Aping around: Locomotor behavior of an extinct great ape

A great ape that roamed Spain 10 million years ago got around like no other hominids known before or since, researchers conclude, based on a unique mosaic of skeletal features that suggest a combination of suspensory and quadrupedal behaviors.

The authors of the study, led by David Alba of the Catalan Paleontology Institute, analyzed bones from the elbow area, shoulder girdle, rib cage, and forelimb of a partial Hispanopithecus laietanus skeleton. They found features suggesting multiple different types of locomotion patterns for the extinct ape, including both swinging through the branches by the arms and walking among the branches on all four feet. The precise combination of features and behaviors, they write, is totally unique among known extinct and extant ape species.

Based on these results, they call the species a ”transitional state,” in that the combination of features simultaneously allowed the ape to maintain balance on all fours while also allowing it to move toward more suspensory behavior, which ultimately took over as the predominant mode of locomotion for the lineage.

This study probably doesn’t have immediate implications for the hotly debated question of how and why human bipedalism evolved, but sometimes it’s nice to take a step back from our relentlessly anthropocentric view and simply appreciate our ape cousins for what they are – and what they were millions of years ago. And, in a broader sense, this study also serves as a reminder that we must be careful to remember that we can’t conceptualize extinct species based only on “the biased evidence provided by their few and very specialized remaining living representatives,” as the authors write. The true evolutionary history is simply much too complex.

Citation: Alba DM, Almécija S, Casanovas-Vilar I, Méndez JM, Moyà-Solà S (2012) A Partial Skeleton of the Fossil Great Ape Hispanopithecus laietanus from Can Feu and the Mosaic Evolution of Crown-Hominoid Positional Behaviors. PLoS ONE 7(6): e39617. doi:10.1371/journal.pone.0039617

New articles online for Food and Energy Security

We are delighted to share with readers two papers which have recently published in Food and Energy Security. Included among these is the journal’s first original research paper by Paulo Mazzafera. We hope that you enjoy reading these articles.

Toward two decades of plant biotechnology: successes, failures, and prospects
Nigel G. Halford
A review of the genetically modified crop varieties and traits that have been launched in the last 18 years, the issues of regulation and consumer acceptance that still have to be overcome, and the prospects for the future development of plant biotechnology.

Which is the by-product: caffeine or decaf coffee?
Paulo Mazzafera
The market for caffeine has increased continuously over the last years while the production of decaf coffee, the main source of natural caffeine, has been almost steady. Synthetic caffeine might replace natural caffeine, but the market for natural and health products demands the latter.

Food and Energy Security is a new open access journal published in association with the Association of Applied Biologists. It publishes original research on agricultural crop and forest productivity to improve food and energy security.

Latest Article Alert from Harm Reduction Journal

The latest articles from Harm Reduction Journal, published between 08-Jun-2012 and 22-Jun-2012

For articles which have only just been published, you will see a ‘provisional PDF’ corresponding to the accepted manuscript.
A fully formatted PDF and full text (HTML) version will be made available soon.

Brief report
Societal images of Cannabis use: comparing three countries
Cunningham JA, Blomqvist

Drug Discovery course at Nijmegen – hands-on

I’ve spent a day and a half at Nijmegen, and have given a presentation on Semantic Science. Since much of the course is hands on, I’ve put together 3 simple web-based examples:

• Run chemicaltagger on abstracts from EGU’s Atmospheric Chemistry and Physics to pick up geo-locations.
• Run Quixote (http://quixote.ch.cam.ac.uk ) to find structures of benzene calculated at different levels of theory (use the SMILES search c1ccccc1)

And many thanks for a great time here!

Finch Fiasco in Figures

The Finch Report, under strong and palpable influence from the publishing lobby, instead of recommending extending and optimizing the UK’s worldwide lead in providing Green OA, cost-free, through institutional and funder self-archiving mandates, has recommended abandoning Green OA and Green OA mandates and instead spending extra money (£50-60 million yearly) on paying publishers’ Gold OA fees as well as a UK blanket national site-license fee to cover whatever is not yet Gold OA (i.e., all the journals that UK institutions currently subscribe to, rather like the “Big Deals” publishers have been successfully negotiating with individual institutions and consortia):

Finch on Green: “The [Green OA] policies of neither research funders nor universities themselves have yet had a major effect in ensuring that researchers make their publications accessible in institutional repositories? [so] the infrastructure of subject and institutional repositories should [instead] be developed [to] play a valuable role complementary to formal publishing, particularly in providing access to research data and to grey literature, and in digital preservation [no mention of Green OA]?”

Finch on Gold: “Gold” open access, funded by article charges, should be seen as “the main vehicle for the publication of research”? Public funders should establish “more effective and flexible arrangements” to pay [Gold OA] article charges? During the transition to [Gold] open access, funding should be found to extend licences [subscriptions] for non-openaccess content to the whole UK higher education and health sectors?

Now here are some of the actual figures behind the above assertions. Let readers come to their own conclusions about the relative success, cost, benefits, cost-effectiveness, growth potential and timetable of mandating Green OA vs funding Gold OA:

1. Mandated vs. Unmandated Green OA (20% vs 70%+):

2. Rise of Green Mandates:

3. Rise of Green OA, 2009-2011:

4. Rise of Gold OA 2003-2011 (from Nature, 2012)
(N.B.: Re-scaled at right for accurate comparison with rise of Green, above):

5. Projected rise of Gold OA (70% in 2020 or 2026; 100% in 2022 or 2029):

6. Relative Green and Gold OA Worldwide in 2010

7. Relative Green and Gold OA in United Kingdom in 2010 (from Nature, 2012)

8. The OA Citation Impact Advantage: (OA vs. non-OA)

9. The OA Economic Advantage for the United Kingdom:

Gargouri, Y., Hajjem, C., Lariviere, V., Gingras, Y., Brody, T., Carr, L. and Harnad, S. (2010) Self-Selected or Mandated, Open Access Increases Citation Impact for Higher Quality Research. PLOS ONE 5 (10) e13636

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

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

Harnad, S. (2011) Gold Open Access Publishing Must Not Be Allowed to Retard the Progress of Green Open Access Self-Archiving Logos: The Journal of the World Book Community 21(3-4): 86-93

YOU must Support Intellectual Property Reform in UK

The UK government commissioned the Hargreaves report into Intellectual Property Reform and their recommendations (summarised by RLUK) were:

Professor Hargreaves’ Review made a number of important recommendations, including that exceptions at national level should include format shifting (vital for preservation), non-commercial research, and library archiving, and that EU exceptions should support text and data mining. There were also proposals on orphan works, which will allow a pragmatic solution to the question of how to digitize older material while still respecting rights holders

The Intellectual Property Office then asked anyone (this is useful modern democracy) to comment and got over 450 replies:

including one from me, and one from the Open Knowledge Foundation Open Science Group.

Worth reading but most sections include “both sides” of the case. “Both sides”? Don’t we all want reform? Well some people are very happy with the status quo. They have good businesses, especially scholarly publishers where universities give them content, they add near-zero value and then sell it back to the world. And the UK is very strong in this area – we have lots of wealth-generating publishers. Wealth-generating? Income generating, perhaps. But adding value?

Anyway there is substantial resistance to Hargreaves from publishers. Why should people like me be allowed to mine the scientific literature? It could destroy British industry. The Royal Society of Chemistry’s view (on this blog) is that I can only text-mine “RSC content” if I can guarantee they won’t lose business. And I can’t guarantee this.

Well if its’ that fragile, it’ll crash anyway.

So a number of MPs have tables an “Early day motion”. This is Houses-of-Parliament-speak for something the MPs want, rather than the government. The RLUK has provided some background:

They need support (ONLY FROM BRITS, I am afraid – anyone can write to Obama but it doesn’t work in reverse).

So you can write to them using www.writetothem.com

I don’t need to as our MP used to work in our lab.

BUT YOU DO. And RLUK’ll expect 100% effort from UK librarians on this.

And everyone else needs to as well.

Latest Article Alert from BMC Public Health

The latest articles from BMC Public Health, published between 14-Jun-2012 and 21-Jun-2012

For articles which have only just been published, you will see a ‘provisional PDF’ corresponding to the accepted manuscript.
A fully formatted PDF and full text (HTML) version will be made available soon.

Study protocol
Rationale, design and methods for a staggered-entry, waitlist controlled clinical trial

Ask EveryONE: Where can I find Supporting Information in a manuscript?

If you’ve just created a manuscript in Editorial Manager and you’re reviewing it before submitting to the PLoS ONE office, or if you’re a reviewer or Academic Editor providing feedback on a paper, you may be asking yourself the above question.

You can access all supporting information at the end of a manuscript through the hyperlinks at the top of the page. It will look something like this:

Our submission system is designed to create these hyperlinks because most often, the kind of data in a supporting information file is quite large, making it far too cumbersome to embed directly into the pdf.

For answers to other questions you may have, visit our Most Common Questions page.  As always, if you still have questions, please don’t hesitate emailing us directly at plosone@plos.org.

#scholpub, PeerJ and Tim O’Reilly

I’ve trailed this post over the last two days. Who / what will be the major revolution in for-profit (FP) #scholpub? (I’m not forgetting PLoS and eLIFE, but I think that there will be a place for responsible private sector participants. And competition in this area will be beneficial.)

I’m currently tipping PeerJ (about which I have all of 1-2 week’s knowledge) (http://peerj.com/ ). So why the rapid jumping on yet another bandwagon?

To be clear I know nothing about PeerJ other than what’s on the web (blog: http://blog.peerj.com/ ). I haven’t spoken to anyone or read insightful blogs. So here’s an introduction:

“If we can set a goal to sequence the human genome for $99, …then why not$99 for scholarly publishing?

That single sentence says it all.

They get it.

In a way that no one else has publicly done. Publishing is a commodity market, and as such is wildly overpriced.

That will cause howls from the mainstream #scholpub. They howled against PLoS (“unfair!!”). They howled against PLoSOne (“unreviewed low quality rubbish”) and they probably howl foul against eLIFE.

But the reality is that scholarly pub has foundered on the conflation of providing a service (which costs 100 USD) and providing Glory. These can be separated. I imagine Nature will continue to prosper – they once hired James Randi the magician to oversee an experiment (http://en.wikipedia.org/wiki/Water_memory -if you don’t know this it’s worth reading!).

So let’s assume that – say – 1 billion of #scholpub goes – somehow – to glamour science. We could have shows, gladiatorial contests, etc.

While PLoSOne and PeerJ (and Acta Cryst) develop commodity publishing.

PeerJ has a very challenging business model: 99USD to publish one paper (against 10,000 in Nature and about >=1500 USD elsewhere). And even more exciting, it’s 300 USD for unlimited papers in your lifetime. Note these charges are per-author. So if I write 2-author papers it costs 200 USD. If I write a 96-author paper(which I have) then it costs 100*(min(12, nauth)) = 1200 USD. But if they have paid their 300 USD that’s then nothing.

The real point is that in a commodity market lots of other avenues open up. The authoring for example. Or re-use of data. Conventional publishers cannot address these as they have hacked authors off with their awful dismissive attitude to authors – simply fodder. A clever publisher will give the author something back – something of value. Mendeley gives something back, for example. What have you got of lasting value after authoring an Elsevier paper? A decimal point.

But the real thing that swung me to PeerJ was a member of its Board, Tim O’Reilly.

If there was one person in the world that I would want to reform #scholpub (and pace Robert Kiley et al) it would be Tim. I’ve met Tim several times – he’s invited me to Foo Camp (http://en.wikipedia.org/wiki/Foo_Camp ) on three occasions. Foo Camp is one of many ways he is transforming the world.

Tim’s a real revolutionary. He wants to create an open world where the key commodity is innovation. If he puts his energy into PeerJ it will transform the landscape. His commitment to Open means he won’t sell out to Springer or anyone else. He knows more about the dynamics of the information world than anyone else I know.

I also know Peter Binfield and Jason Hoyt. They have come up from innovative backgrounds – PloS and Mendeley.

But I hope they won’t mind me saying that it’s Tim’s involvement that is critical.

It won’t be easy for PeerJ. It never is in a stagnant self-congratulatory lawyer-run bloated market. But if they stick to commodities in and beyond #scholpub and foreswear the Glory trail they have a good chance. I reckon that the #scholdata market is even bigger than #scholpub. I doubt that’s news to them.

And, because I hate monopolies, I hope others challenge them.

On fair value, not on reselling someone else’s content.

The coming revolution in STM #scholpub

I have prophesied that there will be a revolution in STM #scholpub and now I can put some flesh on the bones.

If we look at current #scholpub – as the Finch report did – and ask how do we change it, we end up with a mess. The report is a mess and almost all small steps will end up with at least as much mess or even more. The universities have failed to give any sort of moral, organization or technical lead. Their repositories are failures – most have at best a few per cent of their output and academics either ignore them or regard them as a distraction or impediment. No-one uses them to discover scientific information because they are disorganised, have no useful search tools , and do not interoperate.

So STM publishing is probably the most inefficient information market on the planet. Compare it with Amazon, Google, Car insurance, Supermarket products, financial information and more.

Voluntary information resources are better than what the commercial publishers can provide. Compare Wikipedia or Figshare with SpringerImages. Tell me if you disagree.

So let’s get away from the details and see why there must be a catastrophic fracture.

• Anyone who understands the modern information world – Open source/content, communities, open standards, interoperability etc. will look at current closed STM publishing (I’ll call this TollAccess – TA) and see how appallingly inefficient it is.
• The market is very significant – perhaps 15,000,000,000 USD (15 billion). This is largely fuelled by governments (who fund universities), students (who pay fees), research funders (universities strip money off grants to pay for journal subscriptions) and endowments. Up till now this has been an infinite cash cow (yes libraries scream, but expenditure has continued to rise). So it’s worth newcomers coming to get a piece of it
• There has been no change in the market of TA practice for 15 years. No innovation. The Scholarly Kitchen blog, the love-in for TA publishers recently asked itself what the biggest advance was in the last decade. “The Big Deal”. This is a marketing ploy to force libraries to buy more journals than they actually want to buy. (To be fair they also mentioned PLoS).
• The market has failed to follow Moore’s law. This is not because the law doesn’t apply – it’s because it’s been artificially held back by company lawyers, marketeers, timid librarians, indifferent universities and arrogant academics. Even allowing (say) a Moore’s law of 2 years, you end up with a grossly overpriced journal article.
• There is no change in the product (“the journal” and the “artickle”) but there is no restriction requiring this. Lawyers can restrict change in their function through their closed practices and communities. Publishers can’t
• There is no love or respect for publishers. People queue when Apple opens a new store. Do scientists BUY “I love Elsevier” T-Shirts from the “Elsevier Store”?
• There is serious friction between the aspirations of funders and the practice of publishers. Funders want their work made available to all. “TA publishers” base their business model on restricting access.
• 99% of the world, including 99% of the rich world (#scholarlypoor) has no access to #scholpub. Only universities can read it. What other market is so hidebound that it only offers its products to such a restricted customer base? Academia compounds this by suggesting that no-one outside its ivory towers can benefit from #scholpub. This arrogance must not and cannot endure.
• The costs of enforcing TollAccess are a very significant part of the total costs (paywalls, lawyers, etc.). And the hidden costs – to the consumers – are even larger. So much science simply isn’t done because of the TA friction

And the list is probably incomplete.

My point is that any entrepreneur can now see a 15 billion USD market which is ripe for exploitation. You don’t have to be an expert in science.

I can’t see the details of the new market. It will have radically different products. I can guess some. The “journal” will disappear because it has no pupose. There will still be a need for Glory and maybe Nature will still be selling that. Perhaps we shall have TV-based talent contests.

But the article – if it persists – will become a commodity. Here’s my thinking…

There is now mounting evidence that it costs about 100 USD to publish an adequate qualilty open peer-reviewed scientific paper. In total.

My evidence:

* IUCr publishes 3000 OA papers a year (Acta Cryst E), IN FULLY SEMANTIC FORM for 150USD which gives a useful “profit”. They do this because they have engaged the authors who willingly do much of the work for them. Authors do it because IUCr has built the authoring system and it’s far better than anything the main publishers have come up with.

* It costs 7 USD to put a paper in arXiv

* PeerJ charges 99 USD for an open peer-reviewed paper. I believe this figure makes sense.

Nature “has to charge” 10000 USD for an openaccess paper because it is selling glory. Glory commands whatever price people are willing to pay.

Many publishers charge huge amounts for OA because they have an effective monopoly of the subdiscipline and because they are also selling glory.

Anyone can author and publish a scientific paper without a “publisher”. Every student’s thesis is a peer-reviewed piece of science. I know some universities opt out of the process by getting student to publish in closed access journals and then simply collecting the papers. These unievrsities are part of the problem.

Many scientists (particularly in CompSci) run peer-reviewed workshops for dissemination and merit and do the whole lot without publishers. Traditionally they may get the proceedings published through a publisher but this is not necessary.

So;

* publishers are not necessary for top-quality peer review

* publishers are not necessary for the technical creation of high-quality documents

And to reiterate:

Traditional publishers now have exactly two unique selling points:

* they sell perceived glory to universities

* they “persuade” universities and authors to give them highly valuable material and then use the legal mechanisms of the last 200 years to control and resell content.

Both are very fragile. If either crashes then the publisher has very little to sell. If both crash so will the publisher.

If Green OA had been done properly – in 1995 – then I would be a supporter. Basically every university would have required its outputs to be fully posted on the web. Departments and  individuals would be judged on that. Instead of building repositories they should have built publishing systems. By now we would have the whole of STM on the web.

But Green has missed the boat and Gold is slow and expensive.

Enter…

… what or who?