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

Fields Medalist Tim Gowers Takes Action To Stop Cooperating with Anti-Open Science Cartel

Posted on January 26, 2012  Comments (0)

The Fields medal is know as the Nobel of mathematics. Tim Gowers was awarded the Fields medal in 1998 for contributions to functional analysis, making extensive use of methods from combinatorial theory. Tim Gowers is currently the Rouse Ball Professor of Mathematics at Cambridge University. He posted recently on his decision to stop supporting (with his actions, such as submitting paper and reviewing papers) the anti-open-science behavior of Elsevier (a particularly aggressive anti-open-science publisher that also has very bad pricing practices).

Elsevier — my part in its downfall

One method that they have for getting away with it is a practice known as “bundling”, where instead of giving libraries the choice of which journals they want to subscribe to, they offer them the choice between a large collection of journals (chosen by them) or nothing at all. So if some Elsevier journals in the “bundle” are indispensable to a library, that library is forced to subscribe at very high subscription rates to a large number of journals, across all the sciences, many of which they do not want. (The journal Chaos, Solitons and Fractals is a notorious example of a journal that is regarded as a joke by many mathematicians, but which libraries all round the world must nevertheless subscribe to.) Of course, given that libraries have limited budgets, this often means that they cannot subscribe to journals that they would much rather subscribe to, so it is not just libraries that are harmed, but other publishers, which is of course part of the motivation for the scheme.
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Elsevier supports many of the measures, such as the Research Works Act, that attempt to stop the move to open access. They also supported SOPA and PIPA and lobbied strongly for them.
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I also don’t see any argument at all against refusing to submit papers to Elsevier journals.

So I am not only going to refuse to have anything to do with Elsevier journals from now on, but I am saying so publicly. I am by no means the first person to do this, but the more of us there are, the more socially acceptable it becomes

Good for him. All we need is for more and more scientists, mathematicians and engineers to support open science with thier actions and open science will be the way things are. It is as simple as that. The outdated business practices of the old journals will die. Either the existing publishers will finally give up on their extremely outdated practices or they will be replaced.

Related: The Architecture of Access to Scientific Knowledge – Merck and Elsevier Publish Phony Peer-Review Journal – The Future of Scholarly Publication (2005) – Science Journal Publishers Stay Stupid (2007) “It is time for the scientific community to give up on these journals and start looking to move to work with new organizations that will encourage scientific communication and advancement”

Royal Society Journal Embraces Open Access

Posted on January 23, 2012  Comments (0)

Royal Society journal archive made permanently free to access

The Royal Society…journal archive – which includes the first ever peer-reviewed scientific journal – has been made permanently free to access online.

Around 60,000 historical scientific papers are accessible via a fully searchable online archive, with papers published more than 70 years ago now becoming freely available.
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reasures in the archive include Isaac Newton’s first published scientific paper, geological work by a young Charles Darwin, and Benjamin Franklin’s celebrated account of his electrical kite experiment.

The move is being made as part of the Royal Society’s ongoing commitment to open access in scientific publishing.

Good for them. Slowly more and more are realizing clinging to old fashion publishing models are contrary to promoting science and scientific literacy.

Related: 340 Years of Royal Society Journals Online – Britain’s Royal Society Experiments with Open Access (2006) – 8-10 Year Olds Research Published in Royal Society Journal

A Possible Explanation for the Faster Than Light Result Anomaly

Posted on October 14, 2011  Comments (2)

Faster-than-Light Neutrino Puzzle Claimed Solved by Special Relativity

So what is the satellites’ motion with respect to the OPERA experiment? These probes orbit from West to East in a plane inclined at 55 degrees to the equator. Significantly, that’s roughly in line with the neutrino flight path. Their relative motion is then easy to calculate.

So from the point of view of a clock on board a GPS satellite, the positions of the neutrino source and detector are changing. “From the perspective of the clock, the detector is moving towards the source and consequently the distance travelled by the particles as observed from the clock is shorter,” says van Elburg.

By this he means shorter than the distance measured in the reference frame on the ground.

The OPERA team overlooks this because it thinks of the clocks as on the ground not in orbit.

How big is this effect? Van Elburg calculates that it should cause the neutrinos to arrive 32 nanoseconds early. But this must be doubled because the same error occurs at each end of the experiment. So the total correction is 64 nanoseconds, almost exactly what the OPERA team observes.

It is great to see the scientific process at work. Those is support of the scientific method support open access science and this explanation is available via arxiv: Times Of Flight Between A Source And A Detector Observed From A GPS Satellite.

Related: Faster Than Light Speed Anomaly Reported by CERN – More Dark Matter Experiment Results – The Architecture of Access to Scientific Knowledge

The Architecture of Access to Scientific Knowledge

Posted on April 28, 2011  Comments (1)

The Architecture of Access to Scientific Knowledge from lessig on Vimeo.

Larry Lessig speaks at CERN about the proper use of copyright and the moral case for open access. As I have written many times, I strongly believe our society is better off when science is open. I believe we now are allowing a few greedy institution (that seek to restrict science for the benefit of their organization) to pay our politicians to damage society for the benefit of a few donors.

Related: The Future of Scholarly Publication – Toward a More Open Scientific Culture - Why Copyright Extension is a Very Bad Idea – Patent Gridlock is Blocking Developing Lifesaving Drugs – Bad Government, Closed Access – John Conyers Against Open Science – Science Commons – Public Library of Science

Why do we Need Dark Energy to Explain the Observable Universe?

Posted on September 27, 2009  Comments (2)

Why do we need dark energy to explain the observable universe?

Against all reason, the universe is accelerating its expansion. When two prominent research teams dropped this bombshell in 1998, cosmologists had to revise their models of the universe to include an enormous and deeply mysterious placeholder they called “dark energy.” For dark energy to explain the accelerating expansion, it had to constitute more than 70 percent of the universe. It joined another placeholder, “dark matter,” constituting 20 percent, in overshadowing the meager 4 percent that make up everything else—things like stars, planets, and people.
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An accelerating wave of expansion following the Big Bang could push what later became matter out across the universe, spreading galaxies farther apart the more distant they got from the wave’s center. If this did happen, it would account for the fact that supernovae were dim- they were in fact shoved far away at the very beginning of the universe. But this would’ve been an isolated event, not a constant accelerating force. Their explanation of the 1998 observations does away with the need for dark energy.
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And Smoller and Temple say that once they have worked out a further version of their solutions, they should have a testable prediction that they can use to see if the theory fits observations.

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

Merck and Elsevier Publish Phony Peer-Review Journal

Posted on May 3, 2009  Comments (1)

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:

Merck cooked up a phony, but real sounding, peer reviewed journal and published favorably looking data for its products in them. Merck paid Elsevier to publish such a tome, which neither appears in MEDLINE or has a website, according to The Scientist.
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What’s sad is that I’m sure many a primary care physician was given literature from Merck that said, “As published in Australasian Journal of Bone and Joint Medicine, Fosamax outperforms all other medications….” Said doctor, or even the average researcher wouldn’t know that the journal is bogus. In fact, knowing that the journal is published by Elsevier gives it credibility!

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

Posted on March 23, 2009  Comments (2)

MIT faculty open access to their scholarly articles

In a move aimed at broadening access to MIT’s research and scholarship, faculty at the Massachusetts Institute of Technology have voted to make their scholarly articles available to the public for free and open access on the Web.

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

Resurrection of the Human IRGM Gene

Posted on March 8, 2009  Comments (0)

Interesting open access paper on Death and Resurrection of the Human IRGM Gene. Author summary:

The IRG gene family plays an important role in defense against intracellular bacteria, and genome-wide association studies have implicated structural variants of the single-copy human IRGM locus as a risk factor for Crohn’s disease. We reconstruct the evolutionary history of this region among primates and show that the ancestral tandem gene family contracted to a single pseudogene within the ancestral lineage of apes and monkeys.

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

Open Science: Explaining Spontaneous Knotting

Posted on March 4, 2009  Comments (0)

Shedding light on why long strands tend to become knotted

Anyone who has ever put up Christmas lights knows the problem: Holiday strands so carefully packed away last year are now more knotty than nice. In fact, they have become an inextricable, inexplicable, seemingly inevitable mess. It happens every year, like some sort of universal law of physics.

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.

Above a critical string length, the probability P of knotting at first increased sharply with length but then saturated below 100%. This behavior differs from that of mathematical self-avoiding random walks, where P has been proven to approach 100%. Finite agitation time and jamming of the string due to its stiffness result in lower probability, but P approaches 100% with long, flexible strings.
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As L [length] was increased from 0.46 to 1.5 m, P increased sharply. However, as L was increased from 1.5 to 6 m, P saturated at 50%.
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Tripling the agitation time caused a substantial increase in P, indicating that the knotting is kinetically limited. Decreasing the rotation rate by 3-fold while keeping the same number of rotations caused little change in P.
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We also did measurements with a stiffer string and observed a probability of finding a knot would approach 100% with an substantial drop in P.

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

John Conyers Against Open Science

Posted on March 4, 2009  Comments (1)

Lawrence Lessig once again has written a good blog post: John Conyers and Open Access

Open access journals, such as, for example, those created by the Public Library of Science, have adopted a different publishing model, to guarantee that all all research is freely accessible online (under the freest Creative Commons license) immediately, to anyone around the world. This guarantee of access, however, is not purchased by any compromise in academic standards. There is still a peer-review process. There is still even a paper-based publication.

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

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

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