Category Archives: Open Access

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.

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particular hardware or software, Unplugged activities can be used anywhere, and the ideas they contain will never go out of date.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.

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

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.

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

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].
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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.
Continue reading →

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
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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)

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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.

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
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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.”

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.
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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.”

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.