Monthly Archives: November 2012

Editorial board appointed for Food and Energy Security

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Food and Energy SecurityWe are delighted to announce that Food and Energy Security has recently appointed an international editorial board to compliment and support the activities of the existing senior editor team. Each new editor is an expert in their field, providing unique insight into a specific area of food and energy security, and its associated disciplines. 

The editorial board now includes 8 Chinese editors, 4 of which are based at the Chinese Academy of Sciences. The strength of representation from China is in keeping with the journals ambition to attract the best research from this key region and with interests as varied as Weiming Shi’s study into Root Biology and Rhizosphere Processes for Sustainable Agriculture and Yihua Zhou’s focus upon the production of biofuel and new energy we feel confident the journal is now well positioned to achieve this goal.

Sally Wilkinson, one of five editors from the UK, is focused on developing and improving perennial non-food biomass and bioproduct crops. Her research is directly involved in several large international projects funded by the European Commission. Li Laigeng, at the same time, is committed to exploring plant biomass as an important renewable source for energy, fiber material and biochemicals. Gail Taylor at the University of Southampton has a long standing interest in the use of woody plants as sources of renewable energy for heat, power and more recently for liquid biofuels such as bioethanol. To further the possibility of biomass becoming a real fuel source, Ashutosh Mittal, based at the National Renewable Energy Centre at the US, is currently leading research to develop the conversion of biomass into fuel in a cost-effective manner.

Several of the new editorial board have a particular interest in drought, and research into the drought tolerance of plants. Andrew Leakey is currently investigating the genetic basis of drought tolerance in C4 grasses at the University of Illinois, while Chun-Peng Song’s research at Henan University in China centres on plant response to abiotic stress such as drought stress. Ruilian Jing is leading several national projects at the Institute of Crop Germplasm, CAS, aiming to improve crop drought tolerance and water use efficiency. Zhizhong Gong’s research into plant defence at the China Agricultural University s also focused on three aspects of the salt, drought and cold hardiness of the plant.

A select number of the editorial board specialise in nutrition improvement in crops. Chun-Ming Liu at the renowned Institute of Botany at CAS uses rice and Arabidopsis as models for research on seed development and Adam Price at the University of Aberdeenis involved in the release of a better-rooted rice cultivar in India produced via marker assisted selection. Gustavo A. Slafer (University of Lleida, Spain) is focused on the mechanisms, at the crop level of organization, underlying the responses of grain crops to environmental and genetic factors.

Our two South American editors – Paulo Mazzafera of the University of Campinas in Brazil and María Patricia Benavides of the University of Buenos Aries, Argentina – are both interested in secondary metabolism . María Patricia Benavides is currently involved in a study of nitrogen metabolism under heavy metal stress. Meanwhile Nigel Halford’s work at Rothamsted Research UK concerns the genetics of metabolic regulation in crop plants, particularly how environmental stresses affect plant metabolism.

Both Leon Terry (University of Cranfield, UK) and Umezuruike Linus Opara (Stellenbosch University, South Africa) are concerned with the processes surrounding the harvest. Opara, the first board member from Africa, is currently leading research projects on design of the ‘Packaging of the Future’ supported by the South African Postharvest Innovation Programme. Terry’s research is similarly committed to reducing waste and increasing food security around the world.

For a full list of the editorial board members please visit the Food and Energy Security website. To submit your paper to Food and Energy Security visit our online submission site.

Beyond the Problem of Access: Democracy Closing in Hungary

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On Monday November 26 2012, a Hungarian MP, Márton Gyöngyösy, deputy leader of the extreme right “Jobbik” Party, called for the creation of a race-based list, on the grounds of risk to Hungarian national security.

This all-too-familiar burst of base bigotry from the Jobbik party in Hungary’s parliament has deflected attention from an even more ominous event that passed unnoticed, in the very same place, on the very same day: Electoral gerrymandering designed to keep the governing Fidesz Party in power.

As Marton Dornbach points out below in his remarkably insightful commentary from the Hungarian Spectrum — reproduced in full and slightly updated by the author — Fidesz is just playing “good cop” to Jobbik’s “bad cop”.

The two right-wing parties are only distinguishable by the fact that Jobbik’s hallmark is psychopathic bigotry, whereas Fidesz’s hallmark is psychopathic opportunism. Both are sinking Hungary deeper and deeper, downward and backward, toward an ugly, resentful autocracy and xenophobia to which Hungary is no stranger, and from which it has not yet made the sincere effort to dissociate itself that has been made by the other nations of Europe.

Hungary has a majority of decent, fair-minded people, like every other nation in the world. It is not beyond hope that world outrage at this pair of incidents may help them to rally against these two pernicious parties, Fidesz and Jobbik, that have already done Hungary so much harm, and oust them decisively, once and for all, in the next election, despite Fidesz’s shameless and disgraceful efforts to make this so much more difficult to do.

“The thing that is really important here, in my opinion, is not that Márton Gyöngyösi is a Nazi. Most of us realized a while ago that Jobbik is a virulently racist Neo-Nazi party. This is no news. It is also no news, unfortunately, that the ruling party is willing to go to great lengths to avoid unequivocal and firm condemnation of Nazi talk (incidentally, the most disgracefully equivocal part of Zsolt Németh?s response was the formulation he chose: he said the number of Jews in government ?is not particularly closely related? to the severity of the conflict in the Middle East /?nem nagyon kapcsolódik ahhoz?/)

“No, the most newsworthy aspect of this incident is the timing. Gyöngyösi?s statements came five days after the ceasefire in Gaza was announced. So there was nothing particularly topical about his sick proposal. In any case, thugs like him never needed a pretext for Jew-baiting. Why now then?

“Well, it so happens that, on the very same day that MGy made this demented proposal, the Fidesz supermajority put a stake through the barely-beating heart of Hungarian democracy by abolishing universal voting rights and introducing an exceptionally restrictive form of mandatory voter registration. You wouldn?t know this from the foreign media coverage of the Monday parliamentary session; but that?s precisely the point. Especially in the international media, but in Hungary too, the abolition of universal voting rights was completely eclipsed by this Nazi provocation. After all, viewed from London or Washington or Brussels it is so much easier to relate to Nazism than to election technicalities in a small country. So much easier for journalists to cover the former than the latter.

“But let?s put things in perspective. Unfortunately, there always were and perhaps there always will be sick racists who harbor genocidal fantasies. The fact that Hungarian society as a whole fails to ostracize such people and/or treat them as psychiatric cases is a sign of a civilizational breakdown. However, there is no real danger of Gyöngyösi?s proposal being implemented (although in this respect we all know that nothing is impossible). Without denying that anti-Semitism is alarmingly widespread in Hungary and has a potential to produce violent outbursts, I think it is safe to say that the only group of people in Hungary that faces systematic discrimination and harassment on account of ethnic origins is the Roma. So we should see MGy?s statement as a purely symbolic act of transgression whose sole purpose was to shock and draw attention.

“Unlike MGy?s proposal, the election law passed on the very same day is certain to have very real future consequences. It drastically reduces the chances of Orban?s opposition. Let?s be clear about this: the introduction of severely restrictive voter registration rules in a country with a perfectly well-functioning central registry is an unprecedented disgrace. It is the most overt violation of basic democratic principles even in the sordid record of the Orban regime?s power grab. This is the outrage that is being overlooked amid the (absolutely justified) uproar about the latest Nazi provocation by Jobbik. Look at the foreign coverage of what happened on Monday in the Hungarian parliament: there is no reference to the election law, no reference to Zsolt Nemeth?s appalling non-response, while most outlets state that the Hungarian government has condemned the provocation ?in the strongest terms? (if only!) The whole story is a PR coup for Fidesz. In keeping with the line of defense adopted by numerous diplomatic and journalistic apologetes of the regime, this incident has given Fidesz yet another opportunity to play good cop to Jobbik’s bad cop.

To conclude, I find it almost impossible not to raise the obvious, admittedly speculative, question: Cui bono? Who is benefitting from all of this? To my mind at least the timing of this crass provocation invites the conjecture that there may be (tacit or not-so-tacit) co-operation between the Neo-Nazi Jobbik party and the ruling Fidesz supermajority. And let?s not forget here two points: it is not inconceivable that Fidesz may need to form a coalition with Jobbik to stay in power after 2014; and Jobbik is the other party, beside Fidesz, which stands to gain from the new voter registration rules. [original comment edited by MD]

Marton Dornbach

Here is some background reading on last year’s signs of Hungary’s downward trajectory already noted in this blog:

Wednesday, February 23, 2011

Hungary’s Philosophy Affair: Bringing It All Out Into The Open

Open Letter to President of Hungarian Academy of Sciences

Response of President of Hungarian Academy of Sciences

The Hungarian Philosopher Affair: On Nyiri on Martyrdom

The Hungarian Philosopher Affair: On Hornok on 1919

The Hungarian Philosopher Affair: On Vancsó on Smoke Screens

The Hungarian Philosopher Affair: On “Magyar” On White Collar Crime

Quod Erat ad Demonstrandum (QED)

For animals, ‘Value meals’ are not just about quantity

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Animals that hunt or forage for prey can be just as picky as humans about their food, and recent studies show that their choices are based on the quality of food they consume rather than its quantity.

For example, some bugs and spiders have a Spidey sense for regulating their diet to get the nutrients they need without gorging on less nutritious prey. In a recent paper published in PLOS ONE, scientists fed wolf spiders with flies that had been raised on either nutrient-rich or nutrient-poor diets. They found that the spiders hunted both kinds of flies, but chose which ones to eat based on the nutritional quality of the flies, and the spiders’ own dietary history.

Though such carefully controlled experimental diets aren’t always possible in the wild, two other recent studies rely on observations of how changes in food availability affect mammals in oceans and tropical forests.

Unlike wolf spiders, marine mammals are frequently believed to thrive eating any kind of fish, as long as there is enough of it. However, another study published this month in PLOS ONE questions this idea by analyzing the food habits of 11 species of dolphins, whales and porpoises.

These researchers discovered that although some marine mammals ate most kinds of prey, others were more finicky, and only ate certain fast-moving varieties of fish.  Fast-moving fish are more energy-rich as food than slower moving species, but it also takes more effort to catch them. This energy expenditure is, quite literally, the price that marine animals pay for their dinner. According to this study, these preferences appear linked to the muscle performance of the predators- faster moving predators require high-energy prey, while others can afford to be more liberal in their food choices.

Marine life is widely affected by climatic shifts, global warming and fishing, which are causing the populations of high-energy fish to drop and increasing the numbers of low-energy species, a phenomenon the authors describe as “the emergence of junk-food in the ecosystem.” This ‘junk-food’ is likely to have a greater impact on more selective eaters, and the authors suggest that understanding the dietary preferences of these marine mammals could help manage and prioritize conservation efforts.

Changing weather also causes land animals to adopt different diets. Several monkey species switch to fallback foods when the foods they prefer are out of season, and a study published today found that these behavioral changes can have effects beyond just simple changes in nutritional value. Scientists studying blue monkeys in tropical forests found that levels of a stress marker increased in female monkeys when they had to eat lower-quality fallback foods like leaves instead of their first preference of insects or fresh fruit. The dietary change also affected the female monkeys’ reproductive health, although that of the males remained unchanged.

These and other studies reveal how animals’ dinner decisions aren’t just about quantity but quality, and how changes in their food habits impact their health. Read other PLOS ONE papers to learn about salt-loving flies, how brightly colored birds choose foods with more pigments, why pandas eat bamboo, and more.

Photo credits:

Burger by Ewan-M on flickr, wolf spider by jack_246, dolphin by Brian Branstetter, Cercopithecus by Steffen Foerster 

Citations:

Schmidt JM, Sebastian P, Wilder SM, Rypstra AL (2012) The Nutritional Content of Prey Affects the Foraging of a Generalist Arthropod Predator. PLoS ONE 7(11): e49223. doi:10.1371/journal.pone.0049223

Spitz J, Trites AW, Becquet V, Brind’Amour A, Cherel Y, et al. (2012) Cost of Living Dictates what Whales, Dolphins and Porpoises Eat: The Importance of Prey Quality on Predator Foraging Strategies. PLoS ONE 7(11): e50096. doi:10.1371/journal.pone.0050096

Foerster S, Cords M, Monfort SL (2012) Seasonal Energetic Stress in a Tropical Forest Primate: Proximate Causes and Evolutionary Implications. PLoS ONE 7(11): e50108. doi:10.1371/journal.pone.0050108

One of world’s giant textbook publishers bought by private equity firm that "gives Wall Street a bad name"

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Updated November 27, 2012

McGraw Hill, one of the world’s top textbook publishers, was just sold for $2.5 billion to Apollo Global Management, according to Inside Higher Ed.  Debra Borchardt, in The Street, describes Apollo Global Management as a private equity firm that “gives Wall Street a bad name. And that’s saying something”.

From Inside Higher Ed:  “Waterhouse said that the company would continue to expand in digital education, and that – as a private company – “we won’t need to worry about short-term focus and pressures”.

Comment: a Wall Street bad apple expanding into higher education is something we should be watching – and take note of the long term focus.

While this announcement is not directly relevant to open access or education, those working in either area should be aware of this and of strategies that could be deployed by a company like this, whether now or in the future. 

For example, a company like this could move into open education for the short term, giving away textbooks or courses with a view to out-competing existing higher educational institutions, then charging substantial amounts for their courses later on. This is something to watch for – a company designed to reap profits giving things away may well be strategizing for maximum profits at a later date.

For open access advocates, this development is important because one question we should be asking ourselves is – could be possibly be worse off than with the existing owners of scholarly publisher such as Elsevier? Elsevier, Springer, etc., have their disadvantages for scholarship, but these companies have a long history with the scholarly tradition and changing ownership to companies with experience in the financial industry might make things worse for scholarship.

Aside from outright sales of existing publishers, this is a cautionary tale for those who promote the Creative Commons – Attribution license (CC-BY), which gives third parties commercial rights and comes with no strings requiring reciprocity or ongoing free access. When scholars give away their works with this license, they can be used by companies like this whose strategy might be to outcompete our employers, which threatens the employment of scholars. For this reason, here is my advice:

Faculty and teachers: DO NOT GIVE AWAY YOUR WORK FOR COMMERCIAL RIGHTS. If you are using CC licenses, use Noncommercial.

Update: here is the link to the news release McGraw-Hill to sell education business to Apollo for $2.5 billion from the McGraw-Hill website.

Excerpt: NEW YORK, Nov. 26, 2012 /PRNewswire-FirstCall/ — The McGraw-Hill Companies (NYSE: MHP) (“the Company”) today announced it has signed a definitive agreement to sell its McGraw-Hill Education business to investment funds affiliated with Apollo Global Management, LLC (NYSE: APO) (collectively with its subsidiaries, “Apollo”), for a purchase price of $2.5 billion, subject to certain closing adjustments.

Waterhouse said that the company would continue to expand in digital education, and that — as a private company — “we won’t need to worry about short-term focus and pressures.”

Read more: http://www.insidehighered.com/quicktakes/2012/11/27/mcgraw-hill-education-sold-25-billion#ixzz2DSLQp6e5
Inside Higher Ed

Waterhouse said that the company would continue to expand in digital education, and that — as a private company — “we won’t need to worry about short-term focus and pressures.”

Read more: http://www.insidehighered.com/quicktakes/2012/11/27/mcgraw-hill-education-sold-25-billion#ixzz2DSLQp6e5
Inside Higher Ed

Waterhouse said that the company would continue to expand in digital education, and that — as a private company — “we won’t need to worry about short-term focus and pressures.”

Read more: http://www.insidehighered.com/quicktakes/2012/11/27/mcgraw-hill-education-sold-25-billion#ixzz2DSLQp6e5
Inside Higher Ed

Gold OA Costs: Pre-Green vs. Post-Green

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Claudio Aspesi, BernsteinResearch: ?We estimate that a full transition to OA could lead to savings in the region of 10-12% of the cost base of a subscription publisher.?

Richard Poynder, on the Global Open Access List (GOAL): “The key question: if that estimate is accurate, will those savings be passed on to the research community?”

I think that what Richard is worrying about here is whether the cost-cutting that a transition from subscription publishing to Gold OA publishing would make possible (e.g., curtailing the print edition) would be reflected in lower Gold OA charges to the author/institution or they would simply be absorbed by the publisher (Aspesi’s (2012) test case being Elsevier), leaving Gold OA charges higher than they need to be.

I join this speculation and counter-speculation only reluctantly, for two reasons:

(1) I think there are significant transition factors that none of the economic analyses has yet fully taken into account, and hence that the potential savings are still being considerably underestimated.

(2) I also think this focus on predicting the costs of Gold OA just reinforces the excessive preoccupation with estimating the costs and benefits of pre-emptive Gold OA rather than the costs and benefits of OA itself, and what is needed, practically, for facilitating a transition to OA itself, rather than just a direct transition to Gold OA in particular.

Post-Green Gold will cost far less than the pre-emptive pre-Green Gold that the economic analyses keep estimating.

We keep counting the “savings” from generic Gold OA publishing without reckoning how to get there, and whether the transition itself might not be a major determinant in the potential for savings (from OA as well as from Gold OA).

I am not an economist, so I will not try to do anything more than to point out the main factor that I believe the economic analyses are failing to take into account:

If Green OA self-archiving in institutional repositories is mandated globally by institutions and funders, this will have two major consequences:

I. First, not only will globally mandated Green OA provide universal OA (and all of its benefits, scientific and economic) alongside subscription publishing, at minimal additional cost (because (a) repositories are relatively cheap to create and maintain, (b) most research-active institutions have created repositories already, and (c) have done so for multiple purposes, OA being only one of them).

II. Second, mandating Green OA globally (unlike pre-emptive Gold OA) also puts competitive pressure on subscription publishers to cut obsolete costs, because the universal availability of the Green OA version makes it much easier for cash-strapped institutions to cancel their journal subscriptions.

Not only can the print edition and its costs be phased out under cancelation pressure from global Green OA, but so can the publisher’s online edition and version of record: The worldwide network of Green OA repositories and their many central harvesters are perfectly capable of generating, hosting, archiving and providing access to the version-of-record. No more PDF or XML needed from the publisher; nor archiving; nor access provision; nor marketing; nor fulfillment. Nor any of their associated expenses.

All that’s needed from the publisher is the service of managing the peer review (peers review for free) and the certification of its outcome with the journal’s title and track-record.

That’s post-Green Gold OA publishing. Compared to that, all the economical estimates of savings are under-estimates.

Nor will there be any need — with post-Green Gold OA — for mega-publishers (like Elsevier), publishing vast fleets of unrelated journals; nor for mega-journals (like PLoS ONE), publishing vast flocks of unrelated articles. There are many narrow research specialities, a few wider ones, and a few even wider, multidisciplinary ones. They each have their own peers, and they each need their own peer-reviewed journals; depending on the size of the field, some fields will several journals, forming a pyramid of quality standards, the most selective (hence smallest) at the top.

There may have been economies of scale for multiple journal production, in the Gutenberg days. But in the PostGutenberg era, with post-Green Gold OA journals, providing only the service of peer review, there will be no need for generic refereeing being mass-marketed by generic editorial assistants for mega-publishers or mega-journals, where no one other than the referee (if competently selected!) knows anything about the subject matter.

So besides scaling down to the post-Green OA essentials, post-Green Gold OA journals will also revert to being the independent, peer-based titles that they were before being jointly bought up for by the post-Maxwellian publisher megalopolies. The online-era economies will come from restoring journals’ own natural speciality scale rather than from agglomerating them into generic multiple money-makers.

Aspesi, C (2012) Reed Elsevier: Transitioning to Open Access – Are the Cost Savings Sufficient to Protect Margins? BernsteinResearch November 26

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

Harnad, S. (2009) The PostGutenberg Open Access Journal. In: Cope, B. & Phillips, A (Eds.) The Future of the Academic Journal. Chandos.

Harnad, S. (2010a) No-Fault Peer Review Charges: The Price of Selectivity Need Not Be Access Denied or Delayed. D-Lib Magazine 16 (7/8).

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

Houghton, John W. & Swan, Alma (2012) Planting the green seeds for a golden harvest. Comments and clarifications on ?Going for Gold?

Worth a Thousand Words: On Elephants, Literally

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Ever wonder what purpose the sparse, coarse hairs covering an elephant’s skin serve? Authors from Princeton University wondered the same and recently published their findings in the paper “What Is the Use of Elephant Hair?” Body hair is typically thought of as an evolutionary advantage functioning mainly for insulation. Given that elephants typically inhabit warm climates and have a great need for heat loss due to their high body-volume to skin-surface ratio, insulation seems an unlikely explanation. We’ve all observed elephants using a variety of behavioral mechanisms to cool themselves down, (flapping their ears, bathing in dust, or spraying water and mud on themselves) but these alone are not sufficient in extreme heat conditions. It turns out that these little rough hairs are actually very important for keeping elephants cool.

From the Abstract:

The idea that low surface densities of hairs could be a heat loss mechanism is understood in engineering and has been postulated in some thermal studies of animals. However, its biological implications, both for thermoregulation as well as for the evolution of epidermal structures, have not yet been noted. Since early epidermal structures are poorly preserved in the fossil record, we study modern elephants to infer not only the heat transfer effect of present-day sparse hair, but also its potential evolutionary origins. Here we use a combination of theoretical and empirical approaches, and a range of hair densities determined from photographs, to test whether sparse hairs increase convective heat loss from elephant skin, thus serving an intentional evolutionary purpose. Our conclusion is that elephants are covered with hair that significantly enhances their thermoregulation ability by over 5% under all scenarios considered, and by up to 23% at low wind speeds where their thermoregulation needs are greatest. The broader biological significance of this finding suggests that maintaining a low-density hair cover can be evolutionary purposeful and beneficial, which is consistent with the fact that elephants have the greatest need for heat loss of any modern terrestrial animal because of their high body-volume to skin-surface ratio. Elephant hair is the first documented example in nature where increasing heat transfer due to a low hair density covering may be a desirable effect, and therefore raises the possibility of such a covering for similarly sized animals in the past. This elephant example dispels the widely-held assumption that in modern endotherms body hair functions exclusively as an insulator and could therefore be a first step to resolving the prior paradox of why hair was able to evolve in a world much warmer than our own.

And while on the topic of elephants, be sure to check out the videos accompanying the paper “Visualizing Sound Emission of Elephant Vocalizations: Evidence for Two Rumble Production Types” which capture the oral and nasal rumbles of elephants with an acoustic camera. The oral rumble of an elephant at 25 frames per second is below but you can watch the rest on our YouTube Channel here.

 

Citation: Myhrvold CL, Stone HA, Bou-Zeid E (2012) What Is the Use of Elephant Hair? PLoS ONE 7(10): e47018. doi:10.1371/journal.pone.0047018

Citation: Stoeger AS, Heilmann G, Zeppelzauer M, Ganswindt A, Hensman S, et al. (2012) Visualizing Sound Emission of Elephant Vocalizations: Evidence for Two Rumble Production Types. PLoS ONE 7(11): e48907. doi:10.1371/journal.pone.0048907

Open Access and the Prisoner’s Dilemma

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Unilateral Gold OA instead of Green
is the losing choice
in a non-forced-choice Prisoner’s Dilemma
(think about it!)

UniGreen (World): UniGold (World):
UniGreen (UK): win/win win/lose
UniGold (UK): lose/win win/win

Houghton & Swan 2012:

“If OA were adopted worldwide, the net benefits of Gold OA would exceed those of Green OA.

However, we are not in 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 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.” [emphasis added]

Houghton, John W. & Swan, Alma (2012) Planting the green seeds for a golden harvest: Comments and clarifications on ?Going for Gold?

Gross Domestic Clean Water

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 Alternative text: why not measure Gross Domestic Clean Water because this is more essential than Gross Domestic Product. If you’re not convinced, try going a couple of days without clean water, in any form. This word picture is dedicated to the public domain.

This is an alternative metric.

Altmetrics – thoughts about the purpose

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Should altmetrics take a step back and reconsider what the main purpose / research question is? I should suggest that what we need is an alternative to the current power of the impact factor in assessing the work of scholars. This may or may not involve metrics of any kind. My suggestion for starters is that we need a system that is not as reliant on metrics of any kind.

Having said that, some metrics studies that might actually be useful:
–  does an emphasis on quantity of publication increase duplication of content and/or reduce quality? With respect to the latter, this is what I have heard from senior experts in scholarly publishing and I think both Brown and Harley touch on this in their reports – at least with respect to books, pushing scholars to publish two books rather than one to get tenure means pressure to publish in less time than it takes to write a good book. So pushing for quantity seems likely to correlate with reduced quality (a hypothesis worth testing?)

One advantage to studying the disadvantages of pushing for quantity is that if the hypothesis (quantity correlates negatively with quality) is correct, then that is evidence that can reduce the workload of scholars – something I expect that scholars are likely to support

Other possibilities:
– scholars might want to know about journals:
– average and range of time from submission to decision
– level of “peer” doing the peer review (grad student? senior professor?)
– extent and quality of contents (this has to be qualitative analysis; sampling makes sense)

Shifting from a print-based scholarly communication system to an open access knowledge commons, while retaining or increasing quality and reducing costs, is possible – but it’s not easy. It is worth taking the time to think things through and get at least some stuff right.

CC-BY reflects a small subset of open access. Claims of "emerging consensus" on CC-BY are premature

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The Open Access Scholarly Publishers’ Association’s “Why CC-BY page” http://oaspa.org/why-cc-by/ refers to an “emerging consensus on the adoption of CC-BY”. My comment:

Re: CC-BY – emerging consensus. OASPA refers to an “emerging consensus” that CC-BY is the best license for open access. I argue that the evidence suggests that CC-BY is a peripheral phenomenon and very far from consensus.

From Peter Suber’s SPARC Open Access Newsletter, June 2012 – in brief only 11% of the journals listed in DOAJ use CC-BY, and outside of full gold OA publishing as illustrated by the journals in DOAJ, the proportion of OA that is CC-BY is lower still.

“Libre OA through repositories has been rare because most repositories are not in a position to demand it or even to authorize it. Hence, you might think that libre OA through journals would be common because all journals are in a position to do both. But unfortunately that would be wrong. The power of journals to demand and authorize libre OA means that libre gold could be common, and should be common. But scandalously, it doesn’t mean that libre gold is already common…Only 917 journals in the DOAJ have the SPARC Europe Seal of Approval, which requires CC-BY. That’s only 11.8% of the full set”.
http://www.doaj.org/?func=sealedJournals

Suber, Peter. SPARC Open Access Newsletter, June 2012 http://www.earlham.edu/~peters/fos/newsletter/06-02-12.htm#libre

Why open access does not need CC-BY: the Human Genome Project example

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The Open Access Scholarly Publishers’ Association explanation of Why CC-BY http://oaspa.org/why-cc-by/ presents the Human Genome Project as an illustration of why CC-BY is needed for open access. Following is my comment (not yet appearing on the OASPA site, no doubt awaiting moderation).

It is interesting that OASPA’s explanation of “why CC-BY” points to the Human Genome Project as an example of why CC-BY is needed. The HGP ran for 13 years, ending in 2003. Creative Commons is looking forward to its 10th birthday in December. In other words, HGP was completed shortly after CC began. This means that HGP is an awesome example of how science can advance rapidly and in the spirit of libre open access, without any need for Creative Commons licensing at all. [emphasis added]

For HGP details see:
http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml

Delightful irony: students for free culture adamantly opposed to license used for Lessig’s Free Culture

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Larry Lessig’s book, Free Culture, was the inspiration for the Free Culture movement, released as a paperback as well as a free online book, using the license CC-BY-NC 1.0 ( creativecommons.org/licenses/by-nc/1.0).

How ironic that Students for Free Culture consider the Noncommercial license to be “proprietary” and incompatible with free culture? http://freeculture.org/blog/2012/08/27/stop-the-inclusion-of-proprietary-licenses-in-creative-commons-4-0/

I wonder how many of them read the free online version – noncommercial license and all? 

Thanks very much to Creative Commons for keeping up the fight for free culture; note that after fulsome discussion, CC has elected to retain the noncommercial license in version 4.0, with no change in definition.

Some Quaint Elsevier Tergiversation on Rights Retention

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Preamble: If you wish to sample some of the most absurd, incoherent, pseudo-legal gibberish on the subject of “rights” retention, “systematicity” and free will, please have a look at what follows under “Elsevier Article Posting Policies” below. (And bear in mind that an institution only provides a tiny fraction of any journal’s content.)

Any author foolish enough to be intimidated by this kind of garbled double-talk deserves everything that’s coming to him.

My Advice to Authors: Ignore this embarrassing, self-contradictory nonsense completely and exercise your retained “right” to post your final refereed draft (“AAM”) in your institutional repository immediately upon acceptance, whether or not it is mandatory, secure in the knowledge that from a logical contradiction anything and everything (and its opposite) follows! (And be prepared to declare, with hand on heart, that as an adult, every right you exercise with your striate musculature is exercised “voluntarily.”)

[By the way, as long as Elsevier states that its authors retain the right to post “voluntarily”, Elsevier, too, remains on the Side of the Angels insofar as immediate, unembargoed Green OA self-archiving is concerned. It’s just that the Angels are a bit glossolalic…]

Elsevier Article Posting Policies

Accepted author manuscripts (AAMs)

Definition: An accepted author manuscript (AAM) is the author’s version of the manuscript of an article that has been accepted for publication and which may include any author-incorporated changes suggested through the processes of submission processing, peer review, and editor-author communications. AAMs do not include other publisher value-added contributions such as copy-editing, formatting, technical enhancements and (if relevant) pagination.

Policy: Authors retain the right to use the accepted author manuscript for personal use, internal institutional use and for permitted scholarly posting provided that these are not for purposes of commercial use or systematic distribution…

Permitted scholarly posting: Voluntary [emphasis added] posting by an author on open websites operated by the author or the author’s institution for scholarly purposes, as determined by the author, or (in connection with preprints) on preprint servers…

…Elsevier believes that individual authors should be able to distribute their AAMs for their personal voluntary [emphasis added] needs and interests, e.g. posting to their websites or their institution’s repository, e-mailing to colleagues. However, our policies differ regarding the systematic aggregation or distribution of AAMs to ensure the sustainability of the journals to which AAMs are submitted [emphasis added]. Therefore, deposit in, or posting to, subject-oriented or centralized repositories (such as PubMed Central), or institutional repositories with systematic posting mandates [emphasis added] is permitted only under specific agreements between Elsevier and the repository, agency or institution, and only consistent with the publisher’s policies concerning such repositories. Voluntary [emphasis added] posting of AAMs in the arXiv subject repository is permitted.

Systematic distribution means: policies or other mechanisms designed to aggregate and openly disseminate, or to substitute for journal-provided services, including:

— The systematic distribution to others via e-mail lists or list servers (to parties other than known colleagues), whether for a fee or for free…

— Institutional, funding body or government manuscript posting policies or mandates that aim to aggregate and openly distribute the work by its researchers or funded researchers…

#ami2 #opencontentmining: AMI reports progress on #pdf2svg and #svgplus: the “standard” of STM publishing

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AMI has been making steady progress on two parts of AMI2:

  • PDF2SVG. A converter of PDF to SVG, eliminating all PDF-specific information. This has gone smoothly –AMI does not understand “good” so “steady” means a monotonically increasing number of non-failing JUnit tests. AMI has also distributed the code, first on Bitbucket at:

    http://www.bitbucket.org/petermr/pdf2svg

    and then on the Jenkins continuous integration tool at PMR group machine in Cambridge:

    http://hudson.ch.cam.ac.uk – see https://hudson.ch.cam.ac.uk/job/pdf2svg/

    [Note: Hudson was open Source but it became closed so the community forked it and Jenkins is the new Open branch]. Jenkins is very demanding. AMI starts by developing tests on Eclipse, then runs these on maven, and then on Jenkins. Things that work on Eclipse often fail on maven, and things that work on maven can fail on Jenkins.

    AMI has also created an Issue Tracker: https://bitbucket.org/petermr/pdf2svg/issues?status=new&status=open Here humans write issues which matter to them – bugs, ideas, etc. PMR tells AMI what the issues are and translates them into AMI-tasks, often called TODO. PMR tells AMI he is pleased that there is feedback from outside the immediate group.

  • SVGPlus. This takes the raw output of PDF2SVG and turns into into domain-agnostic semantic content. Most of this has already been done so it is a questions of refactoring. AMI requires JUnit tests to drive the development. SVGPlus has undergone a lot of refactoring (AMI notes changes of package structure, deletion of large chunks and addition of smaller bits. The number of tests increases so AMI regards that as “steady progress”.

AMI now has a lot of experience with PDFs from STM publishers and elsewhere. AMI works fastest when there is a clear specification against which she can write tests. AMI works much slower when there are no standards. PMR has to tell her how to guess (“heuristics”). Here’s their conversation over the last few weeks.

AMI: Please write me some tests for PDF2SVG.

PMR: I can’t.

AMI: Please find the standard for PDF documents and create documents that conform.

PMR. I could do that but it’s no use. Hardly any of the STM publishers conform to any PDF standards.

AMI. If the deviations from the standard are small we can add some small exceptions.

PMR. The deviation from the standard is enormous.

AMI. If you read some of the documents we can create a de facto standard and code against that. It will be several times slower.

PMR. That won’t be useful. Every publisher does things differently.

AMI. How many publishers are there?

PMR. Perhaps 100.

AMI. Then it will take 100 times longer to write PDF2SVG. Please supply me with the documentation for each of the publishers’ PDFs.

PMR. There is no documentation for any of them.

AMI. Then there is no systematic quality way that I can write code.

PMR. Agreed. Any conversion is likely to have errors.

AMI. We may be able to tabulate the error frequency.

PMR. We don’t know what the correct output is.

AMI. Then we cannot estimate errors properly.

PMR. Agreed. Maybe we can get help from crowdsourcing.

AMI. I do not understand.

PMR. More people, creating more exams and tests.

AMI. I understand.

PMR. I will have to make it easy for them.

AMI. In which can we may be able to work faster. We may also be able to output partial solutions. Can we identify how the STM publishers deviate from the standard?

PMR. Let’s try.

AMI. Wikipedia has http://en.wikipedia.org/wiki/Portable_Document_Format . Is that what we want?

PMR. Yes

AMI. Is the standard Open?

PMR. Yes, it’s ISO 32000-1:2008.

AMI. [reads}

ISO 32000-1:2008 specifies a digital form for representing electronic documents to enable users to exchange and view electronic documents independent of the environment they were created in or the environment they are viewed or printed in. It is intended for the developer of software that creates PDF files (conforming writers), software that reads existing PDF files and interprets their contents for display and interaction (conforming readers) and PDF products that read and/or write PDF files for a variety of other purposes (conforming products).

AMI. Does it make it clear how to conform?

PMR. Yes. It’s well written.

AMI. Is it free to download?

PMR. Yes (Adobe provide a copy on their website)

AMI. Are there any legal restrictions to implementing it? [AMI understands that some things can’t be done for legal reasons like patents and copyright.]

PMR. Not that we need to worry about.

AMI. Do the publishers have enough money to read it? [AMI knows that money may matter.]

PMR. It is free.

AMI. So we can assume the publishers and their typesetters have read it? And tried to implement it.

PMR. We can assume nothing. Publishers don’t communicate anything.

AMI. I will follow the overview in Wikipedia:

File structure

A PDF file consists primarily of objects, of which there are eight types:[32]

  • Boolean values, representing true or false
  • Numbers
  • Strings
  • Names
  • Arrays, ordered collections of objects
  • Dictionaries, collections of objects indexed by Names
  • Streams, usually containing large amounts of data
  • The null object

Do the PDFs conform to that?

PMR: They seem to since PDFBox generally reads them

AMI. Fonts are important:

Standard Type 1 Fonts (Standard 14 Fonts)

Fourteen typefaces—known as the standard 14 fonts—have a special significance in PDF documents:

These fonts are sometimes called the base fourteen fonts.[34] These fonts, or suitable substitute fonts with the same metrics, must always be available in all PDF readers and so need not be embedded in a PDF.[35] PDF viewers must know about the metrics of these fonts. Other fonts may be substituted if they are not embedded in a PDF.

AMI: If a PDF uses the 14 base fonts, then any PDF software must understand them, OK?

PMR. Yes. But the STM publishers don’t use the 14 base fonts.

AMI. What fonts do they use?

PMR. There are zillions. We don’t know anything about most of them.

AMI. Then how do I read them? Do they use Type1 Fonts?

PMR. Sometimes yes and sometimes no.

AMI. A Type1Font must have a FontDescriptor. The FontDescriptor will tell us the FontFamily, whether the font is italic, bold, symbol etc. That will solve many problems.

PMR. Many publishers don’t use FontDescriptors.

AMI. Then they are not adhering to standard PDF.

PMR. Yes.

AMI. Then I can’t help.

PMR. Maybe we can guess. Sometimes the FontName can be interpreted. For example “Helvetica-Bold” is a bold Helvetica font.

AMI. Is there a naming convention for Fonts? Can we write a regular expression?

PMR. No. Publishers do not use systematic names.

AMI. I have just found some publishers use some fonts without FontNames. I can’t understand them.

PMR. Nor can anyone.

AMI. So the PDF renderer has to draw the glyph as there is no other information.

PMR. That’s right.

AMI. Is there a table of glyphs in these fonts.

PMR. No. We have to guess.

AMI. It will take me about 100 times longer to develop and write a correct PDF2SVG for all the publishers.

PMR. No, you can never do it because you cannot predict what new non-standard features will be added.

AMI. I will do what you tell me.

PMR. We will guess that most fonts use a Unicode character set. We’ll guess that there are a number of non-standard, non-documented character sets for the others – perhaps 50. We’ll fill them in as we read documents.

AMI. I cannot guarantee the results.

PMR. You have already done a useful job. We have had some positive comments from the community.

AMI. I don’t understand words like “cool” and “great job”.

PMR. They mean “steady progress”.

AMI. OK. Now I am moving to SVGPlus.

PMR. We’ll have a new blog post for that.

 

 

 

 

 

 

 

 

 

Semana del acceso abierto en la Universitat Politècnica de València (UPV)

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La Biblioteca de la Universitat Politècnica de València quiere unirse a este acontecimiento como una manera de promocionar el acceso abierto, no sólo como concepto, si no como realidad, materializada en nuestro caso tanto en la Política de Acceso Abierto de la Universitat Politècnica de València como en las diferentes herramientas desarrolladas siguiendo este modelo:

• RiuNet, el repositorio institucional de la UPV. Taller

• PoliPapers, portal de las revistas electrónicas en abierto de la UPV. Taller

Durante la Semana de Acceso Abierto estas actuaciones se concretarán en varios talleres, en la presentación de Polipapers y en el comienzo de una nueva etapa para el blog PoliScience, herramienta de comunicación que nos permitirá reunir y difundir información sobre el Acceso Abierto y publicación científica en general; PoliScience completa su oferta de difusión con la creación de una cuenta de twitter.

Los talleres se realizarán en el aula de formación de la biblioteca. El material de los talleres estará a disposición de la comunidad universitaria a la mayor brevedad posible a través de PoliScience.

  • Qué es el Acceso Abierto
  • RiuNet: Repositorio Institucional de la UPV
  • Propiedad intelectual en el Open Access
  • Publicar en la UPV
  • Publica y se visible

Esperamos que estas iniciativas nos permitan difundir el acceso abierto entre la comunidad universitaria de la UPV

Un saludo