Currently browsing the Open Access Category
Open access science and engineering is similar to open source software. Open access journals share ideas over the internet available to anyone. This continues the historical practice of sharing knowledge to advance scientific innovation.
Recommended posts: The Future of Scholarly Publication - Open Access Engineering Journals - Open Access Legislation - Open Access Education Materials Related: Science and Engineering Webcast Libraries - Open Source Management Innovation

Study on Citation of Open Access Papers v. Closed Access Papers

Posted on February 23, 2009  Comments (1)

Open Access to Scientific Papers May Not Guarantee Wide Dissemination

To test this theory, James A. Evans, an assistant professor of sociology at the University of Chicago, and Jacob Reimer, a student of neurobiology also at the University of Chicago, analyzed millions of articles available online, including those from open source publications and those that required payment to access.

The results were surprising. On average, when a given publication was made available online after being in print for a year, being published in an open source format increased the use of that article by about 8 percent. When articles are made available online in a commercial format a year after publication, however, usage increases by about 12 percent.

“Across the scientific community,” Evans said in an interview, “it turns out that open access does have a positive impact on the attention that’s given to the journal articles, but it’s a small impact.”

Yet Evans and Reimer’s research also points to one very positive impact of the open source movement that is sometimes overlooked in the debate about scholarly publications. Researchers in the developing world, where research funding and libraries are not as robust as they are in wealthier countries, were far more likely to read and cite open source articles.

The University of Chicago team concludes that outside the developed world, the open source movement “widens the global circle of those who can participate in science and benefit from it.”

So while some scientists and scholars may chose to pay for scientific publications even when free publications are available, their colleagues in other parts of the world may find that going with open source works is the only choice they have.

I remain a strong advocate for open science. The out of date model of publishing research in closed journals does not make sense. Especially not for any government funded research or any research supported by foundations, universities or others that aim to promote science.

The quote above and the interview webcast also provide unclear data on what the actual impact is (on how often a paper is cited in other papers). Maybe the article would be clearer but I can’t tell because it is closed access. This link has some worthwhile comments: Generalizing the OA impact advantage.

Related: Toward a More Open Scientific Culture – Open Access Journal Wars – Dinosaurs Fighting Against Open Science

Canada Film Board Provides Open Access

Posted on February 4, 2009  Comments (3)

The National Film Board of Canada is marking its 70th anniversary in 2009 with a gift to Canadians and Web users: a new online Screening Room providing free home viewing of over 700 productions, films, trailers and clips from the NFB’s world-renowned collection.

“This new online Screening Room is the latest example of how the NFB plays a major role in the free exchange of ideas through cinema,” said Tom Perlmutter, Government Film Commissioner and Chairperson of the National Film Board of Canada. “At a time when issues are inter-connected and global communications are mobile and instantaneous, Canada needs a voice. More than ever, the NFB provides that voice: empowering Canadians to share their concerns, express their points of view, tell Canada’s stories. The world is changing – our stories continue.”

From historical films dating back to 1928 to current contemporary releases, including award-winning documentaries, animation and fiction, this initiative invites Canadians from all regions, to browse, discover and be entertained by the stories that bind us together.

The NFB has also opened its vaults to bring forgotten gems to light: archival works that offer rare glimpses back into our past, from Canada’s sacrifices during World War II to traditional communities, exploring the changing face of Canada over the decades.

The site includes many science and nature films including: Life on Ice – Kluane National Park – In Search of the Bowhead Whale – The Enduring Wilderness (Canada’s Natural Parks)

The National Film Board of Canada showing far more vision than many others clinging to outdated models. The internet provides a great opportunity for sharing and using open access to share ideas.

Related: Meteorite, Older than the Sun, Found in Canada – Fishy Future? – Arctic System on Trajectory to New, Seasonally Ice-Free State

Science Commons: Making Scientific Research Re-useful

Posted on January 26, 2009  Comments (1)

Science Commons is a project of Creative Commons. Like other organizations trying to support the advancement of science with open access they deserve to be supported (PLoS and arXiv.org are other great organizations supporting science).

Science Commons has three interlocking initiatives designed to accelerate the research cycle – the continuous production and reuse of knowledge that is at the heart of the scientific method. Together, they form the building blocks of a new collaborative infrastructure to make scientific discovery easier by design.

Making scientific research re-useful, help people and organizations open and mark their research and data for reuse. Learn more.

Enabling one-click access to research materials, streamline the materials-transfer process so researchers can easily replicate, verify and extend research. Learn more.

Integrating fragmented information sources, help researchers find, analyze and use data from disparate sources by marking and integrating the information with a common, computer-readable language. Learn more.

NeuroCommons, is their proof-of-concept project within the field of neuroscience. The NeuroCommons is a beta open source knowledge management system for biomedical research that anyone can use, and anyone can build on.

Related: Open Source: The Scientific Model Applied to Programming – Publishers Continue to Fight Open Access to Science – Encyclopedia of Life – Science 2.0 – Biology

Dolphins Using Tools to Hunt

Posted on December 10, 2008  Comments (6)

photo of a dolphin with a sponge it uses to huntPhotograph of dolphin with a sponge it uses to hunt, courtesy of Ewa Krzyszczyk, PLoS, high resolution.

Cool open access research from PLoS One, Why Do Dolphins Carry Sponges?

Tool use is rare in wild animals, but of widespread interest because of its relationship to animal cognition, social learning and culture. Despite such attention, quantifying the costs and benefits of tool use has been difficult, largely because if tool use occurs, all population members typically exhibit the behavior. In Shark Bay, Australia, only a subset of the bottlenose dolphin population uses marine sponges as tools, providing an opportunity to assess both proximate and ultimate costs and benefits and document patterns of transmission.

We compared sponge-carrying (sponger) females to non-sponge-carrying (non-sponger) females and show that spongers were more solitary, spent more time in deep water channel habitats, dived for longer durations, and devoted more time to foraging than non-spongers; and, even with these potential proximate costs, calving success of sponger females was not significantly different from non-spongers. We also show a clear female-bias in the ontogeny of sponging. With a solitary lifestyle, specialization, and high foraging demands, spongers used tools more than any non-human animal. We suggest that the ecological, social, and developmental mechanisms involved likely (1) help explain the high intrapopulation variation in female behaviour, (2) indicate tradeoffs (e.g., time allocation) between ecological and social factors and, (3) constrain the spread of this innovation to primarily vertical transmission.

The dolphins use the sponge to push along the ocean floor and disturb fish, that are hidden. Once the fish start swimming away the dolphin abandons the sponge and catches and eats the fish. Then the dolphin goes back and gets the sponge and continues.

Related: Do Dolphins Sleep? – Orangutan Attempts to Hunt Fish with Spear – Dolphin Rescues Beached Whales – Savanna Chimpanzees Hunt with Tools – Chimps Used Stone “Hammers” – open access papers

HHMI on Science 2.0: Information Revolution

Posted on December 3, 2008  Comments (0)

The Howard Hughes Medical Institute does great things for science and for open science. They have an excellent article in their HHMI Bulletin – Science 2.0: You Say You Want a Revolution?

Cross-pollination among research disciplines is in fact at the core of many other popular science blogs. Michael Eisen, an HHMI investigator at the University of California, Berkeley, is an avid blog reader who particularly enjoys John Hawks’ site on paleoanthropology, genetics, and evolution. A recent post there discussed a new sequencing of Neanderthal mitochondrial DNA. “It’s like a conduit into another whole world,” says Eisen.
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The current extreme of collaboration via Science 2.0 is OpenWetWare.org. Begun in 2003 by Austin Che, who was then a computer science and biology graduate student at MIT, this biological-engineering Website uses the wiki model to showcase protocols and lab books: everything is open and can be edited by any of its 4,000 members.
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“Most publishers wish open access would go away,” says Brown. It won’t. Major research-funding organizations, including NIH, HHMI, and the Wellcome Trust, now require their grantees to post their findings on openaccess Websites such as PLoS or PubMed Central within 12 months of publication in traditional journals. Publishers are pushing back, however, and in September, the House Judiciary Committee began holding hearings on whether the federal government should be allowed to require grantees to submit accepted papers to a free archive.

Related: $600 Million for Basic Biomedical Research from HHMI – Tracking the Ecosystem Within Us – Publishers Continue to Fight Open Access to Science – $1 Million Each for 20 Science Educators

Toward a More Open Scientific Culture

Posted on November 9, 2008  Comments (4)

Michael Nielsen wrote a great post, The Future of Science, which is also the topic of a book he is writing. He discusses how scientific advancement has often been delayed as those making discoveries did not share them openly. And how 300 years ago scientific journals and reward systems created ways for scientists to be rewarded for publication. And he continues with the need for the process to again change and promote more open sharing of scientific knowledge, which I agree with and have written about previously: Publishers Continue to Fight Open Access to Science, Science Journal Publishers Stay Stupid, The Future of Scholarly Publication, etc..

Why were Hooke, Newton, and their contemporaries so secretive? In fact, up until this time discoveries were routinely kept secret.
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This cultural transition was just beginning in the time of Hooke and Newton, but a little over a century later the great physicist Michael Faraday could advise a younger colleague to “Work. Finish. Publish.” The culture of science had changed so that a discovery not published in a scientific journal was not truly complete. Today, when a scientist applies for a job, the most important part of the application is their published scientific papers.

This has been a great advance. Now we need to continue that advance to use the internet to make that publication open and increase the advantage of shared knowledge to society.

The adoption of the journal system was achieved by subsidizing scientists who published their discoveries in journals. This same subsidy now inhibits the adoption of more effective technologies, because it continues to incentivize scientists to share their work in conventional journals, and not in more modern media.
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This means: making many more types of content available than just scientific papers; allowing creative reuse and modification of existing work through more open licensing and community norms; making all information not just human readable but also machine readable; providing open APIs to enable the building of additional services on top of the scientific literature, and possibly even multiple layers of increasingly powerful services. Such extreme openness is the ultimate expression of the idea that others may build upon and extend the work of individual scientists in ways they themselves would never have conceived.
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To create an open scientific culture that embraces new online tools, two challenging tasks must be achieved: (1) build superb online tools; and (2) cause the cultural changes necessary for those tools to be accepted.

I agree we need to take advantage of the new possibilities to advance the practice of science. His full post is well worth reading.

Related: Open Source: The Scientific Model Applied to Programming – The Future of Science is Open by Bill Hooker – Dinosaurs Fight Against Open Science – Open Access Journal Wars – I Support the Public Library of Science – Does the Data Deluge Make the Scientific Method Obsolete?

Best Research University Rankings – 2008

Posted on September 9, 2008  Comments (8)

The annual ranking of research Universities are available from Shanghai’s Jiao Tong University. The methodology values publications and faculty awards which provides a better ranking of research (rather than teaching). Results from the 2008 rankings of Top 500 Universities worldwide, country representation of the top schools:

location Top 100 % of World
Population		 % of World GDP % of top 500
USA 54     4.6%   27.2%  31.6%
United Kingdom 11  0.9  4.9 8.3
Germany   6  1.3  6.0 8.0
Japan   4  2.0  9.0 6.2
Canada   4  0.5  2.6 4.2
Sweden   4  0.1  0.8 2.2
France   3  0.8  4.6 4.6
Switzerland   3  0.1  0.8 1.6
Australia   3  0.3  1.6 3.0
Netherlands   2  0.2  1.4 2.4
Denmark   2  0.1  0.6 0.8
Finland   1  0.1  0.4 1.2
Norway   1  0.1  0.7 0.8
Israel   1  0.1  0.3 1.2
Russia   1  2.2  2.0 0.4
China  20.5  6.6 6.0
India  17.0  1.9 0.4

There is little change in most of the data from last year, which I think is a good sign, it wouldn’t make much sense to have radical shifts over a year in these rankings. Japan lost 2 schools in the top 100, France lost 1. Denmark (Aarhus University) and Australia (University of Sydney) gained 1. Last year there was a tie so there were 101 schools in the top 100.

The most dramatic data I noticed is China’s number of top 500 schools went from 14 to 30, which made me a bit skeptical of what caused that quick change. Looking more closely last year they reported the China top 500 totals as (China 14, China-Taiwan 6 and China-Hong Kong 5). That still gives them an impressive gain of 5 schools.

Singapore has 1 in the 102-151 range. Taiwan has 1 ranked in the 152-200 range, as do Mexico, Korea and Brazil. China has 9 in the 201-302 range (including 3 in Hong Kong). India has 2 in the 303-401 range.

University of Wisconsin – Madison is 17th again :-) My father taught there while I grew up.
Continue reading →

ASU Science Studio Podcasts

Posted on April 14, 2008  Comments (1)

Science Studio offers podcasts by the Arizona State University School of Life Sciences with professors discussing science; it is another excellent source of science podcasts. Podcasts include:

  • Of Whales, Fish and Men: Managing Marine Reserves – With 90% of the world’s fisheries in a state of collapse, the questions around establishing marine reserves, monitoring, and species/stock recovery take on critical dimensions. But how do decision-makers, stakeholders, and the public formulate effective conservation policies; ones right for their community?
  • Biology on Fire – Regents’ Professor, Mac Arthur Fellow, author and a world’s expert on fire and fire ecology Stephen Pyne talks about how fire, its use, misuse, and its biological nature have shaped our world, before and because of man, and learn how policies of the past still reverberate in our present, in Arizona and globally.
  • Giant Insects: Not just in B movies – Professor Jon Harrison sheds light on the evolution of his scientific career and nature’s biggest order: arthropods. How big is big? In the Paleozoic, cockroaches were the size of housecats and dragonflies the size of raptors.
  • Special Feature: Building a science career – One of the most highly cited ecologists in the world, Jane Lubchenco trod her own unique path to success. In this live recording with the Association for Women in Science, she explains how assertiveness, the art of negotiation, and knowing the currency for promotion and tenure can make the difference between achieving balance between family and career and dropping out the leaky academic pipeline that leads to advancement.

These podcasts are great way to use the internet to serve the mission of universities: to educate. And a great way to promote science.

Related: Lectures from the Stanford Linear Accelerator Center – UC-Berkeley Course Videos – Science Podcast Libraries – Communicating Science to the Public

Computer Science Unplugged

Posted on April 9, 2008  Comments (0)

Computer Science Unplugged offers a free, interesting collection of activities designed to teach the fundamentals of computer science without requiring a computer. Because they’re independent of any particular hardware or software, Unplugged activities can be used anywhere, and the ideas they contain will never go out of date. Unplugged activities have been trialled and refined over 15 years in classrooms and out-of-school programs around the world maintained by the University of Canterbury in Christchurch New Zealand.

Topics include: Binary Numbers, Text Compression, Error Detection, Searching Algorithms, Sorting Algorithms, Steiner Trees and Public Key Encryption.

Related: Leadership Initiatives for Teaching and Technology – Fun k-12 Science and Engineering Learning – Education Resources for Science and Engineering – k-12 Engineering Education

Antarctic Fish “Hibernate” in Winter

Posted on March 6, 2008  Comments (0)

Antarctic Fish “Hibernate” in Winter

This is the first time fish have been seen actively becoming torpid—a state similar to hibernation in land animals—as part of an annual cycle. “A lot of freshwater fish go [unexpectedly] dormant in winter because a drop in temperature lowers their metabolism,” said study co-author Hamish Campbell, a zoologist at the University of Queensland, Australia.

“By contrast, these Antarctic fish actively reduce their ‘cost of living,’” he said… “The fish became 20 times less active in winter compared to summer,”… About every week or so the cod wake up and swim around for a few hours, the team observed. “This is quite similar to ‘denning’ in bears, where the hibernation isn’t so deep and the animals can be disturbed, then spend some time awake before going back to bed,” Fraser said.

Full paper: Hibernation in an Antarctic Fish: On Ice for Winter – Arctic Sharks – Antarctic Robo-sub

Related: Fish Breathes Air for Months at a Time

Harvard Liberal Arts Faculty Votes to Make Their Research Open Source

Posted on February 13, 2008  Comments (0)

Harvard Liberal Arts Faculty Votes to Distribute Research Free

Harvard’s decision lends support to the growing open-access movement in academia, an approach opposed by journal-industry representatives who say bypassing journals and their peer-review process may harm the quality of published research.

“This is a large and very important step for scholars throughout the country,” Stuart Shieber, a computer science professor who sponsored the motion to adopt the new policy, said in a statement released after the vote. “It should be a very powerful message to the academic community that we want and should have more control over how our work is used and disseminated.”

Discussion of a similar move by the faculties of law, medicine and business are “well under way,” and the other faculties, such as education and government, are expected to consider it, Peter Kosewski, a spokesman for Harvard’s library system, said in an e-mail. No other votes are scheduled.

The policy would spur professors to distribute work free on a Harvard Web site, rather than through journals that charge subscribers “enormous amounts of money,” said Harry Lewis, a professor of computer science at the university. Authors could choose not to share their work on the site and could publish in a traditional journal.

Another good step for those that support science. As I have stated publicly funded universities should require open access. Privately funded universities I believe should decide to do so also, but it should be their choice. Government funded research should require open access publication.

Related: The Future of Scholarly Publication (written in 2005, the future is now) – Howard Hughes Medical Institute Takes Big Open Access Step – Open Access Legislation – Harvard to collect, disseminate scholarly articles for faculty – Science Journal Publishers Stay Stupid – I Support the Public Library of Science – Open Access Journal Wars

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