Listen to expert speakers and download powerpoint presentations from this two-day symposium held at the Claremont Hotel in Berkeley, California on April 12-13, 2012. Made possible through the efforts of the Berkeley Digital Library Copyright Project and generous support from the Alfred P. Sloan Foundation.
I dropped in to see our computer officers today – they’ve just had an aircon failure and I was offering sympathy – they have a lot to deal with. While there I noticed this splendid spanner (== wrench/US). I love tools and this one has a majesty of its own in a computer office. It’s about 40 cm long (see ruler) and we guess it’s about 2 kilos.
I naturally assumed it was for something like bolting units to the floor or something like that, but that’s not why it was ordered. The reason is gently amusing – perhaps you can make some guesses).
Meanwhile tomorrow I’ll be blogging about text-mining. I’ve been hacking code furiously over the last 5 days and feeling it. There is a lot I need to write about but textmining is the priority.
Fingerprints are as unique as snowflakes – or so we’re taught in elementary school. Identical twins, though, provide an interesting caveat to this rule: Not only do they look alike, they are also more likely than non-twins to have similar fingerprint patterns.
These similarities raise potential complications for biometrics-based security systems and crime solvers, but a PLoS ONE paper published Friday suggests there’s no reason to worry.
The study, conducted by an international team of researchers from the Chinese Academy of Sciences and the University of Iowa, looked at fingerprints from 83 pairs of identical twins. They collected each print six times, rather than the single impression that is usually collected, and used two different identification methods, called P071 and VeriFinger 6.1, and novel analytical methods to evaluate the prints. They found that identical twins’ fingerprints had a 74% probability of being the same type (though not identical), as compared to a 32% probability for a random pair of prints, but they also showed that the fingerprints could be distinguished using the sophisticated identification methods.
Based on these results, it looks like identical twins may not be the perfect criminals after all. Nevertheless, they seem to have a leg up on the rest of us – maybe something to keep in mind the next time you’re trying to solve that thorny art heist.
Citation/Image source: Tao X, Chen X, Yang X, Tian J (2012) Fingerprint Recognition with Identical Twin Fingerprints. PLoS ONE 7(4): e35704. doi:10.1371/journal.pone.0035704
The claim is often made that researchers (peers) have as much access to peer-reviewed research publications as they need — that if there is any need for further access at all, it is not the peers who need it, but the general public.
1. Functionally, it doesn’t matter whether open access (OA) is provided for peers or for public, because OA means that everyone gets access.
2. Strategically, however, it does matter, because currently OA is not being provided in anywhere near sufficient numbers spontaneously by researchers (peers).
3. This means that policies (mandates) from peers’ institutions and funders are needed to induce peers to provide OA to their publications.
4. This means that credible and valid reasons must be found for peers’ institutions and funders to mandate providing OA.
5. For some fields of research — especially health-relevant research — public access is a strong reason for public funders to mandate providing public access.
6. But that still leaves all the rest of research, in all disciplines, funded and unfunded.
7. Most research is technical, intended to be used and applied by peer researchers in building further research and applications — to the benefit of the general public.
8. But most peer-reviewed research reports themselves are neither understandable nor of direct interest to the general public as reading matter.
9. Hence, for most research, “public access to publicly funded research,” is not reason enough for providing OA, nor for mandating that OA be provided.
10. The evidence that the primary intended users of peer-reviewed research — researchers — do not have anywhere near enough access is two-fold:
11. For many years, the ARL published statistics on the journal subscription/license access of US research universities:
12. The small fraction of all peer-reviewed journals that any university can afford to access via subscriptions/licenses has since become even smaller, despite the “Big Deals”:
13. The latest evidence comes from the university that can afford the largest fraction of journals: Harvard University
14. Researchers’ careers and funding as well as research progress depend on the accessibility, uptake and impact of the research output.
15. Open Access maximizes accessibility and enhances uptake and impact.
16. Hence peer access, rather than just public access, is the reason (all) researchers (funded and unfunded, in all disciplines) should provide OA — and the reason their institutions and funders should mandate that they provide OA.
Enabling Open Scholarship
The list of recommendations I made was strategic. The objective was to maximize OA deposits and maximize OA deposit mandates.
The issue is not about how many members of the general public might wish to read how many peer-reviewed journal articles.
The issue is strategic: What provides a viable, credible, persuasive reason for researchers to provide OA and for institutions and funders to mandate providing OA in all fields of research, funded and unfunded, in all disciplines.
My point was that providing access for the the general public is a viable, credible, persuasive reason for providing and mandating OA in some fields (notably health- related research, but there may be other fields as well) — but it is not a viable, credible, persuasive reason for providing OA in all fields, nor for all research.
It is not difficult to find anecdotal evidence of nonspecialist interest in specialized research; one’s own interests often go beyond one’s own area of expertise.
But that is user-based reasoning, whereas providing OA and mandating OA require reasons that are viable, credible and persuasive to providers of research — and not some providers, sometimes, but all providers, for all research.
The only reason for providing OA to research that is valid, credible and persuasive for all research and researchers is in order to ensure that it is accessible to all of its intended users — primarily peers — and not just to those whose institutions can afford to subscribe to the journal in which it was published.
The issue is strategic. It is a great mistake to construe giving priority to reasons for providing peer access over reasons for providing public access as somehow implying that public access should be denied: Public access automatically comes with the territory with OA. So public access denial is not the issue.
The strategic issue is whether researchers (and their institutions and funders) are more likely to be induced to provide and mandate OA by the argument that the public wants and needs access or by the argument that peers want and need access.
Peer access provides research progress and impact. It is an appeal to researchers’ self-interest to stress the beneficial effects of OA on the uptake and impact of their research.
Most researchers of course also have a secret yearning that their research should appeal not only to their peers, but to the general public. But they also know that that is probably just wishful thinking in most cases. And in any case, public access does not have the direct affect on their careers, funding, and research progress that peer access has.
So it is not that the enhancement of public access should not be listed among the reasons for providing OA. It is just that it should not be promoted as the first, foremost, or universal reason for providing OA, because it is not: for many or most researchers, that argument simply will not work.
Ditto for the argument that researchers need to provide OA because journal subscriptions cost too much. The eventual solution to the journal affordability crisis will probably also come from providing and mandating OA. But, like public access, journal affordability is not a sufficiently compelling or universal rationale for providing OA.
The public access rationale for providing OA appeals to politicians and voters. Good. Use it in order to help get OA mandate legistlation adopted by research funders. But the rationale is much less convincing to researchers (peers) themselves, and their institutions.
The journal affordability rationale for providing OA appeals to librarians and institutions, but it is much less convincing to researchers (peers).
In contrast, providing OA in order to maximize research progress and impact, by maximizing researcher (peer) uptake, usage, applications and citations — if backed up by evidence — is the way to convince all researchers, funded and unfunded, in all disciplines, that it is in their own best interests to provide OA to their research.
Today’s internationally recognized tree holiday was founded in 1872 by J. Sterling Morton, former Secretary of Agriculture to US President Grover Cleveland, and avid tree enthusiast. The holiday is generally observed on the last Friday in April, and today marks over 135 years of tree planting and conservation efforts across the globe. Highlighted below are some of PLoS ONE’s arboreal related articles. Take a moment to read about the critical role trees have in our global ecosystem.
Sudden Oak Death, caused by a pathogen introduced to California forests, continues to disturb local oak populations. This research explores the clonal reproductive behavior of the pathogen, Phytophthora ramorum.
Researchers at the University of Toronto have collected samples from Panamanian rainforest tree species to estimate total carbon content in tropical ecosystems. Read more here.
The fascinating colonization of Juniper trees, Juniperus brevifolia, a native species to the Azores archipelago, has been explored in the following article.
Recent analysis indicates that although forested areas have declined globally, the overall tree density in such areas has increased. Read more about how this is important in the sequestration of atmospheric carbon.
Logging practices in wood-producing forests pose risks for many endangered flora and fauna. Managing these areas sustainably could help conserve such species, as well as increase carbon storage. Read more here.
To find ways to get involved, or to learn how to plant a tree in your community, visit www.arborday.org
Evolutionary Applications has now published issue 5.4. As for all the other 2012 issues, this issue is open access – free to read, download and share.
This issue contains two excellent papers on plant-pathogen interactions. The first of these is ‘Genetic structure and local adaptation of European wheat yellow rust populations: The role of temperature-specific adaptation’ by Mamadou Mboup and colleagues. Yellow stripe rust of wheat is a major concern for wheat farmers. It’s typically thought that variation in the ability of this pathogen to infect different populations of wheat was due to genetic changes among strains of the rust. This paper shows that differences in the environment can also play a key role in whether or not the rust can infect wheat populations.
The second highlighted papers is ‘The Red Queen and the seed bank: pathogen resistance of ex situ and in situ conserved barley’ by Helen R. Jenson and colleagues. This paper addresses the question of whether it is more important to conserve crop plants on the farm or to store in a seed bank. Although it is seen that seeds conserved on the farm can adapt to changes in genetic strains of parasites, the authors argue that it might be important to store seeds away in a bank because the seeds may contain rare alleles that confer resistance to parasites that farm plants are no longer resistant to. Evidence is given to show that both predictions are seen.
Want to know when a new issue of the journal is available online?
Sign up for e-toc alerts.
Signing up is easy:
Register or Log in: when prompted, log in to your Wiley Online Library account. If you need to create an account, register for free!
Today is the day, our Right to Research Coalition Day of Action in support of the Federal Research Public Access Act!
If you haven’t already, please take a few moments to draft an op-ed or letter to the editor explaining FRPAA and how it would benefit you and your campus community, then submit it to your local newspapers. These articles are very effective advocacy tools and demonstrate to your representatives and your local community the importance of this issue and this legislation. Furthermore, you will help raise awareness of the bill and inspire others to contact their representatives, providing a significant boost to FRPAA and its chances to become law.
You can find more details in our post announcing the day of action as well as talking points and tips for writing to your newspaper.
We’re excited to see pro-FRPAA articles appear in campus and local newspapers across the country over the next week, and don’t forget to send a link to nick [at] arl [dot] org when your story is run.
Thanks for your help in making the FRPAA Day of Action a success and bringing FRPAA one step closer to becoming law!
Today is the fifth annual World Malaria Day, commemorated every April 25 to recognize and encourage global efforts to control malaria. This year’s theme, “Sustain Gains, Save Lives: Invest in Malaria,” alludes to the many important advances against the malaria parasite that have been achieved in recent years, but also includes a warning: we must continue to invest in malaria research and maintain our vigilance to ensure that painstakingly earned gains are not surrendered to complacency.
Based on the 251 malaria-related PLoS ONE papers published since last year’s World Malaria Day, it’s pretty clear to us that the research community is maintaining its commitment to this disease. Instead of trying to provide an overview of all of these articles, which cover perspectives as diverse as public health, ecology, and microbiology, we decided to observe the day by highlighting a single article that, like this year’s theme, emphasizes the importance of continued research as the parasite proves itself to be a constantly evolving target.
The study, published last October, monitors drug resistance in the causative parasite Plasmodium falciparum in Mozambique over five years, from 2006 to 2010, as the recommended drug treatment was adjusted. The researchers, led by Jaishree Raman of the South African Medical Research Council, found that the incidence of parasitic resistance to the originally recommended drug regimen increased significantly over the course of the study, from 56.2% at the start up to 75.8% in 2010. This approximately 20% leap in resistance suggested that the preferred treatment at the time would become much less effective as its use increased.
However, the Mozambican Ministry of Healthy preempted this scenario by changing their recommended front-line drug treatment in 2008. The authors weren’t able to study the full impact of this policy change, though, because it was not fully deployed until 2010, at which point the study was winding down – further highlighting the need for continued careful monitoring as new treatments are introduced.
Citation: Raman J, Mauff K, Muianga P, Mussa A, Maharaj R, et al. (2011) Five Years of Antimalarial Resistance Marker Surveillance in Gaza Province, Mozambique, Following Artemisinin-Based Combination Therapy Roll Out. PLoS ONE 6(10): e25992. doi:10.1371/journal.pone.0025992
Image source: eyeweed on Flickr
Advances in Open Access à la Nature Publishing Group
With its recent launch of Light: Science and Applications, an open access (OA) physical sciences journal, and several more OA specialist publications planned for this year, Nature Publishing Group (NPG) is moving forward with its plan to include this publishing model in the center of its business. Though not every NPG journal is fair game for open access, it seems – top-tier publications will remain under a subscription-based model – specialist titles may be a place for further expansion as open access continues to develop.
For some years I have seen the primary literature as an enormous untapped resource of scholarly information. We humans are very good at some aspects of “reading the literature” but there are many areas where machines are better and should be used. These include scale (hundreds of thousands of manuscripts), checking, validation, transformation (e.g. scientific units), deduction (many papers have implicit semantics), aggregation of knowledge, and much more. We are now reaching the time when the technology of “text-mining” is mature enough to deploy and, for example, my group and I have developed among the best tools in the world for mining chemistry. I am now expanding that to other fields which I will describe in later posts.
In general the readers of the scholarly literature (who may include the #scholarlypoor) have been seriously frustrated by the restrictions imposed by publishers and universally agreed by librarians. Most subscriptions to most major journals have terms forbidding readers to mine/crawl/index/extract etc. This is not a consequence of copyright – it is an additional restriction imposed by published and apparently automatically assented to by academic purchasing systems (mainly libraries). This automatic assent has done scholarship a grave disservice, so I give the library community a chance to correct the historical record:
Moving on, the UK Hargreaves report has recommended removing these restrictions (which are not legally required) and also modifying copyright law. My grapevine suggests there is a high probability that significant changes will be made and that “text-mining” will become widely available without requiring explicit permission. We should prepare for this, and any responsible publisher and library/purchaser should be preparing for this.
A month ago I and colleagues in OKF submitted cases to the Hargreaves process. As part of that I asked 6 major publishers whether I could “text-mine” their journals. Naomi Lillie of OKF is summarising the results and I will keep you in suspense till then. It’s fair to say some were helpful, some were not and some were fuzzy (for whatever motivation).
A number of publishers said we should discuss it with the library. There is no need for this. I and my group can text mine material by myself – in one week Daniel Lowe extracted 500,000 chemical reactions from the US Patent Office without needing any help. Nick Day has built PubCrawler and extracted 200,000 crystal structures from supplemental information without any help. The only thing I need is:
- An assurance I won’t be sued for behaving like a responsible scholar
- An assurance that my institution won’t get cut off for (my) responsible behaviour
In case anyone in the publishing or library communities doesn’t understand what “responsible” means, it means:
- I do not intend deliberately to re-publish the publishers manuscripts (“the PDF”) in bulk without valid scholarly reason.
I am a responsible scholar. I conform to health and safety. I obey the law of the UK. I do not steal. I can justify the expenditures on my grants. I attempt to value and promote human equality in my scholarship. I try to give credit where it is due. Responsible scholarship is a fundamental principle which I believe applies to almost all readers of the scholarly literature. Occasionally I and others fail – there are ample mechanisms for addressing these without forbidding textmining.
So this post asserts my absolute right as a subscriber to the scholarly literature to carry out textmining and to disseminate the results to anyone. I do not need any other permissions.
A number of details follow which I’ll address in later posts.
At present, therefore, a group of us – under the aegis of the Open Knowledge Foundation – is drafting a set of principles for textmining. They include:
- Heather Piwowar. Heather has written several blogposts (http://researchremix.wordpress.com/ ) about text-mining. They include negotiations with Elsevier (which include the need for Elsevier and librarians to give her permission) and more recently a manifesto (http://researchremix.wordpress.com/2012/04/20/new-fron/ ).
- Maximilian Haussler. See (http://blogs.ch.cam.ac.uk/pmr/2012/03/09/textmining-update-max-haussler%E2%80%99s-questions-to-publishers-they-have-a-duty-to-reply/ ). Max was quoted 85,000 USD by NPG to mine their content (I think this has been altered to 0?) . He and colleagues have fought for the right and he has submitted a detailed case to the US government
- Diane Cabell and Jenny Molloy, OKF. Diane is a specialist in intellectual property law and has helped to craft the OKF open-science response to Hargreaves.
- Ross Mounce. Panton fellow (http://about.me/rossmounce ). Ross has created a superb and damning summary of publishers distortion of the term “Open Access” in paid hybrid journals. Ross and I are now working on the technology and strategy of textmining.
We shall come up with a manifesto/set-of-principles. This will be a statement of our rights and our responsibilities. It is not a negotiation, anymore than Tom Paine or the Founding fathers negotiated in the construction of their declarations. Or, more recently, the BBB declarations of Open Access. Those declaration are priceless – it’s just a pity that there are not enough who believe in them enough to push for their universal acceptance. We shall not make the same mistake with the principles of textmining.
Although the nationally celebrated Earth Day has just passed, it’s important to consider our impact on the environment every day. In their recently published article “Proliferation of Hydroelectric Dams in the Andean Amazon and Implications for Andes-Amazon Connectivity,” authors Matt Finer and Clinton N. Jenkins highlight a constant environmental concern; meeting the world’s growing energy demands. Finer and Jenkins developed a strategic ecological impact assessment of planned dams from the Andes to the Amazon. Their findings point to the need for this kind of heightened environmental awareness every day.
Due to rising energy demands and abundant untapped potential, hydropower projects are rapidly increasing in the Neotropics. This is especially true in the wet and rugged Andean Amazon, where regional governments are prioritizing new hydroelectric dams as the centerpiece of long-term energy plans. However, the current planning for hydropower lacks adequate regional and basin-scale assessment of potential ecological impacts. This lack of strategic planning is particularly problematic given the intimate link between the Andes and Amazonian flood plain, together one of the most species rich zones on Earth. We examined the potential ecological impacts, in terms of river connectivity and forest loss, of the planned proliferation of hydroelectric dams across all Andean tributaries of the Amazon River. Considering data on the full portfolios of existing and planned dams, along with data on roads and transmission line systems, we developed a new conceptual framework to estimate the relative impacts of all planned dams. There are plans for 151 new dams greater than 2 MW over the next 20 years, more than a 300% increase. These dams would include five of the six major Andean tributaries of the Amazon. Our ecological impact analysis classified 47% of the potential new dams as high impact and just 19% as low impact. Sixty percent of the dams would cause the first major break in connectivity between protected Andean headwaters and the lowland Amazon. More than 80% would drive deforestation due to new roads, transmission lines, or inundation. We conclude with a discussion of three major policy implications of these findings. 1) There is a critical need for further strategic regional and basin scale evaluation of dams. 2) There is an urgent need for a strategic plan to maintain Andes-Amazon connectivity. 3) Reconsideration of hydropower as a low-impact energy source in the Neotropics.
It’s been an exciting week in Pantonia. I have been very active with our new Panton Fellows (http://science.okfn.org/2012/04/03/introducing-our-panton-fellows/) Last Monday Ross Mounce came over to Cambridge and we looked in depth about liberating information about phylogenetic trees. This is exciting and keeps me up at night and active on train journeys. And yesterday I took the train to Oxford to visit Sophie Kershaw who’s putting together a radically different course for Graduates, with emphasis in reproducible computing. I’m deliberately downplaying both of these here, as they’ll be telling you all about what they are doing.
Part of yesterday was an evening meeting run by Jenny Molloy – a new Open Science groups with about 12 of us in the Oxford eResearch Centre (OeRC) where we met Dave de Roure who took us out the dinner in the Royal Oak. While there we discussed in some depth what need to be done for text-mining including Diane Cabell and Dave Shotton. It’s really great to see critical mass in this way. I will have a LOT to write about textmining.
So today I met with Ayumi Koso (above) from Tokyo. Ayumi works with the Japanese government in Tokyo on the National Bioscience Database Centre (NBDC). She has already translated the Panton Principles into Japanese (http://pantonprinciples.org/translations/#Japanese ). She’s staying in Cambridge and so today has a chance to meet some OKF people. Here’s our visit to the Panton Arms, preceded by a visit to Hinxton/Sanger Centre to visit Tim Hubbard (OKF advisory). And this afternoon Laura Newman will be coming round to meet.
I am really fortunate to be living in the middle of all this.
(We’ve decided today that the Panton hashtag is #pantonscience)
It is scandalous that much of our collective knowledge about alternative energy and renewable technologies is kept locked behind an Elsevier paywall! This is one area where clearly everyone anywhere on the planet with the inclination to read about the possibilities and push for solutions, whether through developing more basic knowledge or transferring knowledge to the business sector, should have immediate, barrier-free access. This is one area where the need is too great to permit for ANY embargo period.
Science works in step-wise fashion, like a detective mystery. One scientist discovers a clue; another builds on the discovery, until we have a new body of knowledge or real-world implementations, or both. If a useful discovery sequence takes six steps, with about 6 months of research for each step, then with no embargoes, the process takes 3 years. With a one-year embargo at each step, the whole sequence takes 9 years (3 years for research, 6 years for embargoes). Consider the impact of 6 more years of increasing greenhouse gases on climate change, and it is easy to see why the public good of rapid advancement in this area far outweighs an outmoded, print-based business model.
Here are the 29 journals Elsevier publishes in this area, from this page:
Total impact is a set of alternative metrics for scholarship. Total impact looks at a number of factors, including social networking tools such as Facebook and Twitter. As a research tool, Total Impact has a lot of potential, to explore how works are used and what impact they have. As an alternative metric to evaluate the quality of scholarship – an alternative to impact factor – there are a number of potential serious problems to consider.
First, there is the question of whether the current push towards quantitative metrics makes any sense at all. I have talked about the problems of this kind of instrumental rationality is my book chapter, The implications of usage statistics as an economic factor in scholarly communication https://circle.ubc.ca/handle/2429/954 (In brief, usage stats are likely to have significant negative impacts, from discouraging use to discouraging important but not necessarily popular entire fields of research); and the second chapter of my draft thesis http://pages.cmns.sfu.ca/heather-morrison/chapter-two-scholarly-communication-in-crisis/ (search for irrational rationalization).
One example, from an interview study of scholarly monograph publishers I did recently, is the impact of pushing scholars to publish more books to obtain tenure. This pressure is not consistent with the time it takes to write books that are really worth publishing and reading; so in this instance, we have a quantitative metric intended to improve quality and productivity (of our academic staff) which appears to be lowering quality (more mediocre books, more book production when the problem for all of us is not enough reading material, but rather not enough time to read).
Research, both quantitative and qualitative, is my recommendation before putting too much stock in Total Impact or other alternative metrics as a replacement for Impact Factor in evaluating the quality of scholarship. Note that I do not recommend retaining Impact Factor, but rather minimizing or eliminating quantitative approaches to evaluating the quality of scholarship.
The use of social networking tools may be particularly problematic. One research area that I recommend is examining the effects of traditional biases. I would hypothesize that social networking tools would be likely to exhibit the following biases prevalent in modern society:
- men would show more impact than women
- minorities would have lower impact
- developing country authors would have lower impact
- introverts would have lower impact than extraverts
- authors adept at social networking tools would have more impact than authors less comfortable with these media
In addition, I would suggest that metrics based on social networking tools could easily be manipulated, not only by authors but also by interested others. It doesn’t take much to imagine corporate polluters in favor of climate denial upping the impact of their preferred pseudo-science, or for drug companies to drive up the impact of studies making the drugs that they sell look good.
Another area to consider (for all kinds of tools, not just social networking tools), is the impact of funding considerations. If universities are relying more on corporate funders at a time in society such as today when the political will seems to be on the side of the wealthy who wish to cut spending on social justice, it is reasonable to hypothesize that there will be a smaller proportion of funding for social justice issues. What happens to research on poverty issues and its impact if there is less funding for research and academic positions in this area (hence fewer researchers), at the same time that there is less funding for government services and social workers (fewer potential readers and tweeters), and many of those poverty research is meant to help have lost their homes and jobs and may find it difficult to get internet access?
This week British Columbia is mourning the passing of notable citizen and philanthropist Irving K. Barber. This post celebrates a small part of the achievements made possible by his generosity, the Small Business Accelerator program of the Irving K. Barber Learning Centre.
The Small Business Accelerator program is a highly innovative program and partnership of the University of British Columbia with BC’s public and other libraries and the BC business community.
From the website:
Business success depends on obtaining access to reliable information. The Small Business Accelerator is curated by business librarians and is your gateway to freely available business information, education, and assistance that is both current and trustworthy.
It is my hope that this small token of appreciation will encourage others to consider this model of cooperation, which is also a great model to illustrate how libraries and the business community can work together cooperatively, making use of open access resources, to benefit business and local communities (by making business accelerator programs available throughout the province.
[Disclosure: the Irving K. Barber Learning Centre is a key partner of the BC Electronic Library Network where I serve as Coordinator].