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.

Latest Article Alert from Breast Cancer Research

The latest articles from Breast Cancer Research, published between 12-Feb-2012 and 26-Feb-2012For research articles that have only just been published you will see a ‘provisional PDF’ corresponding to the accepted manuscript. Fully formatted PDF and full-text (HTML) versions will be made available soon.Research articleHonokiol activates AMP-activated protein kinase in breast cancer cells via LKB1