Monday, 9 December 2013

Update: Elsevier's Knowledge Lockdown

In Open Access, Accountability, and For-Profit Publishing I wrote about the publisher Elsevier and its continual efforts to restrict access to published research by locking it behind expensive subscriptions, without any explanation as to why access was so prohibitively expensive in the first place (besides making $$$). I mentioned that authors who publish in Elsevier's publications can choose to make their articles openly accessible to everyone, but that
Elsevier's revenue model currently dissuades researchers from sharing by charging authors who wish to make their work open access $3,000 per article (the actual amount varies depending on the journal - it's £400 per page in The Lancet and $5,000 for Cell Press titles).
However, it's been common practice among researchers to disregard this technicality and publish their papers on their own websites as well - free of charge. And Elsevier's legal team must be extra restless right now, because they served up a bunch of take-down notices, nicely summed up over at Sauropod Vertebra Picture of the Week:
Preventing people from making their own work available would be insane, and the publisher that did it would be committing a PR gaffe of huge proportions. Enter Elsevier, stage left. Bioinformatician Guy Leonard is just one of several people to have mentioned on Twitter this morning that took down their papers in response to a notice from Elsevier. explained its actions with the following notification, laying the responsibility squarely and fairly at the feet of Elsevier:

Hi Guy
Unfortunately, we had to remove your paper, Resolving the question of trypanosome monophyly: a comparative genomics approach using whole genome data sets with low taxon sampling, due to a take-down notice from Elsevier. is committed to enabling the transition to a world where there is open access to academic literature. Elsevier takes a different view, and is currently upping the ante in its opposition to academics sharing their own papers online.

Over the last year, more than 13,000 professors have signed a petition voicing displeasure at Elsevier’s business practices at If you have any comments or thoughts, we would be glad to hear them.
          The Team

So, there. The battle lines were contractually drawn a long time ago, and big publishing is simply entrenching itself further.

Big thanks to Mike Taylor and SV-POW for bringing this to our attention

Wednesday, 4 September 2013

Optimism Without Reserves

Peak Oil Is Dead, Long Live Peak Oil

Less than a month ago, geologist Euan Mearns wrote a piece called "Three Nails in the Coffin of Peak Oil". The article was posted on The Oil Drum, a website that has been a source of peak oil information and debate for nearly a decade, but is now being mothballed and indefinitely put to rest.

This is emblematic of the state of peak oil today. The idea that a peak in oil production rates is imminent seems to appear much less in the media now than during the oil price spike of 2005-2008, and the graph below suggests that public interest in it is waning as well.

When peak oil does appear in the media these days, it is often dismissed or outright ridiculed. A widely cited report from Harvard University put the ivory seal of academia on peak oil's death sentence. The June 2012 report, which can be read in full here, contends that global oil production will rise until 2020 at rates that have not been seen since the 1980s. Most of this growth is attributed to an increase in shale/tight oil production, especially in North America, where Montana and North Dakota could become "a big Persian Gulf producing country within the United States".

Taking a slightly different angle, The Economist recently argued that the world will soon figure out out how to reduce its oil dependency through a mix of fuel efficiency improvements and switching to newly abundant natural gas, meaning a peak in demand, rather than supply, is expected. There have even been calls to shut down the U.S's Strategic Petroleum Reserve, a massive oil storage facility put in place after the 1973-1974 embargo, implying that the kind of oil worries started in the '70s have been put to rest once and for all.

This lack of concern with oil supply constraints is generally regarded as good news, although taken from another perspective, the idea that we might manage to keep up (or even increase) the rate at which we're burning oil for decades to come is perhaps not particularly appealing. Some of those who reject the peak oil hypothesis aren't thrilled about it either. One of the most prominent names to have switched sides in the debate, journalist George Monbiot, wrote a piece shortly after the Harvard report came out called "We were wrong on peak oil. There's enough to fry us all". However, while the more severe effects of climate change are still decades away according to most predictions, a dip in the supply of oil could have immediate and far-reaching repercussions: about 95% of global transportation energy is petroleum-based, meaning pretty much everything you eat or use has been moved around using oil at some point in its life. Personally, with my parents living more than 7000 km away from me, any decrease in the availability of affordable transportation would have a significant impact on my life. As a species with a relatively-short lifespan, it's not hard to guess how far on the horizon our priorities are going to lie.

Of course, all this pre-supposes that the combination of science and speculation behind this production/demand optimism is accurate. Look for another post coming down the pipeline which critically examines what, exactly, is lending credence to these reports.

Thursday, 2 May 2013

Experimental Lakes Area Bailed Out, Still Living Paycheque to Paycheque

Temporary Respite from the War on Science

The Experimental Lakes Area (ELA) is a series of 58 lakes and a research facility in northwestern Ontario where scientists study the effects of pollutants and other stressors in a naturally-occurring ecosystem. In other words, it's a literal massive wet-lab. The world-class testing facility, unique to Canada, allows scientists to introduce chemicals into entire lakes monitor the effects in a natural ecosystem, rather than in a smaller artificial lab setting. Some of the globally recognized work to come out of the ELA includes the investigation of algae blooms which led to the ban of high-phosphate laundry detergents and phosphorous use at sewage treatment plants in the 1970s.
Last summer, however, the federal government announced it would no longer be funding the facility, effective March 31, 2013.

The reasons for the decision were never clearly articulated, the usual fall guy of budget cuts being touted, alongside claims that the ELA, which was under the operational umbrella of the Department of Fisheries and Oceans, no longer fell under the department's mandate. Since then there has been rampant speculation about the fate of the ELA, and at one point it was being sold to the UN's International Institute for Sustainable Development.

It would cost the federal government $2 million a year to continue funding the ELA, with an additional $600,000 in operation costs, but as MP for the area Greg Rickford concedes, this really isn't about the money:
“We do intend to withdraw our role in the ELA. The motivation for that is because the federal government must have flexibility to move certain types of research, including some that has gone at the ELA, to other parts of the country where there is the potential for monitoring new environmental factors that are more proximal to resource development in Western Canada. That research is continuing, it’s just moving to other areas of the country where it’s required.”
As it turns out, this bullshit response can be refuted by the very history of the Experimental Lakes Area itself. In the 1970s, the acid rain research conducted at the ELA was initially funded by the Government of Alberta's Oil Sands Research Program, with the intent of investigating the long-term impacts of developing the oil sands. They were  able to secure money for the first three years of the research from the program because, lo and behold, "their freshwater ecosystems had a lot of the same species that we did at ELA and their most sensitive lakes were like ours" (from a great interview with the renowned scientist David Schindler, former ELA director).

It seemed that efforts to save the area had failed, when last week the Government of Ontario announced that it would work with the Government of Manitoba, the federal government, and "other partners" to keep the ELA operational for the rest of 2013. It's still unclear what the long term plans are, but as of right now Ontario seems to willing to cover operating costs, at least for now. It's a temporary victory, but a relief for the scientists who currently have federal grant money to study the effects of nanosilver on lakes - $800,000 to be exact, which perhaps the federal government would have been fine writing off as a cost of war.

Conservatives Vote "No" to Science

The mounting frustration regarding the federal government's handling of the ELA, and science in general, reached its apex this March with the following vote put forward during Parliament, which is now in the midst of federal budget discussions. From Vote No. 631 on March 20, 2013:
That, in the opinion of the House: (a) public science, basic research and the free and open exchange of scientific information are essential to evidence-based policy-making; (b) federal government scientists must be enabled to discuss openly their findings with their colleagues and the public; and (c) the federal government should maintain support for its basic scientific capacity across Canada, including immediately extending funding, until a new operator is found, to the world-renowned Experimental Lakes Area Research Facility to pursue its unique research program.
The vote, sponsored by NDP MP Kennedy Stewart, is a particularly loaded piece of political savvy. By tacking on the call for the government to continue its support for the ELA, Stewart guaranteed its defeat at the hands of the 157 Conservatives in Parliament. In short, the Government of Canada voted that it is against science, a very catchy soundbite which fits perfectly into 140 characters and makes for a great screen cap. Of course, this is accomplished through a bit of circular logic not uncommon to political rhetoric. But in light of the policy pushed through by this government, the vote is not an inaccurate representation of the prevailing attitudes of the current government at all. The Unmuzzled Science has a brief takedown of how the Conservatives have opposed each point present in the motion.

Not Scientists, Just Doctors of Spin

The advocacy group Democracy Watch released a report in January of this year, alleging that the Government of Canada has been systematically limiting access to government information, specifically federal scientists from the departments of Environment, Fisheries and Oceans, and Natural Resources. Spin and the restriction of information is, of course, not unique to this government, but the unabashed, unapologetic way in which the Harper Government does so is downright insulting. Democracy Watch has subsequently filed a complaint along with the University of Victoria's Environmental Law Centre to the Information Commissioner of Canada, asking for an investigation into the government's obstruction of information. Until then, here's to hoping that public backlash will continue the stay of execution of further campaigns against science.

Tuesday, 23 April 2013

Betrayal in the Banana Republic

Or, The Short Version of Why Open Access Matters

In Open Access, Accountability, and For-Profit publishing, I wrote about how the lack of model transparency and access to data prevented researchers from replicating others' results, leading to an over-reliance on the peer-review process to vouch for a piece of research's validity. I also mentioned how peer-reviewers are not required to audit the veracity of a model or verify its results, and that this lack of oversight could result in inaccurate information influencing policymakers.

Now, researchers Thomas Herndon, Michael Ash, and Robert Pollin have called into question the conclusions of the economics paper "Growth in a Time of Debt" for exactly these reasons. Written in 2010 by Carmen Reinhart (University of Maryland) and Kenneth Rogoff (Harvard), the paper has played a not-insignificant role in the public discourse on economic policy during the current recession. As Mike Konczal of Next New Deal summarizes:
This has been one of the most cited stats in the public debate during the Great Recession. Paul Ryan's Path to Prosperity budget states their study "found conclusive empirical evidence that [debt] exceeding 90 percent of the economy has a significant negative effect on economic growth." The Washington Post editorial board takes it as an economic consensus view, stating that "debt-to-GDP could keep rising — and stick dangerously near the 90 percent mark that economists regard as a threat to sustainable economic growth."
Their findings also provided the basis of Reinhart's testimony before the Senate Budget Committee on Feb. 9, 2010, and have been used to support the argument for austerity in Europe and the United States.

Initially it would seem that access to data isn't an issue, as Reinhart and Rogoff provide the historical data they used along with their sources on their website. But publicly-available data is meaningless without context, and the authors don't provide any clarity on which dataseries and methodology they used. This is why model access is equally important to experiment repeatability and accountability. (There is some discussion on whether or not "Growth in a Time of Debt" was ever actually peer-reviewed, but as noted above, there's a good chance it would have passed review without anyone ever having to look at the model and datasets anyway.)

From Herndon, Ash and Pollin (pg 5):
We were unable to replicate the RR results from the publicly available country spreadsheet data although our initial results from the publicly available data closely resemble the results we ultimately present as correct. Reinhart and Rogoff kindly provided us with the working spreadsheet from the RR analysis. With the working spreadsheet, we were able to approximate losely the published RR results. While using RR's working spreadsheet, we identifi ed coding errors, selective exclusion of available data, and unconventional weighting of summary statistics.
Reinhart and Rogoff's work demonstrated a seemingly straight-forward, data-driven analysis linking causation from a country's public debt to GDP growth, which is great talking-head bait and support for austerity economics. But, as succinctly put by Herndon, Ash and Pollin, "A necessary condition for a stylized fact is accuracy".

Update: Now with video! 
Reinhart/Rogoff debacle reaches fever pitch with Steven Colbert going to town.

Friday, 22 March 2013

Greenwashing Blitz: Métro

Bref Vert, or Briefly Green

Cut down a bunch of trees, mill them into paper, paint it turquoise, put a bizarre picture of a monkey doing monkey business on the cover, say a few words about how cute animals are awesome and therefore they will save the planet, and there, you've got yourself a "Green Special". Never mind that one of the ways these animals are supposed to save the planet is through ecotourism, which involves rich people spending half a year's worth of SUV emissions on a flight to some tropical paradise to swim with the turtles or whatever.  Either the people who are editing this daily pastime for the short-of-attention are completely unaware of what global environmental challenges are, or they just decided to make a mockery of it by praising the virtues of "panda diplomacy"- an actual political term which has less to do with saving the planet and more with sending over furry animals in exchange for natural resource access.

For some reason, I feel like the former is the explanation, and the latter is the outcome.

Wednesday, 13 March 2013

Open Access, Accountability, and For-Profit Publishing

This post originated from the specific frustration of trying to evaluate suspiciously accurate energy assessment models and looking for ways to improve others. Every time I was stonewalled by a lack of access to the models and datasets, I would stupidly ask why and subsequently discover more ways in which the current state of academia fails the public, the government, and the academic community. 

Banana Republic: The Failed State of Academic Publishing

How does academic publishing - a mechanism which should encourage the open exchange of information and dissemination of knowledge - get away with doing the exact opposite? By operating in a manner not dissimilar to a banana republic.  Public resources, including funding and institutions, incur the costs of producing research and the burden to continue supporting them, while the dictators (publishing companies) exploit the power imbalance between themselves and the academic contributors, made possible by the priorities of the current academic system - the quota of publications. As is the case with banana republics, the result is that the system's currency - citations in the academic world - becomes devalued, while the only gains made are outside this currency system and are for the publishing monopolies, in the form of actual money. Publishing companies have held the academic population and public resources hostage by exploiting the citation-focused criteria of academia.

One of these "dictators" is publishing giant Elsevier (sub-sect of Reed Elsevier), which puts out roughly 2000 scholarly journals and includes the online access portal ScienceDirect.  Because of their massive market share and subsequent influence (including in front of government committees), I'm going to pick on their business practises in particular as an example of the state of academic publishing. Elsevier makes money by selling subscriptions to its large depository of publications to universities, governments, corporations,  or charging members of the public to access articles, and it is starting to get territorial. The Chronicle of Higher Education has a good piece  on the influence publishers wield politically, the fight for open access, and Aaron Swartz:
"The academic publisher Elsevier has contributed to many U.S. Congressional representatives, pushing the Elsevier-supported Research Works Act, which among other things would have forbidden any effort by any federal agency to ensure taxpayer access to work financed by the federal government without permission of the publisher."
The Research Works Act is one in a series of reactionary measures to restrict control on taxpayer-funded research in the U.S. The result was backlash from the academic community, including The Cost of Knowledge online petition, which academics publicly signed and vowed to abstain from either publishing, reviewing, or doing editorial work for Elsevier. The petition was successful, and Elsevier withdrew its support on February 27, 2012 (without acknowledging the boycott, naturally). Prior to that on Feb. 3, however, the publisher issued this statement to the academic community:
"The costs of publishing services need to be met and are in addition to the costs of doing the research. Publishers invest heavily to add value to research reports and draft manuscripts through the publishing process. Academics do too through the peer review process, but without publishers and peer reviewers the 3 million manuscripts submitted each year would not be transformed into the 1.5 million articles published each year. Researchers function more efficiently and effectively because of the value that is added by all of us through publishing processes."
(There is some Schadenfreude in the statement's panic to justify itself, and is worth the read. The Cost of Knowledge is ongoing in its boycott and has drawn over 13,000 signatories to date.)

The most important part of preserving the peer review process is the peers who are willing to review, in my estimation. And those peers are not reimbursed by Elsevier, except for some occasions where they are incentivized with book vouchers.  So where then does this "value-added" come from? It's true that ScienceDirect is a nice interface to use and search through, because they own many, many publications. And that requires development and maintenance, and administration. But apart from that, I'm not sure where the money goes, except to "cost of sales" and other dubiously ambiguous accounting terms (their financials can be found here).  Of course they're willing to play ball: "Elsevier is happy to work with any sustainable business model for publishing services". The problematic word here is "sustainable" - corporations left to define sustainable for themselves is like putting a jar of cookies in front of a 5 year old and letting them decide how many they should reasonably consume. And then wondering why they're puking chocolate chips.

In 2011 the U.S. Office of Science and Technology Policy put out a call for recommendations from interested parties on the subject of open access to peer-reviewed scholarly publications. You can view responses from different stakeholders here, but suffice it to say, the universities and individuals fell on the side of supporting open access, and the publishers in opposition, arguing that to do so would hurt their revenue streams and ultimately provide a loss of service for American researchers. (One of those things may be true, but as for the other: ).

Elsevier responded to the Office of Science and Technology predictably:
"Incentives, rather than mandates, are needed to overcome data access challenges. There is currently a disparity between a researcher's willingness to use shared data and to supply it. Many researchers agree it is necessary, but decline to share their own data. An example is documented in a survey prepared for the launch of the Economists Online repository in 2010 that indicated a majority of economists were in favor of accessing datasets, but when asked if they would post their own data only 15% indicated that they would be prepared to do so.  Publishers can play a role to incentivize the deposit and reuse of data - just as we help to incentivize academics to publish by enabling them to register their scientific discoveries in widely accessed, cited, and respected journals. We have made data available alongside publications and support initiatives to help researchers to share data (e.g. Pangaea, CCDC and DRYAD)." Page 4
"Incentives, rather than mandates" is reiterated throughout the response, without explaining why incentives would be more effective than mandates. But to be clear, this is a call for governments and funding bodies to incentivize researchers, lest the publishers' revenue models be disrupted. In fact, Elsevier's revenue model currently dissuades researchers from sharing by charging authors who wish to make their work open access $3,000 per article (the actual amount varies depending on the journal - it's £400 per page in The Lancet and $5,000 for Cell Press titles). Elsevier's justification for these not-insignificant sums: "This fee covers the costs involved during the peer review process and publication."  As mentioned a few paragraphs back, peer reviewers are not paid to review articles, so I'd be interested in seeing that number broken down into publishing costs.  Elsevier does have some established agreements with funding bodies, including the NIH, Wellcome trust and UK Research Councils regarding open access for research done with their grants, and researchers can appeal to their funding bodies and institutions to be reimbursed for the fee, but as long as Elsevier retains its current position of monopolistic power it can get away with charging what it likes.

Meanwhile, Elsevier maintains that one of the biggest obstacles to open access is the research and academic community itself. Their response cites the statistic that while a majority of economists are interested in accessing others' datasets, only 15% are willing to share, a number supposedly coming from the final report of the NEEO project.  NEEO (Network of European Economists Online) provides open access to economics publications from European research institutions through the portal Economists Online.  The aforementioned report includes the results of studies conducted by the NEEO to assess the researcher/user requirements, but nowhere have I been able to locate Elsevier's 15%, which the footnote indicates as coming from section 7.3.5. A figure which does seem to correspond to Elsevier's point is 29% - researchers indicated that dataset availability through Economists Online could be a key feature, but only 29% indicated they would be willing to submit all their datasets to an institutional repository (pg 32). Furthermore:
"Dataset creators appear to have two main concerns in relation to submitting their work to EO: the risk of not being credited for their work and losing the opportunity of producing more results based on their creations. Even if a researcher had already produced an article, giving away his/her data may allow other researchers to produce a similar piece of work more quickly than the dataset creator. In addition to losing the opportunity of producing more research outputs, participants also feared that free access to datasets may facilitate a widespread use of their work without any recognition. The central role datasets play in empirical research means they were not seen solely as an input for publications but also as a product in themselves whose authorship needs to be credited. The general consensus, then, was that researchers would be willing to include datasets in EO only if creators are guaranteed proper acknowledgement. The most common mechanism by which participants thought both previous concerns (loss of publication opportunities and lack of recognition) could be somewhat minimised was to wait until their own research was released, preferably through an article in a peer-reviewed journal." Page 32
To wit: Elseiver recognizes that researchers believe there is a benefit to sharing but are reluctant to do so, making incentives are necessary, rather than mandates, which would cut into their revenue stream, and is therefore the job of someone without shareholders to answer to. Elsevier does understand the importance of paying lip-service to the principles of open access (here's a list of their initiatives ) as long as someone else is picking up the tab. Oh, and Elsevier does support access by publishing the authors' work in the first place, so you're welcome.

Tuesday, 5 February 2013

Nature Drinks the Pipeline Koolaid

An editorial in last week's issue of Nature - the  prestigious, oft-cited scientific magazine founded in 1869 - seems to have announced a bold departure for the publication, away from science and towards garbage. Beginning benignly enough, the editorial congratulates Obama's "generic" and "pragmatic" call for innovation in clean energy, and states that Obama needs to "break out of the mould and lay the foundation for something larger" if he is to cement his legacy in the climate debate. Fair enough.

Though the discerning reader may note an ominously questionable tone in the ones preceding, it's in the fourth paragraph where the transformation truly begins. Writing in regards to the approval of the Keystone pipeline, the author helpfully suggests Obama ensures the project adheres to environmental regulations and cuts the ribbon on it already. After all, "oil produced from the Canadian tar sands [is not] as dirty from a climate perspective as many believe (some of the oil produced in California, without attention from environmentalists, is worse)". This being a truth so fundamental, the author has no need to insert supporting citations.

But it's more the blasé acknowledgement of the following which warrants such outrage over a sloppily-written, lackadaisically-presented contribution to "science":
Tar-sands development raises serious air- and water-quality issues in Canada, but these problems are well outside Obama’s jurisdiction. 
Well then. Problem solved, because it's not the good ol' U.S. of A's issue. Your grandchildren will be thankful that you had the foresight to commit to artificially cheap energy sources, irrespective of the quality of air in Northern Montana (Alberta naturally being the only province annexed in the aftermath of the Drone Resource Wars of 2060).

Keeping in mind Nature's self-proclaimed mission is to "ensure that the results of science are rapidly disseminated to the public throughout the world, in a fashion that conveys their significance for knowledge, culture and daily life". Keeping in mind that, under its submission criteria, the magazine proudly announces it "does not employ an editorial board of senior scientists, nor is it affiliated to a scientific society or institution, thus its decisions are independent, unbiased by scientific or national prejudices of particular individuals." Sure, it's an editorial, but it's an editorial in service to a magazine which promotes itself to the most exalted levels of objective scientific discovery.

For an article which refers to the "tar sands" throughout (as opposed to "oil sands"), this is a pretty balls-y stance.  I would like to duly congratulate the author on his/her quest to bring utter garbage to the discourse surrounding energy policy and the environment, but unfortunately, in their modesty, no name has been attached to the editorial.