Science and Engineering: Innovation, Research, Education and Economics
Open Access (Open Source) 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
April 14, 2008

ASU Science Studio Podcasts

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

April 9, 2008

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.

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

March 6, 2008

Antarctic Fish “Hibernate” in Winter

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

February 13, 2008

Harvard Liberal Arts Faculty Votes to Make Their Research Open Source

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

February 1, 2008

Great Self Portrait

photo of astronaut's faceplate reflecting earth

Photo by, and of, Astronaut Clay Anderson, Expedition 15 flight engineer. He used a digital camera to expose a photo of his helmet visor during the mission’s third planned session of extravehicular activity (EVA) on the International Space Station (15 August 2007). Also visible in the reflections in the visor are various components of the station and a blue and white portion of Earth. During the 5-hour, 28-minute spacewalk, Anderson and astronaut Rick Mastracchio (out of frame), STS-118 mission specialist, relocated the S-Band Antenna Sub-Assembly from Port 6 (P6) to Port 1 (P1) truss, installed a new transponder on P1 and retrieved the P6 transponder.

NASA provides their content, photos etc. online in an open access spirit. When linking to content (especially images) it is best to provide context (and with the internet the easiest way to do is so is relevant links). You can find many low resolution pictures of the image above around the internet. Trying to find the context around the image is not so easy - it took me quite awhile to do so. I try to provide the context and links. Lately some more sites will link to some original sources but this is still done far to infrequently.

There are also still far too many pointy haired bosses (PHB) making decisions to break the web by killing pages: web pages must live forever. Those PHB’s decisions do reduce the great benefit of linking but it is still worth doing for those cases where web sites are managed by people with the knowledge and ability to manage an internet resource properly.

Photo: NASA - high resolution version

Related: Van Gogh self portrait - Mars Rovers Getting Ready for Another Adventure - NASA Robotics Academy

January 27, 2008

From Ghost Writing to Ghost Management in Medical Journals

Ghost Management: How Much of the Medical Literature Is Shaped Behind the Scenes by the Pharmaceutical Industry?

As discussed below, a substantial percentage of medical journal articles (in addition to meeting presentations and other forms of publication, which are not the focus here) are ghost managed, allowing the pharmaceutical industry considerable influence on medical research, and making that research a vehicle for marketing.

Ghost writing and honorary authorship are not in and of themselves scientific problems, though they become so when they shape science to meet particular interests [1]. Some honorary authors are senior professors and chairs of departments, who are added to articles because of local academic politics rather than at the request of drug companies [15,16].

It has been repeatedly and firmly established that pharmaceutical company funding strongly biases published results in favor of the company’s products [17–19]. Ghost management amplifies that bias, because when one set of commercial interests exerts influence at multiple stages of research, writing, and publication, it will shape the resulting article.

This PLoS published essay includes 52 citations of studies in this area.

While they are clear to distinguish drug company influence on authors and other influence, I can see no justification for honorary authorships. Why can’t people just be honest. Is that really too high an expectation for scientists? Academic politics should not trump truth - especially for scientists. I can understand that traditionally claiming authors that were not actually authors has not been uncommon. But what reason is there to be dishonest in this way now? I don’t know of a good reason. Therefore it seems to me this practice should be seen as any other dishonest practice and those interested in finding the truth should stop making dishonest claims of authorship.
(more…)

January 23, 2008

Plants, Unikonts, Excavates and SARs

image of 4 biology supergroups

The Tree of Life Has Lost a Branch

“The results were pretty astounding. All non-bacterial life on Earth - called eukaryotic life - can now be divided into four main groups instead of the five groups that we have been working with up to now,” says Kamran Shalchian-Tabrizi, an associate professor from the University of Oslo’s Department of Biology

All life on Earth can be divided into two essentially different life forms—eukaryotes and prokaryotes. The eukaryotes gather their genetic material in a nucleus, while the prokaryotes (bacteria and archaea) have their genetic material floating freely in the cell. Eukaryotic organisms—such as humans—can, as a result of the new findings, be divided into the following four categories:

  • Plants (green and red algae, and plants)
  • Opisthokonts (amoebas, fungi, and all animals—including humans)
  • Excavates (free-living organisms and parasites)
  • SAR (the new main group, an abbreviation of Stramenophiles, Alveolates, and Rhizaria, the names of some of its members)


Three billion years ago, there was only bacteria and Archaea. Eukaryotic life, which comprises all multi-celled organisms, developed in the sea—probably between 1.2 and 1.6 billion years ago. It was not before about 500 million years ago that the first creatures crept onto land.

Related: research article Phylogenomics Reshuffles the Eukaryotic Supergroups - Evolution is Fundamental to Science - The Decline and Fall of the Animal Kingdom

January 17, 2008

In Tunguska, Siberia 99 Years Ago

Just What Happened 99 Years Ago in Tunguska, Siberia?

in the morning of 30 June 1908, a few native peoples in Siberia reported seeing a blue light in the sky that was as bright as the sun and hearing a series of loud explosions, accompanied by fierce winds and fire. These explosions, which flattened the pristine Siberian Taiga for 770 miles (2,000 kilometers) around, are estimated to have had the power of 2000 Hiroshima atomic bombs. However, this area is so remote and Russia was experiencing so much political turmoil that no one was able to investigate the scene until 1927

Gasperini’s team says their data suggest that a 10 meter (33 foot) wide fragment of the celestial object was blasted free by the explosion and continued traveling in the same direction that the original object was moving in. This fragment traveled slowly, about 1 kilometer a second (0.6 mile) per second. When the fragment plowed into the marshy terrain five miles north of the explosion epicenter, it created a long, trenchlike depression.

“It splashed on the soft, swampy soil and melted the underlying permafrost layer, releasing CO2 [carbon dioxide], water vapor, and methane that broadened the hole, hence the shape and size of the basin, unusual for an impact crater,” argues Gasperini, adding that “our hypothesis is the only one that accounts for the funnel-like morphology of Lake Cheko’s bottom.”

Related: research paper A possible impact crater for the 1908 Tunguska Event - Meteorite, Older than the Sun, Found in Canada - NASA Tests Robots at Meteor Crater

January 6, 2008

Mapping Where Brains Store Similar Information

CMU finds human brains similarly organized

Based on how one person thinks about a hammer, a computer can identify when another person also is thinking about a hammer. It also can differentiate between items in the same category of tools, be it a hammer or screwdriver.

The study makes two important scientific advances: “[T]here is an identifiable neural pattern associated with perception and contemplation of individual objects, and that part of the pattern is shared” by people.

The study reveals that patterns of thought extend into different regions of the brain, reflecting its complexity. It proves that a simple image can invoke thoughts in various regions of the brain, including how to use the object and experiences one has had with the object.

The study also helps to explain how the brain organizes thoughts, and the commonality of that process. “I want a complete mapping of brain states and thoughts,” Dr. Just said. “We’re taking tiny baby steps, but anything we can think about is represented in the brain.”

Related: PLoS One research paper - Using fMRI Brain Activation to Identify Cognitive States Associated with Perception of Tools and Dwellings - How Brain Resolves Sight - Regular Aerobic Exercise for a Faster Brain - How The Brain Rewires Itself

December 20, 2007

Great Physics Webcast Lectures

One great example of MIT’s Open Course Ware initiative is Physics I: Classical Mechanics. This course features lecture notes, problem sets with solutions, exams with solutions, links to related resources, and a complete set of videotaped lectures. The 35 video lectures by Professor Lewin, were recorded on the MIT campus during the Fall of 1999. These are some great lectures by a entertainer and educator. Some lecture topics: Newton’s Laws, Momentum - Conservation of Momentum - Center of Mass, Doppler Effect - Binary Stars - Neutron Stars and Black Holes, The Wonderful Quantum World - Breakdown of Classical Mechanics. What a wonderful web it is.

Related: MIT for Free - Berkeley and MIT courses online - Science and Engineering Webcast Libraries - Inner Life of a Cell: Full Version - Non-Newtonian Fluid Demo - Webcasts by Physics Nobel Laureates - Google Tech Webcasts #3

December 1, 2007

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.

Related: Open Source for LEGO Mindstorms - Young Scientists Design Open-Source Program at NASA - Open-Source Biotech - Publishers Continue to Fight Open Access to Science

November 19, 2007

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 discover 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.”

Related: Extreme Dinosaur: Nigersaurus, the Mesozoic Cow! - Dinosaur from Sahara ate like a ‘Mesozoic cow’ - Nigersaurus: just when you thought you’d seen everything… - Dino’s look is hard to swallow - Bizarre Dinosaur Grazed Like a Cow, Study Says - T-rex Treasure - Most Dinosaurs Remain Undiscovered

November 15, 2007

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).

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.

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

November 3, 2007

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.

Related: Publishers Continue to Fight Open Access to Science - Science Journal Publishers Stay Stupid - I Support the Public Library of Science - Open Access Legislation supported by 25 leading university provosts (2006)

October 23, 2007

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.

Related: Open Access and PLoS - I Support the Public Library of Science - Problems with Bonuses

September 21, 2007

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.

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.

Related: Finding Open Scientific Papers - Open Access Journal Wars - Anger at Anti-Open Access PR - Open Access Article Advantage

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