Category Archives: Open Access

Open Source: The Scientific Model Applied to Programming

xo-laptop: On the Open-Sourcing of Business – interesting post worth reading, though I disagree with some points:

There is no obligation to “give back” anything, though it often makes sense to participate in the community based on a particular open-source project. However, that is a strategic decision for you to make. Your sole obligation is to respect the license terms.

There is a difference between your sole legal obligation and your sole obligation. I agree legally all you are obliged to do is comply with the legal requirements. That does not mean that is your sole obligation. I don’t see any problem making money in efforts involving open source efforts but I do believe that as that happens an obligation (perhaps not legal but real none-the-less) grows to give back to the community (Google’s summer of code is a great example of giving back). Most open source efforts require that any additions you make to the software be given back to the community (those involved in open souce know this, I add this just for the information of those not familiar with open source practices). Legal obligations are the minimum you can be forced to do, not the only obligations one has. Great quote (emphasis mine):

I think the best is one I have often seen expressed by Linus Torvalds, and it was one of the explanations I gave in a talk to the New York City Linux User Group in a talk in December, 1999.

Simply put, free and open-source software is just the scientific model applied to programming: free sharing of work open collaboration; open publication; peer review; recognition of the best work, with priority given to the first to do a meaningful new piece of work; and so forth. As a programmer, it is the best arena in which to work. There are no secrets; the work must stand on its own.

Another great post on this topic: What Business Can Learn from Open Source.

Nigersaurus

photo of the Nigersaurus Jaw Bones

Structural Extremes in a Cretaceous Dinosaur

Nigersaurus taqueti shows extreme adaptations for a dinosaurian herbivore including a skull of extremely light construction, tooth batteries located at the distal end of the jaws, tooth replacement as fast as one per month, an expanded muzzle that faces directly toward the ground, and hollow presacral vertebral centra with more air sac space than bone by volume. A cranial endocast provides the first reasonably complete view of a sauropod brain including its small olfactory bulbs and cerebrum. Skeletal and dental evidence suggests that Nigersaurus was a ground-level herbivore that gathered and sliced relatively soft vegetation, the culmination of a low-browsing feeding strategy first established among diplodocoids during the Jurassic.

This discovery has received a good deal of coverage. Among other things it is great to see this paper is available to everyone who wants to view it because it is published by open access PLoS One. The Nigersaurus was discovered in what is now the Sahara Desert in Niger. When the Nigersaurus was roaming the area, 110 million years ago, the climate was a Mesozoic forest. The dinosaur had a few hundred teeth that were replaced almost monthly (a record). The bones of the head and neck were so minimal and light that the Read more about the Nigersaurus. As the author stated: “One of the stunning things about this animal is how fragile the skull is… Some of the bones are so thin you can shine a light through them.”

New Theory of Everything

Surfer dude stuns physicists with theory of everything

An impoverished surfer has drawn up a new theory of the universe, seen by some as the Holy Grail of physics, which as received rave reviews from scientists. Garrett Lisi, 39, has a doctorate but no university affiliation and spends most of the year surfing in Hawaii, where he has also been a hiking guide and bridge builder (when he slept in a jungle yurt).
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Despite this unusual career path, his proposal is remarkable because, by the arcane standards of particle physics, it does not require highly complex mathematics. Even better, it does not require more than one dimension of time and three of space, when some rival theories need ten or even more spatial dimensions and other bizarre concepts. And it may even be possible to test his theory, which predicts a host of new particles, perhaps even using the new Large Hadron Collider atom smasher that will go into action near Geneva next year.
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Although the work of 39 year old Garrett Lisi still has a way to go to convince the establishment, let alone match the achievements of Albert Einstein, the two do have one thing in common: Einstein also began his great adventure in theoretical physics while outside the mainstream scientific establishment, working as a patent officer, though failed to achieve the Holy Grail, an overarching explanation to unite all the particles and forces of the cosmos.

Now Lisi, currently in Nevada, has come up with a proposal to do this. Lee Smolin at the Perimeter Institute for Theoretical Physics in Waterloo, Ontario, Canada, describes Lisi’s work as “fabulous”. “It is one of the most compelling unification models I’ve seen in many, many years,” he says.

Actual open access paper: An Exceptionally Simple Theory of Everything by A. Garrett Lisi
Reactions: A Theoretically Simple Exception of Everything – Upon further review, surfer’s new Theory of Everything severely deficient
Related: String Theory – CERN Pressure Test Failure – Webcasts by Chemistry and Physics Nobel Laureates

Open Access Legislation May Be Included in HHS Budget Bill

Open Access to Research Funded by U.S. Is at Issue by Rick Weiss:

The idea is that consumers should not have to buy expensive scientific journal subscriptions — or be subject to pricey per-page charges for nonsubscribers — to see the results of research they have already paid for with their taxes. Until now, repeated efforts to legislate such a mandate have failed under pressure from the well-heeled journal publishing industry and some nonprofit scientific societies whose educational activities are supported by the profits from journals that they publish.

But proponents — including patient advocates, who want easy access to the latest biomedical findings, and cash-strapped libraries looking for ways to temper escalating subscription costs — have parlayed their consumer-friendly “public access” message into legislative language that has made it into the Senate and House versions of the new HHS bill.

The opponents of open science are lobbying to keep scientific research funded by taxpayers unavailable to the public. As I have said before it is time to stop supporting those who attempt to stop scientific progress. The out of date thinking behind closed access journals should be discouraged and those journals fighting progress should not be supported. This legislation would bring openness to federal research in a similar manner to the steps taken by Howard Hughes Medical Institute announced for research they fund.

More Dinosaurs Fighting Against Open Science

Controversy at the American Chemical Society by John Dupuis

So, what’s my take on this? First of all, I’m not surprised. Unfortunately there are some scholarly societies that operate more like for-profits when it comes to their publishing arms and ACS is certainly one of the most notable for that sort of thing. While it should be shocking that ACS is acting more like Elsevier than Elsevier at times, sadly it isn’t.

Secondly, what should we, as librarians do about it? Mostly we need to advocate. We need to push our vendors towards business models that favour open access, we need to reassure them that we’re interested in a sustainable model for scholarly publishing

I agree. It is sad that so many organizations distort behavior though poor management structures but that is the world we live in. My management improvement blog focused on how to manage better. And I have posted several times about the need to shift our support to open access science and away from those who want continue outdated strategies that restrict the advancement of scientific ideas.

Publishers Continue to Fight Open Access to Science

Publishers prepare for war over open access

On one side are the advocates of open-access journals – publications that make academic papers freely available and recoup costs by charging authors to publish. The model seems increasingly successful. New open-access journals are springing up weekly and could gain support if the US acts on plans make all its publicly funded health research freely available via a government archive.

Lined up against them are the academic publishers. The idea of open-access journals is frightening for an industry whose profits are based on subscription charges.
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Dezenhall’s strategy includes linking open access with government censorship and junk science – ideas that to me seem quite bizarre and misleading. Last month, however, the AAP launched a lobby group called the Partnership for Research Integrity in Science & Medicine (PRISM), which uses many of the arguments that Dezenhall suggested.

It is sad to see journals that were founded to promote science so flawed in their thinking today. As I said last month in Science Journal Publishers Stay Stupid: “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 (PLoS – arXiv.org – Open Access Engineering Journals) and leave those that seek to keep outdated practices to go out of business.” Organizations can’t ignore principles when choosing tactics. Tactics that might be ok in other situations, should not be acceptable to scientists publishing scientific information. When journals move to harm science to preserve their outdated business practices they deserve to lose the respect of scientists.

I Support the Public Library of Science

I support PLoS graphic

I am a fan of the Public Library of Science, as I have mentioned previous. Yesterday I donated some money to support their great efforts. From the PLoS site:

During this time of transition from traditional to open access publishing, we must develop creative ways to support the launch of new journals, the investment in new publishing technologies, and efforts to increase awareness of, and commitment to, open access.

The Future of Scholarly Publication, 2005
Why Most Published Research Findings Are False by John P. A. Ioannidis, PLoS published, 2005
Inhibition of Mutation and Combating the Evolution of Antibiotic Resistance, PLoS published, 2006
Who Needs Sex (or Males) Anyway? by Liza Gross, PLoS published, 2007
Science Journal Publishers Stay Stupid, 2007
YouTube+ for Science from PLoS, 2007

Science Journal Publishers Stay Stupid

Science publishers get even stupider by Andrew Leonard:

The American Association of Publishers and everyone associated with it should be ashamed of trying to protect their profit margins by slandering the open access movement as government intervention and censorship. Research paid for with government funds should be freely accessible to the general public.

I wish it was amazing that these people have so little grasp of what has been going on in the world the last 5 years (but I must say such failure to adapt seems to be a common trait in too many organizations). Previously I have posted on the importance of continuing the scientific tradition of open debate and open access. In the past there have been distribution complexities that made paid journals an acceptable compromise. That people working at journals don’t see that the internet changes that is going to lead to their rapid irrelevance. They had to figure this out a couple of years ago. Given they still haven’t, I must say that they really don’t seem to have much understanding of science or modern communication methods. Given their industry that is sad. 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 (PLoS – arXiv.org – Open Access Engineering Journals) and leave those that seek to keep outdated practices to go out of business.

“It is not necessary to change. Survival is not mandatory.” Dr. W. Edwards Deming

I do object to scientific knowledge being kept out of the scientific and public community. The ability to use the internet to more effectively communicate new knowledge should not be sacrificed to protect the old model journals had for sustaining themselves. They should find a way to fund themselves and make their material available for free on the internet (I think some delay for free public access would be fine – the shorter the delay the better). Or they should be replaced by others that do so.

Textbook Revolution

Textbook Revolution is a resource on free textbooks and free related course materials. In general, I must say the prices of textbooks seem crazy. This is another tool great open access resource.

At Textbook Revolution, you’ll find links to textbooks and select educational resources of all kinds. Some of the books are PDF files, others are viewable only online as e-books. Most books are aimed at undergraduates, but there are at least a few resources at every level, from kindergarten to post-doc. All of the books are offered for free by their respective copyright holders for online viewing. Beyond that, each book is as individual as the author behind it.

Some examples: The Scientist and Engineer’s Guide to Digital Signal Processing by Steven W. Smith; Light and Matter by Benjamin Crowell; A First Course in Linear Algebra by Robert A Beeze; Programming Ruby: The Pragmatic Programmer’s Guide by
Dave Thomas and Introduction to Statistical Thought by Michael Lavine.

While on the subject of textbooks, I will plug my father’s book: Statistics for Experimenters – it is my blog so I get to do what I want 🙂

Laser Tool Creates “blueprints” of Archeology Sites

Laser mapping tool traces ancient sites

Born in northern Iraq in 1940, Kacyra developed this laser-mapping tool several years ago to solve a problem in construction — keeping accurate records of the real dimensions of factories and power plants when they deviate from the architect’s plans.

The 67-year-old sold his invention in 2001 and now works with his wife, Barbara, to get the $100,000 tool into the hands of archaeological researchers who are using it to create electronic blueprints so accurate that scientists sitting at computer terminals can glean the secrets of ancient monuments remotely. “We both loved the ancient-built environment and we wanted to put high technology to use saving ancient places,” Kacyra said.

Today the Kacyras have created a Web site, at www.cyark.org, that allows anyone to see these blueprintlike images. But that’s just the start. Down the line they would like to superimpose real graphics on top of these geospatial maps — recreating ancient worlds onscreen.

“Using the latest laser-scanning technology, CyArk collects the most accurate 3D model of cultural heritage sites, stores them safely and provides them freely to the world.” More on the laser tool:
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