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Why do we need dark energy to explain the observable universe?
Another interesting example of the scientific inquiry process at work in cosmology.
Shouldn’t the National Academy of Science (NAS), a congressionally chartered institution, promote open science instead of erecting pay walls to block papers from open access? The paper (by 2 public school professors) is not freely available online. It seems like it will be available 6 months after publication (which is good) but shouldn’t the NAS do better? Delayed open access, for organizations with a focus other than promoting science (journal companies etc.), is acceptable at the current time, but the NAS should do better to promote science, I think.
Related: Physics from Universe to Multiverse – Laws of Physics May Need a Revision – Extra-Universal Matter – Cosmology Questions Answered
Elsevier is one of those publishers fighting open science. They try to claim that the government publishing government funded research in an open way will tarnish science. The argument makes no sense to me. Here is another crazy action on their part: they published a “journal” funded by Merck to promote Merck products. Merck Makes Phony Peer-Review Journal:
As I have said the journals fighting open science should have their credibility questioned. They are putting their outdated business model above science. We should not see organizations that are focused on closing science research through deceptive publicity efforts and lobbying efforts as credible.
Related: From Ghost Writing to Ghost Management in Medical Journals – Merck Faked a Research Journal – Medical Study Integrity (or Lack Thereof) – The Future of Scholarly Publication – Fresh questions raised about prominent cardiologist’s role in “ghostwritten” 2001 meta-analysis of Vioxx trials – Science Commons: Making Scientific Research Re-useful – Publishers Continue to Fight Open Access to Science – Misleading or Deceptive Conduct – Peter Suber Response to Rep. Conyers
MIT faculty open access to their scholarly articles
The new policy, which was approved unanimously at an MIT faculty meeting on Wednesday, March 18 and took immediate effect, emphasizes MIT’s commitment to disseminating the fruits of its research and scholarship as widely as possible.
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Under the new policy, faculty authors give MIT nonexclusive permission to disseminate their journal articles for open access through DSpace, an open-source software platform developed by the MIT Libraries and Hewlett Packard and launched in 2002. The policy gives MIT and its faculty the right to use and share the articles for any purpose other than to make a profit. Authors may opt out on a paper-by-paper basis.
MIT’s policy is the first faculty-driven, university-wide initiative of its kind in the United States. While Harvard and Stanford universities have implemented open access mandates at some of their schools, MIT is the first to fully implement the policy university-wide as a result of a faculty vote. MIT’s resolution is built on similar language adopted by the Harvard Faculty of Arts & Sciences in 2008.
It is good to see scientists putting advancing science above outdated journal business models. It is a bit of a shame that we have to be happy for such a small thing but given the state of those fighting against open science it is good to see those in favor of open access to science make progress.
Related: John Conyers Fights Open Science – Anger at Anti-Open Access PR – The Future of Scholarly Publication
Interesting open access paper on Death and Resurrection of the Human IRGM Gene. Author summary:
Phylogenetic analyses support a model where the gene has been “dead” for at least 25 million years of human primate evolution but whose ORF became restored in all human and great ape lineages. We suggest that the rebirth or restoration of the gene coincided with the insertion of an endogenous retrovirus, which now serves as the functional promoter driving human gene expression. We suggest that either the gene is not functional in humans or this represents one of the first documented examples of gene death and rebirth.
Related: 8 Percent of the Human Genome is Old Virus Genes – Old Viruses Resurrected Through DNA – One Species’ Genome Discovered Inside Another’s – posts on genes – Gene against bacterial attack unravelled – Gene Duplication and Evolution
Shedding light on why long strands tend to become knotted
Which, it turns out, it basically is. In October, two UCSD researchers published the first physical explanation of why knots seem to form magically, not just in strands of Christmas lights, but in pretty much anything stringy, from garden hoses to iPod earbud cords to DNA.
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“We’re not mathematicians,” Smith said. “We’re physicists. Physicists do experiments.”
UCSD researchers constructed a knot probability machine that involved placing a single length of string in a plastic box, sealing it, then rotating the box at a set speed for a brief period of time.
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The experiment involved placing a single length of floppy string into a plastic box, sealing it, then rotating the box at a set speed for a brief time. The researchers did this 3,415 times, sometimes changing variables such as box size and string length.
Open access research paper: Spontaneous knotting of an agitated string by Dorian M. Raymer and Douglas E. Smith.
Yet another interesting case of scientists explaining the world around us (and the value of open science).
Related: Toward a More Open Scientific Culture – Electron Filmed for the First Time – Saving Fermilab – Scientists and Engineers in Congress
Lawrence Lessig once again has written a good blog post: John Conyers and Open Access
Pushed by scientists everywhere, the NIH and other government agencies were increasingly exploring this obviously better model for spreading knowledge. Proprietary publishers, however, didn’t like it. And so rather than competing in the traditional way, they’ve adopted the increasingly Washington way of competition — they’ve gone to Congress to get a law to ban the business model they don’t like. If H.R. 801 is passed, the government can’t even experiment with supporting publishing models that assure that the people who have paid for the research can actually access it. Instead, if Conyers has his way, we’ll pay for the research twice.
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The insanity in this proposal is brilliantly described by Jamie Boyle in this piece in the FT. But after you read his peace, you’ll be even more puzzled by this. For what possible reason could Conyers have for supporting a bill that 33 Nobel Prize Winners, and the current and former heads of the NIH say will actually hurt scientific research in America? More pointedly, what possible reason would a man from a district that insists on the government “Buying American” have for supporting a bill that basically subsidizes foreign publishers (for the biggest players in this publishing market are non-American firms, making HR 801 a kind of “Foreign Publishers Protection Act”)?
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the co-sponsors of this bill who sit on the Judiciary Committee received on average two-times the amount of money from publishing interests as those who haven’t co-sponsored the bill.
The damage done to science by dinosaurs fighting progress and corrupt or inept politicians is very disheartening. Thankfully we have been able to achieve great things in spite of politicians trying to favor their donors and harm the scientific community.
Related: Science Journal Publishers Stay Stupid – Howard Hughes Medical Institute Takes Big Open Access Step – From Ghost Writing to Ghost Management in Medical Journals – The A to Z Guide to Political Interference in Science
Open Access to Scientific Papers May Not Guarantee Wide Dissemination
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
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 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
Photograph 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?
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
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?
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
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..
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.
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?
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.
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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:
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 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
“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
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