green as “embargoed OA” has induced (some) publishers to adopt or lengthen Green embargoes. RCUK now cites this effect as if it were a justification for RCUK’s having adopted what in fact caused it in the first place.

RCUK: RCUK has a preference for immediate, unrestricted, on-line access to peer-reviewed and published research papers, free of any access charge and with maximum opportunities for re-use. This is commonly referred to as the ‘gold’ route to Open Access. RCUK prefers ‘gold’ Open Access

Gold OA means the publisher provides the OA. Green OA means the author provides it.

Gratis OA means free online access. Libre OA means free online access plus “maximum opportunities for re-use” (e.g., CC-BY).

Gold OA does not necessarily entail Gold OA APCs and most Gold OA is not Libre OA.

Both Green and Gold OA can be immediate or embargoed.

RCUK conflates “Gold OA” with immediate OA and Libre OA.

RCUK conflates “Green OA” with embargoed OA.

Hence most of the RCUK’s evidence and reasoning amounts to self-justifying definitions and self-fulfilling prophecy.

RCUK: by going directly to the journal web site a reader can be confident that they are accessing the final peer-reviewed and formally published record of research.

By paying publishers a considerable amount of extra money for Gold OA, over and above what publishers are already being paid for subscriptions, the UK can indeed give readers this tiny increase in confidence — But the reader can be almost as confident in the Green OA version, without this vast extra payment.

Strengthening deposit mandates to increase open access

BISCOM: “RCUK should build on its original world leading policy by reinstating and strengthening the immediate deposit mandate in its original policy (in line with HEFCE‘s proposals) and improving the monitoring and enforcement of mandated deposit (paragraph 31).”

RCUK:The current RCUK policy is much stronger in requiring deposit and access within clearly defined time periods. Reinstating individual council policies would be a backward step.

Former council mandates were Green, but weak. They did not require immediate deposit, but only deposit after an allowable embargo period had elapsed, with no monitoring to ensure timely compliance.

A forward step is to upgrade the former council mandates to require immediate institutional deposit, whether or not access to the deposit is embargoed for an allowable period (as HEFCE has since proposed, for eligibility for REF2020). Institutions monitor and ensure compliance with funding conditions and the institutional repository’s request-a-copy Button tides over usage needs during the embargo.

The backward step is to prefer to double-pay for immediate Libre Gold with the UK’s scarce research funds — and to portray Green OA as meaning embargoed Gratis OA or a version of which one cannot even be confident. (To have bought into this specious argument is the surest sign of how publisher interests have been allowed to penetrate what ought to have been UK research interests.)

Pure Gold and Hybrid Gold

RCUK is completely silent about the fundamental objections BIS raised against funding hybrid Gold (subscriptions + Gold OA APCs):

(1) Hybrid Gold is arbitrarily over-priced.

(2) Hybrid Gold is double-paid (subscriptions + Gold OA APCs)

(3) Hybrid Gold makes double-dipping possible

(4) Double-dipping subscription rebates to all subscribing institutions worldwide only returns 6% of 6% of UK’s Gold OA APC subsidy to the UK.

(5) Subsidizing and encouraging hybrid Gold encourages publisher adoption and lengthening of Green OA embargoes to pressure authors to pick and pay for Gold.

BISCOM: “Given the importance of ensuring that UK open access policy does not result in reduced access in the UK or worldwide, the Government and RCUK must monitor and evaluate the impact of their open access policy on embargo lengths imposed by UK publishers. The impact on different subject areas must also be carefully monitored. That information must inform future meetings of the Finch Group and RCUK’s reviews of open access policy (paragraph 51).”

RCUK: we welcome the recent reduction in embargo periods by Elsevier, such that the majority of its journals now offer a green option with 12/24 month embargo periods in line with those agreed by the Government for publicly funded research where no funds are available to cover the payment of APCs, as well as a hybrid-gold option.

RCUK is astoundingly ill-informed: Since 2004, well before Finch/RCUK, Elsevier has not embargoed Green OA at all. Under the incentive of the Gold OA funding mandated by Finch/RCUK, Elsevier has now adopted explicit embargoes for Libre Green, as well as some (meaningless) double-talk about Gratis Green (it must be “voluntary” and must not be “systematic“).

Nothing for RCUK to welcome, if RCUK’s interests are with research access rather than publisher profits.

Affordability of APCs for authors and UK research organizations

BISCOM: “We are concerned that the expectation appears to be that universities and research organisations will fund the balance of APCs and open access costs from their own reserves. We look to the Government and RCUK to mitigate against the impact on university budgets. The Government must not underestimate the significance of this issue (paragraph 64).”

RCUK: Publication of research results is an integral part of the research process, and is thus a legitimate part of the cost of undertaking research. RCUK is committed to providing the necessary funding to cover the costs of publishing papers arising from the research funded by the Research Councils.

This re-statement of the Wellcome Trust mantra continues to ignore the fact that the UK (but not Wellcome) also has to pay the costs of journal subscriptions. Hence the Gold APC costs are over and above subscription costs (which are likewise “a legitiame part of the cost of undertaking research”).

That means Gold OA APCs today are needless double-payments: “Fool’s Gold.” The only way they can turn into “Fair Gold” is if Green OA first prevails, eventually allowing subscriptions to be cancelled (and driving down publication costs by offloading access-provision and archiving onto Green OA repositories). Then the price of Gold will drop to a fair, affordable, sustainable level, single-paid out of the institutional subscription cancellation savings, instead of double-paid, needlessly, as now, out of scarce research funds. — Needless, because while subscriptions are still being paid, Green OA can provide the OA.

RCUK: The shared ultimate goal of full Gold open access

The proximal goal (still far away) is 100% Gratis OA; this can be reached by mandating Green OA (with the immediate-deposit clause + Button). The ultimate goal is affordable, sustainable OA, at a fair price, with as many re-use rights as users need and researchers want to provide.

BISCOM: “The Government and RCUK should clarify that Gold open access is the ultimate goal of, rather than the primary route to, their open access policies. We recommend that the Government and RCUK reconsider their preference for Gold open access during the five year transition period, and give due regard to the evidence of the vital role that Green open access and repositories have to play as the UK moves towards full open access (paragraph 70).”

RCUK: RCUK’s preference is for immediate, unrestricted on-line access, aka Gold open access, for reasons defined in section 2 of this response.

Gold OA means publisher-provided OA. RCUK is referring to immediate, fee-based Libre Gold OA — but re-naming it “Gold OA” as if to contrast with Green OA.

Green OA means author-provided OA. RCUK is trying to portray Green OA as embargoed Gratis Green OA. This is publishers’ preferred way of spinning the meaning of “Green OA”: the same publishers that are embargoing Green OA in an attempt to make their definition a self-fulfilling prophecy.

And, regrettably, under the influence of the publishing lobby (unwittingly aided and abetted by the Wellcome Trust as well as the minority of researchers who are in a great hurry for Libre OA), Finch/RCUK have fallen for it, hook, line and sinker.

BISCOM: “RCUK’s current guidance provides that the choice of Green or Gold open access lies with the author and the author’s institution, even if the Gold option is available from the publisher. This is incompatible with the Publishers Association’s decision tree, and RCUK should therefore withdraw its endorsement of the decision tree as soon as possible, to avoid further confusion within the academic and publishing communities (paragraph 71).”

RCUK: ?the ‘decision tree’? represents the post-transition ‘end state’ … institutions now understand the flexibility we are offering during the transition period, and that the ‘decision tree’ has to be seen within the context of this flexibility.

Why attach a decision tree to a new policy, now, that authors are trying to understand, now, when the decision tree does not apply now, but will only apply eventually (maybe)?

(Is this not yet another way of digging heels in with: “My mind’s made up: Don’t confuse me with facts!“)

BISCOM: “If RCUK and the Government continue to maintain their preference for Gold, they should amend their policies so that APCs are only paid to publishers of pure Gold rather than hybrid journals. This would eliminate the risk of double dipping by journals, and encourage innovation in the scholarly publishing market (paragraph 77).”

RCUK: RCUK made an explicit decision not to restrict the RCUK block grants only to covering APC costs for pure Gold journals. To have done so would have restricted the choice of authors as to where they could publish their research by limiting them to pure Gold journals if they wanted to ‘go gold’… RCUK commitment to provide APC funding without restriction has already driven change within the publishing industry, with many major subscription journals now offering a hybrid-gold option for the journals that Research Council authors chose to publish in. It is unlikely that publishers would have made these changes if RCUK had restricted its APC funding to pure Gold journals.

My mind’s made up! Don’t confuse me with facts!” — facts about over-pricing, double-payment, double-dipping, “rebates,” and perverse effects:

Gold payments are in any case double-payments (subscriptions + Gold APCs). If paid to the same publisher (hybrid Gold), they also allow publisher double-dipping. But even if not double-dipped, but instead paid back as a rebate to all subscribing institutions, that just means the UK’s 6% double-payment subsidizes all subscribers worldwide with a 6% subscription reduction! The UK itself only gets back 6% of the Gold APC subsidy it has provided for the rest of the world.

And far from following the UK’s profligacy with this needless foray into paying for Fool’s Gold, the rest of the world — which mandates Green, not Gold — is left saddled with the perverse effects of the UK’s incentives to hybrid Gold publishers: offer hybrid gold, pick your price, and adopt or lengthen embargoes on Green!

RCUK: RCUK considers that publishers need to ensure that subscriptions paid by institutions for hybrid journals reflect any additional revenue that the journal has received through the APCs that the institution has paid in order to publish ‘gold’ papers in that journal.

See above: RCUK thinks that a 6% rebate of a needless 6% double-spend (6% of 6%) is sufficient solace. It is not clear that UK tax-payers would or should see it that way. Nor should UK researchers. (Nor should researchers worldwide, in view of the perverse effects of UK policy on Green OA embargoes worldwide.)

RCUK: Whilst RCUK does not restrict its policy to supporting only pure Gold journals, institutions are free to decide how they allocate their RCUK block grants, and this could include declining to make APC payments to specific hybrid Gold journals that institutions may consider guilty of ‘double-dipping’.

How are institutions supposed to figure out whether publishers are double-dipping?

The best thing institutions can do with the scarce research funds RCUK has needlessly re-directed to double-paying publishers for Fool’s Gold is to make sure all their authors immediately deposit their final, refereed drafts in the institutional repository and make them Green OA as soon as possible.

And instead of wasting the RCUK OA funds on Fool’s Gold, they should spend them on implementing a reliable mechanism for monitoring and ensuring timely compliance with the HEFCE immediate-deposit requirement.

Stevan Harnad

Content-mining: Using Tabula

Extracting tables from PDFs is not fun. But @TabulaPDF have made it possible. So we are going to learn how to extract tables at Jenny’s liberation-fest tomorrow. Here’s how:

Got to http://

(That’s right: NERD POWER. Nerds are good. Nerds are clever). We find:


Tabula is a tool for liberating data tables trapped inside PDF files.

Why Tabula?

If you’ve ever tried to do anything with data provided to you in PDFs, you know how painful this is — you can’t easily copy-and-paste rows of data out of PDF files. Tabula allows you to extract that data in CSV format, through a simple interface. And now you can download Tabula and run it on your own computer, like you would with OpenRefine.

Download and install Tabula

Note: You’ll need a copy of Java installed. You can download Java here.

1. Download the version of Tabula for your operating system:

2. Extract the zip file using the file extractor of your choice (such as 7-zip).

3. Go into the folder you just extracted. Run the “Tabula” program inside.

4. In your web browser, go to http://localhost:8080/ . (This should automatically happen, actually.) There’s Tabula!

5. Upload a file of your choice. Select a section of a table, and go.

That’s it.

It works! Here’s a table (they are Gibbons!) [#animalgarden needs more monkeys…]

We use Tabula. Select the table and we get:

WOW! It’s actually in a CSV table

OK the spaces are occasionally elided, and the italics are gone, but we are working on that…



Tabula is better than #ami2 on tables (AMI relies on the English word “Table” and her tables are currently being refactored). Tabula is developing auto-detect. #ami2 is probably better on italics and spaces.

So we join forces. Everyone gains.



Burning the Candle at Both Ends: Intertidal Ant Species Can Work Night and Day


If you’ve ever experienced rush hour traffic, you know firsthand that most humans base our schedules roughly around the rise and setting of the Sun, during daylight hours. However, the Australian intertidal ant, Polyrhachis sokolova, must instead schedule its busy day of foraging in the mangrove forest according to the rise and fall of the tide. Low tide can occur day or night, and to function effectively in both the brightest and darkest conditions, these ants possess several useful eye structures—not unlike the pupils in our eyes, or night vision goggles—that help them adjust to different light levels so that they can find food.

AntFaceThere are thousands of ant species that can have a variety of habitats, morphologies (shapes), and navigation methods. Australian intertidal ants use vision to identify landmarks like trees, and celestial cues like the angle of starlight to find their way. Low tide, whenever that may be, is the best time for foraging, so these ants need to see in all light levels without the assistance of flashlights or sunhats. Exactly how they manage to adapt to such a wide range of light conditions was investigated and described in a recent PLOS ONE study.

To learn more, researchers made tiny casts of intertidal ants’ eyes using fingernail polish. They flattened the casts and examined them under a microscope. Ants have compound eyes, meaning that their eyes are made of many tiny facets, or eye units, compared to simple eyes like ours that only have one eye unit each. Researchers counted the number of facets in each compound eye and measured each one’s diameter. The eyes were cast at different times—10am and 10pm—to inspect how the eye structures changed in dark versus light conditions. The light sensitivity of the eyes was calculated based on this morphological data.

journal.pone.0076015.g003Intertidal ants’ compound eyes each have around 596 facets and are similar to the eyes of other ant species specifically adapted to darker conditions. Eyes that “see” in the dark tend to have larger lenses and be extremely sensitive to light to get the most out of the little available light. This night vision adaptation would typically limit an ant’s ability to function in daylight because bright light would overload the photoreceptors in these highly sensitive structures, but the researchers found  other mechanisms that protect these ants’ eyes, restricting the amount of light that can enter—like a pupil—by making the openings that allow light to pass smaller. This mechanism helps the ants adapt their night-vision eyes to bright daylight.  This type of pupil is seen in other nocturnal ants but had not been found previously in ants that forage during the day.

Finally, to assist in navigation, the researchers found yet another structure in the ants’ eyes: special light detectors that act like skylights and help determine direction by sensing the angles of light sources in the sky. Therefore, Australian intertidal ants do not have the very best day or night vision, but they instead sacrifice some of their ability to see well in each condition in order to see “adequately” in both.

Citation: Narendra A, Alkaladi A, Raderschall CA, Robson SKA, Ribi WA (2013) Compound Eye Adaptations for Diurnal and Nocturnal Lifestyle in the Intertidal Ant, Polyrhachis sokolova. PLoS ONE 8(10): e76015. doi:10.1371/journal.pone.0076015

Image Credits: Images are from Figures 1, 2, and 3 from the manuscript.

Content-mining the scientific literature into CKAN

CKAN was pioneered by the Open Knowledge Foundation as an Open Source tool to make government and related data more easily available. Governments love it, because it’s good and it’s free and it’s open. But why would we use it for science?

Because it’s good and it’s free and it’s open.

Here’s Wikipedia:

The Comprehensive Knowledge Archive Network (CKAN) is a web-based
open source data management system for the storage and distribution of data, such as spreadsheets and the contents of databases. It is inspired by the package management capabilities common to open source operating systems like Linux, and is intended to be the “apt-get of Debian for data”.[2]

Its code base is maintained by the Open Knowledge Foundation. The system is used both as a public platform on[3] and in various government data catalogues, such as the UK’s,[4] the Dutch National Data Register, the United States government’s “ 2.0″[5] and the Australian government’s “Gov 2.0″.[6]
SOUTH Australian state government has also joined the ranks of many jurisdictions world-wide in making government data freely available to the public on CKAN platform[7]

Well if Barrack Obama uses it, it must be good. But how to use it?

You can use it in private , without permission,of course (that’s what Open Source means). But the OKFN runs a public server and Chuff (@okfn_okapi) spoke very nicely to Mark Wainwright who set up an Organization: November25). Chuff asked for petermr to be an admin.

It’s very easy. You just enter some metadata and tip the data in. And here what it looks like

This is the prototype. The animals know that Hydraena dentipes and H. dentipes are the same, so they’ll replace all H. with Hydraena. (probably before the data gets in). There’s between 5 and 20 species per paper full-text, but often far more in the diagrams and tables (their speciality).

So soon they will have the best collection of published animals in the scientific literature…

.. and the best plants, and bacteria and …

It’s easy to add metadata to CKAN, and we’ll do it by machine. That means we can search the literature by species.

And soon (maybe Wednesday) by:

  • Chemistry
  • Sequences
  • Phylogenetic trees
  • Identifiers.
  • And whatever YOU can contribute (it’s easy)

So if this excites you – and it should – please let us know.

Content-mining: #animalgarden discover CKAN/Datahub and create the November25 declaration of the Right to Mine

A massive day for #animalgarden. They’ve made a huge technical breakthrough. They can now store all the facts from the scientific literature.

They’d been worrying about where to put the data they extracted, now that the STM publishers have blessed Content-mining. Today Mark Wainwright from the OKFN visited and told them about CKAN. It holds very flexible metadata and can also hold the data. CKAN was developed for governments to manage Open Data, but can it manage science? Mark said yes – so they had a try. But before that, Mark said, you need a name for the Datahub project.

#animalgarden? Not quite right. Panton? Again not quite right?

November 25! The November 25 revolution! The first liberated data set in CKAN. That sounded just right.

But if there is a revolution, shouldn’t there be a declaration? Yes, of course. They know it by heart: “The right to READ is the Right to MINE”!

And a proper declaration need to be big and signed by everyone. So here are all our names.


What about the data? No problem. You can see it at

Altmetrics panel discussion at University of Kentucky Libraries

The University of Kentucky Libraries celebrated Open Access Week 2013 with a panel discussion (#Altmetrics: Demystifying the Link between Research Impact and Social Media) on Oct. 22nd.  The videos and presentation slides of the event are now online:

We also created a research guide to introduce the university community to different types of impact metrics. If you have any comments or suggestions, please feel free to contact us.

Robofish: How Color and Tail Wagging Helped Bring a Robot Fish to “Life”

Figure 1

In an age of 3D printing and bionic limbs, distinctions between the manmade and the natural can sometimes blur. Take, for example, the case of the robotic fish depicted above (part A). This little guy is modeled after Notemigonus crysoleucas (image, part B), also known as the golden shiner, and in a recent PLOS ONE study, researchers put it to the test: can a robotic fish influence the behavior of a real fish, and if so, what characteristics enable the robotic fish to do so? According to the researchers at Polytechnic Institute of New York University, answers may depend on the robot fish’s color and the frequency with which it waggles its tail.

To find out more, the authors commissioned the making of two robot fish for this study: one gray and one red. While both physically modeled the golden shiner in many respects, only the gray robot fish was painted to mimic its real-life counterpart. Other than color, the two robots were identical: both consisted of three rigid parts, connected on hinges, and sported silicone tail fins.

pone.0077589 Figure 2

As illustrated above, one robot fish was placed in a water tunnel with a real fish during each trial. The real fish was free to swim in the tunnel while the robot fish “swam,” or waggled its tail fin, in the center of the apparatus. The robotic fish’s tail waggled at various frequencies, ranging from 0 Hz to 4 Hz, as webcams tracked the real fish’s movements. The middle of the tunnel was designated the “focal region” to indicate where fish and robot interaction was likely to occur. The researchers further divided the region behind the fish into four parts, explaining that the robot fish’s tail wagging was likely to affect the water flow, and thus the real fish’s behavior, in this area.

pone.0077589 Figure 4

After reviewing the webcam footage, they found that neither factor (color, tail wagging frequency) working alone had a significant impact on the real fish’s swimming behavior. However, when the gray robot wagged its tail at 3 Hz, the real fish spent a significantly longer time swimming in the center of the tunnel, preferring to spend most of its time swimming right behind the robot. When this happened, the wake created by the robot’s tail wagging could allow the real fish to reduce its energy expenditure while swimming.

What’s so special about wagging your tail fin at 3 Hz, you ask? The researchers ascertained through preliminary research that when golden shiners swim, their tails waggle at 3.32 Hz. In addition, the gray robot’s coloring may have been more attractive to the golden shiner than the red robot’s, as it may have elicited a likeness-related social response in the real shiner. This suggestion is in line with other robot work in comparable fish species.

In other words, the robot fish exerted the most influence—or was the most convincing to the real fish—when its coloring and movements closely corresponded to the coloring and movements of a real fish. Go figure!

If you are interested in learning more, visit our website and see what others had to say.


Citation: Polverino G, Phamduy P, Porfiri M (2013) Fish and Robots Swimming Together in a Water Tunnel: Robot Color and Tail-Beat Frequency Influence Fish Behavior. PLoS ONE 8(10): e77589. doi:10.1371/journal.pone.0077589

Image 1: Figure 1 from the paper

Image 2: Figure 2 from the paper

Image 3: Figure 4 from the paper

Would you share your genome sequence? (can you get to Cambridge?)

Would you?

The next event in Cambridge Open Research is

We are going to be led by Fiona Nielsen who created

The genomic era is at our doorstep together with a lot of promises to personalized medicine – But what exactly is a genome? Do I have to share it? Do I have to share it all? With whom should I share it? What ethical issues might arise? What are my rights concerning my genome?

EVERYONE welcome

The only requirement is possessing a genome.

Big Deals, Big Macs and Consortial Licensing

Ann Okerson (as interviewed by Richard Poynder) is committed to licensing. I am not sure whether the commitment is ideological or pragmatic, but it’s clearly a lifelong (“asymptotic”) commitment by now.

I was surprised to see the direction Ann ultimately took because — as I have admitted many times — it was Ann who first opened my eyes to (what eventually came to be called) “Open Access.”

In the mid and late 80’s I was still just in the thrall of the scholarly and scientific potential of the revolutionarily new online medium itself (“Scholarly Skywriting”), eager to get everything to be put online. It was Ann’s work on the serials crisis that made me realize that it was not enough just to get it all online: it also had to be made accessible (online) to all of its potential users, toll-free — not just to those whose institutions could afford the access-tolls (licenses).

And even that much I came to understand, sluggishly, only after I had first realized that what set apart the writings in question was not that they were (as I had first naively dubbed them) “esoteric” (i.e., they had few users) but that they were peer-reviewed research journal articles, written by researchers solely for impact, not for income.

But I don’t think the differences between Ann and me can be set down to ideology vs. pragmatics. I too am far too often busy trying to free the growth of open access from the ideologues (publishing reformers, rights reformers (Ann’s “open use” zealots), peer review reformers, freedom of information reformers) who are slowing the progress of access to peer-reviewed journal articles (from “now” to “better”) by insisting only and immediately on what they believe is the “best.” Like Ann, I, too, am all pragmatics (repository software, analyses of the OA impact advantage, mandates, analyses of mandate effeciveness).

So Ann just seems to have a different sense of what can (hence should) be done, now, to maximize access, and how (as well as how fast). And after her initial, infectious inclination toward toll-free access (which I and others caught from her) she has apparently concluded that what is needed is to modify the terms of the tolls (i.e., licensing).

This is well-illustrated by Ann’s view on SCOAP3: “All it takes is for libraries to agree that what they?ve now paid as subscription fees for those journals will be paid instead to CERN, who will in turn pay to the publishers as subsidy for APCs.”

I must alas disagree with this view, on entirely pragmatic — indeed logical — grounds: the transition from annual institutional subscription fees to annual consortial OA publication fees is an incoherent, unscalable, unsustainable Escherian scheme that contains the seeds of its own dissolution, rather than a pragmatic means of reaching a stable “asymptote”: Worldwide, across all disciplines, there are P institutions, Q journals, and R authors, publishing S articles per year. The only relevant item is the article. The annual consortial licensing model — reminiscent of the Big Deal — is tantamount to a global oligopoly and does not scale (beyond CERN!).

So if SCOAP3 is the pragmatic basis for Ann’s “predict[ion that] we?ll see such journals evolve into something more like ‘full traditional OA’ before too much longer” then one has some practical basis for scepticism — a scepticism Ann shares when it comes to “hybrid Gold” OA journals — unless of course such a transition to Fool’s Gold is both mandated and funded by governments, as the UK and Netherlands governments have lately proposed, under the influence of their publishing lobbies! But the globalization of such profligate folly seems unlikely on the most pragmatic grounds of all: affordability. (The scope for remedying world hunger, disease or injustice that way are marginally better — and McDonalds would no doubt be interested in such a yearly global consortial pre-payment deal for their Big Macs too?)

I also disagree (pragmatically) with Ann’s apparent conflation of the access problem for journal articles with the access problem for books. (It’s the inadequacy of the “esoteric” criterion again. Many book authors — hardly pragmatists — still dream of sales & riches, and fear that free online access would thwart these dreams, driving away the prestigious publishers whose imprimaturs distinguish their work from vanity press.)

Pragmatically speaking, OA to articles has already proved slow enough in coming, and has turned out to require mandates to induce and embolden authors to make their articles OA. But for articles, at least, there is author consensus that OA is desirable, hence there is the motivation to comply with OA mandates from authors’ institutions and funders. Books, still a mixed bag, will have to wait. Meanwhile, no one is stopping those book authors who want to make their books free online from picking publishers who agree?

And there are plenty of pragmatic reasons why the librarian-obsession — perhaps not ideological, but something along the same lines — with the Version-of-Record is misplaced when it comes to access to journal articles: The author’s final, peer-reviewed, accepted draft means the difference between night and day for would-be users whose institutions cannot afford toll-access to the publisher’s proprietary VoR.

And for the time being the toll-access VoR is safe [modulo the general digital-preservation problem, which is not an OA problem], while subscription licenses are being paid by those who can afford them. CHORUS and SHARE have plenty of pragmatic advantages for publishers (and ideological ones for librarians), but they are vastly outweighed by their practical disadvantages for research and researchers — of which the biggest is that they leave access-provision in the hands of publishers (and their licensing conditions).

About the Marie-Antoinette option for the developing world — R4L — the less said, the better. The pragmatics really boil down to time: the access needs of both the developing and the developed world are pressing. Partial and makeshift solutions are better than nothing, now. But it’s been “now” for an awfully long time; and time is not an ideological but a pragmatic matter; so is lost research usage and impact.

Ann says: “Here?s the fondest hope of the pragmatic OA advocate: that we settle on a series of business practices that truly make the greatest possible collection of high-value material accessible to the broadest possible audience at the lowest possible cost ? not just lowest cost to end users, but lowest cost to all of us.”

Here’s a slight variant, by another pragmatic OA advocate: “that we settle on a series of research community policies that truly make the greatest possible collection of peer-reviewed journal articles accessible online free for all users, to the practical benefit of all of us.”

The online medium has made this practically possible. The publishing industry — pragmatists rather than ideologists — will adapt to this new practical reality. Necessity is the Mother of Invention.

Let me close by suggesting that perhaps something Richard Poynder wrote is not quite correct either: He wrote “It was [the] affordability problem that created the accessibility problem that OA was intended to solve.”

No, it was the creation of the online medium that made OA not only practically feasible (and optimal) for research and researchers, but inevitable.

Stevan Harnad

Legacy publishers! The Berlin moment: your paywalls are history. We want freedom and we want it now!

Yesterday was the Open Access Button ThunderClap:

I’m proud to have been one of the 434 and to have donated 2000+ followers. That means that yesterday they will all have got a tweet like the ones below:

I’d love to see the list . But note our own Cambridge MP Julian Huppert (immediately above) retweeting the clap.

For me this is the Berlin moment. The critical date when the wall started to fall down. A million people telling the conventional publishing system:

Your world is over.

Open access is not fundamentally about free access to the literature (such as Green) or extortion through Hybrid Gold.

It’s about Freedom. Freedom to build our own world where rich corporates and out-of-date rich scholarly societies do not control the means of production. Where everyone, not just academics, feels ownership of the publishing system as a modern means of communication.

Where young people are seen as the wellspring of the future.

As happened yesterday with Joe and David’s great , simple , vision.

I grew up in the time of great political movements. Read John Lewis’ speech to The March On Washington ( ). Read it all. Fifty years ago the issues were different, but this echoes the feeling of many of us in the present:

To those who have said, “Be patient and wait,” we must say that we cannot be patient. We do not want our freedom gradually but we want to be free now.

We are tired. We are tired of being beat by policemen. We are tired of seeing our people locked up in jail over and over again, and then you holler “Be patient.” How long can we be patient? We want our freedom and we want it now.

We do not want to go to jail, but we will go to jail if this is the price we must pay.

Open Access may seem a smaller issue than racism and human rights. But we are fighting for our digital future and if we lose it we may lose our humanity.