High altitude genetic juggling

Tibetans and Incas are so well adapted to their high altitude homes that the low oxygen levels don’t even faze them, but for those of us living near sea level, traveling up to the mountains can put a lot of stress on our bodies.  Even so, we can still do some of our own short-term biological adjustments, and a new study published today in PLoS ONE identifies some of the specific genetic changes that are involved in this high altitude acclimation.

The research team, composed of 26 scientists from institutions in China and Denmark, studied four climbers of Himalayan peak Mount Xixiabangama, which rises 8,012 meters, or 26,286 feet, above sea level. (For comparison, Mount Everest is 8,848 meters tall.)  They collected blood samples before, during, and after the trip, which took almost 30 days, and then determined how the climbers’ gene expression – which genes were “on” or “off” – changed over time.

Changing gene expression is one of the fastest ways to adjust to a new environment or situation. The DNA itself can’t change to accommodate rapidly developing needs, but gene expression is can change quickly and plays a large role in determining how a cell behaves. By looking at the climbers’ gene expression, the researchers aimed to find out which genes were most important for the physiological changes that helped the climbers temporarily adjust to life at high altitude.

The results showed a complex network of expression changes, particularly for genes involved in red blood cells and inflammation, which makes sense given the unique rigors of high altitude climbing. As a climber myself (though not nearly to the same extent as those in this study), I’m now left with the question of how my own gene expression may change while I’m on the wall.

Citation: Chen F, Zhang W, Liang Y, Huang J, Li K, et al. (2012) Transcriptome and Network Changes in Climbers at Extreme Altitudes. PLoS ONE 7(2): e31645. doi:10.1371/journal.pone.0031645

Image source: Rupert Taylor-Price on Flickr

Brain and Behavior and Ecology and Evolution now listed by DOAJ

DOAJWe are pleased to annouce that the first Wiley Open Access titles are now listed by the Directory of Open Access Journals (DOAJ). This directory currently lists 7531 open access journals, with more titles being regularly added. Brain and Behavior and Ecology and Evolution are now listed alongside the other peer reviewed open access journals in DOAJ. Both journals were launched in 2011 and have a large number of high quality articles and several issues live on Wiley Online Library. Their inclusion in this directory will help to increase the visibility of the journals by enabling potential authors and readers to navigate to them directly from the directory. We look forward to working with DOAJ in future to include more of the Wiley Open Access journals throughout 2012.

@ccess for all: Update and Oxford meeting

We now have the Twitter tag @ccess! This is fantastic. Thanks to Tyler Neylon for making this happen.

The progress on http://access.okfn.org and http://whoneedsaccess.org is fantastic. On the latter we are getting daily stories from the #scholarlypoor – people who want to read the scholarly literature and cannot. Read them and see how powerful their stories are – people who leave their job feel a great sense of loss and deprivation, and spending thousands of dollars is not an option.

I’m going to Rhodes House Oxford for : Scientific Evolution, Open Science and the future of publishing www.evolutionofscience.org/ This is a great event and I’ve been asked to ask a question. I’ve sent this in – not sure whether the panellists have seen it so I shan’t put it here but it’s about the #scholarlypoor. The tragedy is that the world is deprived of scholarship and we have to put that right. The first step is to recognise it and cement it in our articles of policy – my approach is http://blogs.ch.cam.ac.uk/pmr/2011/09/30/access-to-scientific-publications-should-be-a-fundamental-right/ .

Then we have to work out how to make it happen. This is where the #scholarlypoor have the power. We – I count myself as part of the #scholarlypoor as the publishers have forbidden me to do the research I want – should mobilise and make our voice heard. If the world trembles when 7000 academics (including me) Boycott Elsevier then how much more the power of the world, feeling the deprivation.

And, yes, unlike the woolliness of most academics this is a hardball fight. The #scholarlypoor have no hIndexes to worry about and their demand is simple (I have been on enough demonstrations to know this by heart!)

  • What do we want?
  • Access.
  • When do we want it?
  • Now

If you can remember this simple chant, join us.

Will Elsevier accidentally unite the open access movement?

We open access advocates are unanimous in the goal of universal open access to the world’s scholarly knowledge (at least in its peer-reviewed journal article form, for now). However, at times we differ about the means. Some of us favor a focus on rapid transition to a fully open access, more efficient and effective scholarly communication system – what some call the gold road of open access publishing, and Harnad refers to as the premature gold rush.  Others, like Harnad himself, favor beginning with the traditional scholarly publishing system as it is, with authors self-archiving in open access archives to expand open access beyond what is provided by library subscriptions.  (I fully agree with both positions!).

So what does this have to do with Elsevier? Simple: Elsevier is “green” on open access and hence the darling of the green roaders. As long as Elsevier supports this approach, the open access archives first supporters are likely to support Elsevier. However, as we saw recently with the Research Works Act, Elsevier is quite capable of doing its best to attack the open access mandates that are critical to the green road. If Elsevier keeps up this attack on open access mandates, it’s a matter of time the green roaders become gold and join us in the Elsevier boycott – where they will be most welcome!

So what are the options for Elsevier? They can either support – or at least not attack – the open access mandates that are coming, particularly the U.S.’ FRPAA and the growing institutional open access mandates movement, and keep the support of the green roaders – or they can attack the mandates, and face a much more united open access movement. I think that this is what people like to call “between a rock and a hard place”.

Of course, Elsevier could follow the lead of other major commercial scholarly publishers such as Springer, Wiley, Nature Publishing Group, and others, and aim to compete in the obviously emerging open access marketplace.  This growing tendency towards OA competition is a topic that I speak to in a bit more depth in the 4th chapter of my draft dissertation, open access as solution to the enclosure of knowledge.

Ecology and Evolution Publishes its 100th Article!

Since its launch in September Ecology and Evolution has received a great number of quality submissions and this month we celebrate publishing our 100th article! 

The change in species richness of savanna bird species between 1990 and 2080

The 100th article published in Ecology and Evolution is Projected changes in distributions of Australian tropical savanna birds under climate change using three dispersal scenarios’ by April E. Reside, Jeremy VanDerWal and Alex S. Kutt. This paper uses species distribution modelling to predict geographic ranges for birds of Australian tropical savannas, and to project changes in species richness and ranges under a future climate scenario in 2080. Projected future range sizes were sensitive to dispersal scenario: ranges decreased for 66% of species if full dispersal was assumed, but for 89% of species when no dispersal was assumed.

See more articles from Ecology and Evolution.

Splitting the Difference on Open Access: Brainlessness Masquerading as "Balance"

New York Times, February 27, 2012: Gulf on Open Access to Federally Financed Research by Guy Gugliotta

The debate between these two extremes has been remarkably vitriolic, in part, perhaps, because neither side has been completely honest. Mr. Adler would not discuss publishers? profit margins, and openaccess advocates frequently say that the journals are low-overhead cash cows that are gouging the public. Open-access scientists, on the other hand, are less than candid about how important it is to their careers to be published in prominent traditional journals. If scientists truly wished to kill the system, all they would have to do is withhold submissions.

Utter nonsense, of course.

(1) Researchers’ need (and reasons) for publishing in journals with high peer review standards are no secret (and nothing to hide or apologize for!)

(2) The objective of OA is not to “kill the system” but to provide OA.

(3) As usual, the false assumption is that OA = Gold OA publishing.

(4) OA has nothing to do with “withholding submissions” or boycotting.

(5) Both bills (FRPAA and RWA) are about mandating Green OA self-archiving.

What’s worth writing an article (or book) about is how this relentless misunderstanding of something so stunningly simple just keeps propagating itself, year after year after year.

And it looks like Congress will yet again wimp out this year on FRPAA, splitting the difference with RWA in much the same clueless spirit as the above sterling example of “balanced” journalism…

So it’s back to yet another year of trying to talk sense into universities about mandating Green OA…

One thing the journalist got right: There is indeed something that researchers are less than candid about: not withholding submissions but about withholding keystrokes

Harnad, S. (2006) Opening Access by Overcoming Zeno’s Paralysis, in Jacobs, N., Eds. Open Access: Key Strategic, Technical and Economic Aspects. Chandos.

Stevan Harnad

Elsevier numbers illustrate – once again – just how much more sense open access makes!

Elsevier today wrote a letter to the mathematics community, hoping to woo scholars away from the still-growing boycott, The Cost of Knowledge, now that Elsevier has publicly disavowed its support for the Research Works Act which would have forbidden the U.S. government from requiring public access to the results of research it pays for. In its letter, Elsevier commits to lowering the costs of articles in its mathematics journals to at or below $11 US per article. This sounds like a pretty reasonable step when you consider that this is just over a quarter of what Elsevier currently charges. However, when you compare this with the potential of open access, you can see how ludicrous this model really is today. If every research library in North America were to purchase a copy of an Elsevier article at $11, this would add up to $1,386 – more than it would cost to pay the PLoS ONE article processing fee for full open access to everyone, everywhere. Or, if an undergrad class of 150 students were required to purchase this article to read for class on a pay-per-use basis, the total would come to $1,650 – that’s $300 more than what is needed to pay for the article to be fully open access through PLoS ONE – for access to just one class. In summary, this move by Elsevier just shows how ludicrous the current model is. Plus – why just math, Elsevier? There are many of us who signed the boycott who are not mathematicians!


In the section on pricing, Elsevier commits to lowering the costs of articles in its mathematical journals to at or below $11 US per article or 50-60 cents per page. 

As a for-profit corporation reporting to shareholders, I think it is reasonable to assume that Elsevier would not make such a commitment unless this cost was sufficient to not only cover costs, but return a profit. Does this mean that the current $37.95 charged for one article in Elsevier’s Advances in Applied Mathematics is close to 4 times more than what Elsevier itself feels is necessary to recoup costs and make a profit? This does seem consistent with Elsevier’s high profit rates.

If every one of the 126 members of the Association of Research Libraries were to pay $11 for an article in mathematics, the total would be $1,386. That’s higher than the article processing fee for a fully open access article at PLoS ONE at $1,350 per article. In other words, a high quality, U.S.-based publisher working out of San Francisco (not a cheap place to live or work, I hear), can provide full open access for everyone in the world at less than it would cost to have one copy of an article at every large North American research library, at Elsevier’s proposed reduced rate which is just over a quarter of what they currently charge. This is yet more proof that this old school business model of Elsevier’s just doesn’t make any sense any more, not even with this little modicum of tweaking after significant pressure from mathematicians like Timothy Gowers.

Another scenario: if an undergrad class of 150 students were required to buy a $11 mathematics article to read for class on a pay-to-read basis, the cost would be $1,650. In other words, the pay-per-view costs for just one class to read an article would exceed the PLoS ONE article processing fee by $300. Multiply that by all the millions of students in the world, and it’s easy to see how the Elsevier model means either outrageous costs or needless barriers to mathematical knowledge, or, more likely (as things stand now) some of both.

The section from the Elsevier letter on pricing:

Mathematics journals published by Elsevier tend to be larger than those of other publishers. On a price-per-article, or price-per-page level, our prices are typically, but not always, lower than those of other mathematics publishers.

Our target is for all of our core mathematics titles to be priced at or below US$11 per article (equivalent to 50-60 cents per normal typeset page) by next year, placing us below most University presses, some societies and other commercial competitors. Where journals are more expensive than this, we will lower our prices, as we already have in recent years for journals such as the Journal of Algebra and Topology and its Applications, among others.

We realize that this is just part of the concerns about pricing -and we will seek to address concerns about the nature and composition of the large discounted agreements, through which most Universities now access journals – but addressing the base line pricing is a necessary first step.

Worth A Thousand Words: Stretchable Spider Silk

Egg sac of the spider Meta menardi.

Spiderman, watch out! There’s a new, super-strength spider silk in town! Researchers from Politecnico di Torino in Italy performed stress tests on the stalks of silk egg sacs produced by the cave spider, Meta menardi (pictured above), and suggest that it could be the most stretchable spider silk ever tested.

The scientists,  led by Dr. Nicola Pugno, collected 15 egg sacs from different caves in Piedmont (a north-western region of Italy), and used a tensile testing machine to pull on the stalk of the sac until the fibers broke. They recorded that silk strands produced by these spiders can stretch up to 7.5 times their original length, which could bode well for future understanding of nano-materials.

The researchers claim that such results may be linked to the fact that these egg sacs were collected from nature, and thus more reflective of actual stresses, as opposed to silk that may have been produced in a lab.

Read the full article here.

What’s the Real Value of a Scholarly Publication? Part I

I’ve been invited to a very timely meeting in Oxford next week to discuss the future of Scholarship. “Open Science and the Future of Publishing” http://www.evolutionofscience.org/webFlyer.pdf . The question I want to ask is (roughly):

“We the public pay 10 billion USD annually in journal subscription fees [*] and 200 billion USD for research; what value do WE get? And what value do WE lose by closed access?”

[*] throughout this post I use guestimates which are probably off by half an order of magnitude either way (i.e. factor of 3). This is partly because much of the information is secret (and some so secret that you will be sued if you divulge it) and partly because academia and we the public don’t yet care enough to find out. I am also removing CC-BY publications from the argument to avoid having to say “except for CC-BY” all the time. It’s about 5% of the market, if that. So I’d like your help.

I am also working this up for a (unfortunately virtual) presentation I am giving in Poland next month. I am taking my text from Wikipedia: http://en.wikipedia.org/wiki/Value_%28economics%29 (This is 6 years old and not disputed so I take it as more-or-less correct. If anyone can fault this, we shall all benefit)

Let me tackle COST and PRICE first.

The COST to the public purse of scholarly publishing is of the order of 10 billion USD. There are also contributions from industrial subscriptions, and from student fees, and 1% from pay-per-view, but the bulk is from taxpayers. In return for this the public get virtually no value or rights. If you the public, you the government, you the NHS want to read a paper you either have to pay again or walk to St Pancras and read it in the British library premises (you cannot get this online because of publisher restrictions – mad and sad but true. The BL even charges me to read my own CC-BY papers if I’m not at St P.).

This is set by the PRICE of electronic journals. This bears no relation to the COST of production. The cost of production can be very low. It’s USD 7 for ArXiV (not peer-reviewed) and about 100 USD for Acta Cryst E (a very high-quality peer-reviewed data journal). In an efficient organisation it’s inconceivable that the COST of production of a journal article is more than 200 USD. Any higher PRICE comes from the following:

  • The ADDED_VALUE that the publishers assert they add
  • Inefficiencies (often gross) in the publishing system. (For example almost all author manuscripts are retyped from scratch).
  • Profits

Publishers like Nature estimate costs-per-paper at 20,000 USD. That is not related to the cost of production but something else. Perhaps the high rejection rate? The basis of these “costs” is kept highly secret.

The PRICE of pay-per-view articles (about 35 USD for one day’s rent) is the only part with real elasticity http://en.wikipedia.org/wiki/Elasticity_%28economics%29 . The only evidence I have is from my FOI requests to Oxford/Cambridge University presses (they are public organizations, parts of the Universities, so have to reply – if you want publishing facts consider University presses).

CUP:  [http://www.whatdotheyknow.com/request/88390/response/224094/attach/html/2/FOI%202011%20236%20Murray%20Rust%20response%20letter.pdf.html ]

In 2010, 13,646 articles were purchased as PPV. In 2010, the total number of articles for potential purchase via CJO was 680,000.  Revenues from PPV approximated to 1.3% of Journal subscription revenues in 2010. 

OUP [http://www.whatdotheyknow.com/request/85085/response/214837/attach/html/2/Murray%20Rust%20Reply%20OUP%20PPV.pdf.html ]

 In 2010, 37,157 PPV articles were purchased [OUP do not know how many purchasable articles they publish]  PPV represents around 1.5% of total journal subscription income. 

I take heart from the consistency of the figures (TWO coincident points!) and surmise that other publishers get 1.5% of their income from Pay-per-view. It’s possible, but unlikely, that the large profits of other publishers comes from Pay-per-view but I and you will doubt that. It’s clear that the price is far too high and it amazes me that publishers still use these levels which were – I assume – set by the cost of paper in interlibrary loans. I’m no economist, but it’s actually stupid to run these prices . If they cut their prices to a fifth – 7USD – and gained 5 times more custom they’d still make the same income, incur no more costs (really!) and gain a great deal of goodwill. And even if they gained no more readers they’d only have lost 1% of their income. But they probably know something about a small subset of customers who have to use this service and they don’t care about everyone else. Which is also inelastic.

If any closed access publisher can give figures here we’d be delighted.

It’s also a serious condemnation of the effort to promote scholarship. Only 2% or all articles are ever purchased each year. I imagine the 680,000 includes historical articles, and if we take this as 50 years, then each modern article is purchased about once each year. Which shows that it’s value to the public is almost zero.

We now need to establish the cost of public (include charity) funded research. I have asked many times without finding authoritative results. So here’s a beer-mat calculation, and allow +- half an order of magnitude. I approach it from these directions:

  • Wellcome Trust allow about 2% of a grant to cover publishing. So if scholarly publishing is USD 10 billion, then public research is 500 billion USD
  • The income for Cambridge, Stanford, etc is ca 500 million. Assume 1000 research universities in the world (can anyone do better?) and a power law and we get ca USD 200 billion
  • The NIH is funded at USD 35 billion. It’s probably the largest, but add in national funders and you are well over USD 100 billion

Let’s use a figure of USD 200 billion (though I am sure it’s higher).

I’m now using VALUE in the sense (from Wikipedia):

Value in the most basic sense can be referred to as “Real Value” or “Actual Value.” This is the measure of worth that is based purely on the utility derived from the consumption of a product or service. Utility derived value allows products or services to be measured on outcome instead of demand or supply theories that have the inherent ability to be manipulated. Illustration: The real value of a book sold to a student who pays $50.00 at the cash register for the text and who earns no additional income from reading the book is essentially zero. However; the real value of the same text purchased in a thrift shop at a price of $0.25 and provides the reader with an insight that allows him or her to earn $100,000.00 in additional income is $100,000.00 or the extended lifetime value earned by the consumer. This is value calculated by actual measurements of ROI instead of production input and or demand vs. supply. No single unit has a fixed value. Value is intrinsically related to the worth derived by the consumer. [Burke(2005)].

And asking “What VALUE do the public get for their 200 billion dollars?”


“what extra VALUE would they get if the research was published openly?”

And again, if you have insights let me know.

JAHA — New Open Access Journal NOW LIVE!

JAHA cover

The American Heart Association/American Stroke Association continues to set the gold standard for publishing cardiology and stroke research with the introduction of a new online-only, peer-reviewed, Open Access publication to its portfolio of 11 scientific journals. Welcome JAHA — Journal of the American Heart Association!

Read the inaugural issue now.

JAHA provides a global forum for basic and clinical research articles and timely reviews on cardiovascular disease and stroke. As an Open Access journal, its content is rapidly and freely available, accelerating the translation of strong science into effective practice.

The journal has launched with five original research articles and three editorials that are free for you to read, download, and share! Of particular note,  ‘Relationship of National Institutes of Health Stroke Scale to 30-Day Mortality in Medicare Beneficiaries With Acute Ischemic Stroke’ by Gregg C. Fonarow and colleagues offers an important insight and will be part of the AHA Emerging Science Series webinar on February 29th.

Sign up for eAlerts to ensure that you are always up to date with the latest content from JAHA.

To submit a manuscript, please visit the JAHA submission site.
A discounted article publication charge is available for AHA/ASA members!
Learn more.

@ccess: #scholarlypoor: Craig Dylke, teacher and artist

There’s an arrogant assumption among many academics that scholarly publishing is produced by academics (maybe 1% of the population) to be read only by other academics (1% of the population) and that no-one else matters. After all why would anyone other than a dinosaur scholar be competent to read a paper on dinosaurs. And surely dinosaur papers have no financial benefit to the world.

WRONG – on both counts.

Mike Taylor has done an awesome – truly awesome – job in pulling together our ideas and hope for the @ccess movement – the imperative to make scholarship available for the #scholarlyporr. Those are the people who don’t have access to a University library. And access doesn’t mean driving to a building, filling pout forms and getting a paper copy. It means online access. Immediate and expansive. Because that’s the only form of access that’s now reasonable for scholarly articles [I deliberately omit books].

Mike’s been interviewing the scholarly poor. I’ve done an interview [http://whoneedsaccess.org/2012/02/18/peter-murray-rust-chemistry-researcher/ ]– just because I’m at a rich university doesn’t mean I can use the electronic library as I want to. My research is stalled because the publishers forbid it. Everyone is scholarly poor when it comes to text-, data- and image-mining. But you know all that.

What’s tremendous is the stories that are emerging. And I get the impression from Mike that he’s got a number yet to be published. So here’s someone who passionately wants to read the dinosaur literature. http://whoneedsaccess.org/2012/02/21/craig-dylke-teacher-and-artist/ You’ll need to read it yourself, best beloved, because I can’t show his dinosaur pictures. Here is he teaching, and I’ll give some exceprts below:


CD: I try to help connect the science of palaeontology to a larger audience. Palaeo-art lets me do this in a way that combines my childhood obsession with palaeontology and my love of digital art. I’ve become so interested in the the philosophy, and methodology of palaeo-art that, together with Peter Bond, I co-founded the community blog ART Evolved where we discuss and encourage palaeo-art of all forms.

But why does Craig need the literature?

When you scientifically reconstruct an animal, every detail of its physical appearance is important. For most prehistoric life, the only place to get details about fossilized remains and informed speculation on what that extinct life might have looked is in the scientific literature. From my perspective as an artist rather than a researcher, the most useful part of papers is the diagrams and photographs of the fossils

Craig cares about getting it right. As simple and as important as that.

… there are times when I would love to have it to check “facts” in popular children’s books. The number of factual mistakes in these books is sometimes quite alarming. Being on top of the most recent publications can also lead to good discussion topics for my students: news outlets only report a fraction of new science discoveries.

And the problems?

The fees for subscriptions, or for single papers are simply outrageous. Many of my digital art software packages cost less!

Limited access to scientific literature has also created an interesting problem in palaeo-art. Without access to source material, many artists resort to referencing other artists. Then you get artistic “memes” in which organisms are consistently shown with characteristics that we have no actual evidence for. (Since the art is the closest thing we have to photographs, they gain an implied credibility when repeated enough times). This runs completely counter to my science education goal.

What changes would you like to see?

Frankly that answer is simple. Either researchers only publish in free access journals or the publishers get with the times and open access to their content.

I’d also like to see more journals offer unlimited illustrations for authors. On any given subject PLoS papers are almost always the superior source material for me as an artist, as the authors tend to fill them liberally with photos and diagrams of their specimens. Too often I’ve been disappointed to track down a critical paper on topic from a mainstream journal only to find there are no diagrams or photos, leaving me at square one on my restoration.

As I have already noted, even a fraction of the scholarly literature is valuable. We’re fighting to get it all, but until that time we are trying to get as much as possible together for Craig.

And there’s no money in dinosaurs, is there? Jurassic Park grossed 900M USD. By depriving the creative #scholarlypoor of the literature we are denying them their full potential.

Darkroom and open disclosure: two library solutions for dealing with copyright extremists

Elsevier, the scholarly publisher currently being boycotted by close to 7,000 researchers, does not appear on the exclusions list of the copyright extremist group Access Copyright. To me, this raises the question: are Elsevier and ilk receiving monies from Access Copyright in addition to the substantial fees paid by libraries for subscriptions, and if so, is this a breach of the typical “entire agreement” clause in a library license? Since Access Copyright does not tell us who they are giving money to, why not ask when we purchase? We could call this an “open disclosure” policy. Whenever libraries are purchasing or subscribing to resources, let’s ask – IS this really the entire agreement, or are you looking for money from copyright collectives, too?

Of course, open disclosure would be most effective if it were practiced by Access Copyright. If people knew who they are representing (rather than who is excluded), then we could take appropriate actions. Such actions could include:

  • not buying their stuff
  • buying their stuff if we must, but putting it away in the most dark, remote corner we can find, in a separate room covered with stern warnings like: “These materials are covered by Access Copyright”. Don’t even THINK about copying!
  • set up a bank of computers that people pass by on their way to the dark room featuring open access resources

Another thought: if Access Copyright and those represented by Access Copyright don’t want to participate in open disclosure, then let’s start by encouraging those who aren’t members of Access Copyright to openly proclaim their non-membership. This could be a selling point! Come of think of it, I wonder if anyone is using that Access Copyright exclusions list as an acquisitions tool?

@ccess is launched!

Today we have launched @ccess – a new site, and more importantly a new community – to make scholarly information REALLY LIBRE available. I’ll stress to start with that this means all disciplines and all types of information and means of communication. Because I’m a scientist I’m concentrating on STEM but it covers everything. By LIBRE we ean free to use, re-use, and redistribute for any purpose. It’s covered by the Open Knowledge Definitions and the actual text of the Budapest Declaration on Open Access 10 years ago.

I’ve blogged about this before. Any information is better visible than not, but simply “being on the web” isn’t good enough for many (I’d say most) modern uses. There are 101 reasons why information must be fully LIBRE and why GRATIS is not good enough. There are 10 million paragraphs on chemical reactions I want to read each year and I must use machines to do this. GRATIS does not work for machines. They can’t work out rights or protect me from being sued. And that’s the reality. If I use a scientific paper beyond what I am allowed to do I’ll be sued and the University of Cambridge will be cut off.

The only way to ensure this is to make sure all the information we want is LIBRE. Free to use, re-use, redistribute for any purpose, commercial as well.

Note that the term “Open Access” is operationally meaningless. The term “fully Open Access” is even worse because it is seriously misused. Some publishers offer “fully open access” and give the reader no rights at all.

The problem is that only about 3-5 percent of current scholarly information is LIBRE. It’s actually very difficult to get a figure, because information isn’t generally labelled with its rights. Print a typical scholarly pub and the print will often tell you very little about the rights. It may not even give the actual copyright owner – so you don’t know whether you can copy it and who will sue you. Some “open access” publishers DO label the material – here’s BMC:

All articles are immediately and permanently available online. Unrestricted use, distribution and reproduction in any medium is permitted, provided the article is properly cited. See our open access charter.

But almost all hybrid papers – where you pay substantial money (perhaps 2000 USD) to make the paper “Open Access” – are neither labelled nor LIBRE. Ross Mounce has shown that only 5% of publishers offer LIBRE “open access” – the rest still impose restrictions or severe restrictions on use. And in my simple study of avian malaria in Pubchem only about 3 papers out of 70 were LIBRE at first glance.

So let’s say 5% of the current published scholarly output can be reused without thinking and without worrying. Because that’s the only guide. If you have to think, then it’s effectively not re-usable on a large scale. Machines can’t understand lawyers. And they can’t interpret information this isn’t given.

What can you do with 5%?

More than you might think at first glance. Much more.

Academics often have a narrow mindset that the only reason for publishing a paper is so some other academic can read your paper. That if we don’t have access to the precise paper we cannot do anything. Sometimes that’s true. But sometimes we just need representative material in that area. Let’s say I want to know the conditions for making an ester (a type of chemical) and there are 500,000 esterifications published a year. 5% of that is 25,000 different reports. My machines will certainly find all the mainstream types of reaction. If I want to know how to grow a common cell type, or prepare a specimen, or find the methods using for recognising motifs in genes or … I’ll certainly find enough examples. If I want to find images of mosquitoes, or a graph of the average rainfall in W Africa the LIBRE literature is almost certainly good enough. If I want to analyse the type of language and terms used in malaria articles the LIBRE literature is more than enough. If I want to find which countries the work is done in the LIBRE literature is all I need.

So we need to label and liberate LIBRE scholarship. And then persuade people to label their articles properly. And hopefully to persuade them of the immense value of LIBRE over GRATIS.

So the recent heroes of our effort have been

  • Tom Olijhoek and Bart Knols. Here’s Tom’s report in Malaria World http://www.malariaworld.org/blog/how-easy-can-you-find-information-you-need . Malaria is a really good place to start as the concept is well contained and we can find everything through UK/PubMedCentral. They have also helped to create the site http://access.okfn.org/ . That’s a really good place to start
  • Mike Taylor, sauropodologist (http://en.wikipedia.org/wiki/Sauropoda ). Mike has campaigned tirelessly and burnt midnight oil to create the site http://whoneedsaccess.org/ which runs in parallel with the @ccess site. He’s collecting interviews, including one from me, on why we need LIBRE @ccess.
  • Mark MacGillivray who continues to add fantastic design and power to http://bibsoup.net . Mark’s Bibserver uses faceted search in an incredibly powerful manner. The technical details are completely hidden from the user. The technology can interact with the Semantic Web / Linked Open data and is a great community builder

Anyone can be a member of this effort – you just need passion and energy and a need to provide LIBRE resources. And if you have a story about how and why you need LIBRE material and can’t get it , then highlight it on the mailing list or help populate the questions on the wiki.