Tag Archives: Open Access

HHMI on Science 2.0: Information Revolution

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.

Toward a More Open Scientific Culture

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.

The Most Trusted Sources in Science

PBS: The Most Trusted Source in Science?

When Americans were asked in 2005 about their views on the credibility of information sources about biotechnology, a clear hierarchy of trust emerged starting at the top with scientific journals (almost 60% of respondents said they trusted journals as credible information ), followed by university scientists who are funded by government (50%), public television (50%), government scientists (40%), the WHO (40%), university scientists funded by industry (35%), biotechnology company scientists (30%), religious leaders (20%), TV networks (18%), biotechnology executives (15%), print media (15%), and political leaders (10%)

The data is from a survey by NSF in 2005. I predict PBS’ influence will grow as they provide valuable, open access, content online (the way the public will get most of their news).

University Web Presence Rankings

The Webometrics Ranking of University Web Sites provides some interesting data. I don’t remember reading this last year, but they state on the site now: “The original aim of the Ranking was to promote Web publication, not to rank institutions. Supporting Open Access initiatives, electronic access to scientific publications and to other academic material are our primary targets.” I support those goals, I am not totally convinced this is the most effective measure to do that but it provides one way of ranking web presence of universities. I am not that convinced this does a good job of ranking the web presences of universities but I think it is of some interest so I decided to post on the results.

graph of universities web presence

Country	% top 200	% top 500	% World Population	Jiao Tong top 101
USA	53	37.8	4.6	54
Germany	7.5	9.4	1.3	6
United Kingdom	5.5	7.2	0.9	11
Canada	8.5	5	0.5	4
Australia	3	2.8	0.3	2
Italy	0.5	2.8	0.9	1
Japan	1.5	2.4	2	6
France	0.5	2.4	0.9	4
Netherlands	4	2.2	0.3	2
Sweden	3	2	0.1	4
Switzerland	2	1.6	0.1	3
Taiwan	0.5	1.6	0.4	0
Finland	0.5	1.4	0.1	1
China	0.5	1.2	20.1	0
Portugal	0	1.2	0.2	0

Eating Breakfast Keeps Teenagers Leaner

Breakfast ‘keeps teenagers lean’

In a five year study of more than 2,000 youngsters, those who skipped breakfast weighed on average 5lbs (2.3kg) more than those who ate first thing. This was despite the fact that the breakfast-eaters consumed more calories in the course of the day. But the study in Pediatrics found they were likely to be much more active.

The University of Minnesota research adds weight to a growing body of evidence that those who eat breakfast – whether young or old – are leaner than those who do not.
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“The real problem is the profusion of messages about obesity. We need to make clear that eating regular meals is vital – and that a proper breakfast is very important. “If you eat well first thing, you’ll feel brighter, you’ll have more get up and go – and that will mean you’ll expend more energy.”

Teenagers are not the only ones who may benefit from sitting down to a proper breakfast. In a study of nearly 7,000 middle-aged people in Norfolk, a team from Cambridge University found that those who ate the most in the morning put on the least amount of weight.

Computer Science Unplugged

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.

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.”

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.