open-access-publishing

sciencealert.com
Researcher illegally shares millions of science papers free online to spread knowledge
Welcome to the Pirate Bay of science.
By Fiona MacDonald

A researcher in Russia has made more than 48 million journal articles - almost every single peer-reviewed paper every published - freely available online. And she’s now refusing to shut the site down, despite a court injunction and a lawsuit from Elsevier, one of the world’s biggest publishers.

For those of you who aren’t already using it, the site in question is Sci-Hub, and it’s sort of like a Pirate Bay of the science world. It was established in 2011 by neuroscientist Alexandra Elbakyan, who was frustrated that she couldn’t afford to access the articles needed for her research, and it’s since gone viral, with hundreds of thousands of papers being downloaded daily. But at the end of last year, the site was ordered to be taken down by a New York district court - a ruling that Elbakyan has decided to fight, triggering a debate over who really owns science.

“Payment of $32 is just insane when you need to skim or read tens or hundreds of these papers to do research. I obtained these papers by pirating them,”Elbakyan told Torrent Freak last year. “Everyone should have access to knowledge regardless of their income or affiliation. And that’s absolutely legal.”

If it sounds like a modern day Robin Hood struggle, that’s because it kinda is. But in this story, it’s not just the poor who don’t have access to scientific papers - journal subscriptions have become so expensive that leading universities such as Harvard and Cornell have admitted they can no longer afford them. Researchers have also taken a stand - with 15,000 scientists vowing to boycott publisher Elsevier in part for its excessive paywall fees.

Continue Reading.

DEAR RESEARCHERS OF TUMBLR

You know what’s awesome?  Research.  You know what’s not awesome?  Not being able to get access to research because it’s stuck behind a paywall and you don’t belong to an institution/your institution doesn’t subscribe to that particular journal.

FEAR NOT.

Here is a list of free, open access materials on a variety of subjects.  Feel free to add if you like!

GO FORTH AND LEARN SHIT, MY FRIENDS.

Directory of Open Access Journals- A compendium of over 9000 journals from 133 countries, multilingual and multidisciplinary.

Directory of Open Access Books- Like the above, but for ebooks.  Also multidisciplinary.

Ubiquity Press- Journals covering archaeology, comics scholarship, museum studies, psychology, history, international development, and more.  Also publishes open access ebooks on a wide variety of subjects.

Europeana-  Digital library about the history and culture of Europe.

Digital Public Library of America- American history, culture, economics, SO MUCH AMERICA.

Internet Archive- In addition to books, they have music and videos, too.  Free!  And legal!  They also have the Wayback Machine, which lets you see webpages as they looked at a particular time.

College and Research Libraries- Library science and information studies.  Because that’s what I do.

Library of Congress Digital Collections- American history and culture, historic newspapers, sound recordings, photographs, and a ton of other neat stuff.

LSE Digital Library- London history, women’s history.

Wiley Open Access- Science things!  Neurology, medicine, chemistry, ecology, engineering, food science, biology, psychology, veterinary medicine.

SpringerOpen-  Mainly STEM journals, looooong list.

Elsevier Open Access-  Elsevier’s kind of the devil but you might as well take advantage of this.  Mainly STEM, also a linguistics journal and a medical journal in Spanish.

Art history straddles the digital divide. Its pedagogical practices have been transformed by digital technology, but its scholarship remains wedded to the printed age. … Art history is invested in the monographic book as the prime vehicle for transmission of knowledge and academic advancement, and this bias is reinforced by tenure and promotion standards that privilege books over other types of publications.
— 

Hilary Ballon and Mariet Westermann. “Art History and Its Publications in the Electronic Age.” Rice University Press (2006). 

There are only a couple open access, online art history journals, but they are limited in scope. ArtHistory.us aims to add to their numbers.  Our field can move past print publication bias, and slowly but surely, it will.

Be a force of change by submitting an article to ArtHistory.us. Let’s create a new kind of journal for an emerging type of art history.

Over the past 100 years, tens of thousands of academic books have been published in the humanities, including many remarkable works on history, literature, philosophy, art, music, law, and the history and philosophy of science. But the majority of these books are currently out of print and largely out of reach for teachers, students, and the public. The Humanities Open Book pilot grant program aims to “unlock” these books by republishing them as high-quality electronic books that anyone in the world can download and read on computers, tablets, or mobile phones at no charge. The National Endowment for the Humanities (NEH) and the Andrew W. Mellon Foundation are the two largest funders of humanities research in the United States. Working together, NEH and Mellon will give grants to publishers to identify great humanities books, secure all appropriate rights, and make them available for free, forever, under a Creative Commons license.
languagelog.ldc.upenn.edu
Language Log » Lingua is dead. Long live Glossa!

Language Log has a good summary post about the latest in exciting linguistics publishing news: 

As many readers of Language Log know by now, the editors and the entire editorial board of a major linguistics journal, Lingua, have resigned en masse, effective when their contractual obligations to their soon-to-be-erstwhile publisher, Elsevier, are concluded at the end of this calendar year. This same editorial team will re-emerge in 2016 as the editors and editorial board of Glossa, a fair Open Access journal to be published by Ubiquity Press

Before resigning, the editorial team proposed to Elsevier that Lingua should become a fair Open Access journal: that the editorial board own the title of the journal, that authors retain copyright of their articles, that all articles be free to all readers, and that article processing charges be low, transparent, and in proportion to the work carried out by the publisher. Elsevier did not agree to this proposal, and insisted that they have the rights to the name Lingua. This is why the new journal will be called Glossa, but in the eyes of the community it is the rightful continuation of Lingua. Elsevier will try to start their own new journal, which they will name Lingua, usurping a name that has a lot of associated goodwill because of the hard work of the editors over many decades. We view this move as disingenuous and deceitful, and as a disservice to the field. The alternative name Zombie Lingua for the Elsevier project has been proposed, and we hope it will stick.

The main purpose of this post is to repeat and amplify these calls for community action:

Support Glossa. Submit your best work to it, agree to review for it, help it get ranked and recognized across the academy.

Do not support Zombie Lingua. The community should not assist Elsevier in standing up a new journal that usurps the Lingua goodwill. Do not serve on the editorial team, do not submit articles, do not review for them.

(Read the rest.)

Or, as one of the commenters suggests, only submit articles to the new Zombie Lingua that are about the language of zombies. (May I recommend double-submitting them to @speculativegrammarian?)

Study: people who believe in innate intelligence overestimate their own

In Understanding overconfidence: Theories of intelligence, preferential attention, and distorted self-assessment, an open access paper published in the Journal of Experimental Social Psychology, psych researchers from Washington State U, Florida State U and Stanford report on their ingenious experiments to investigate how subjects’ beliefs about intelligence affect their own intelligence.

Specifically, the researchers investigated what effect a belief in “fixed” intelligence (the idea that your intelligence is fixed, possibly at birth or before, and doesn’t change over your life) had on problem-solving, versus a belief that intelligence is trainable and can be changed through practice.

The result is a kind of microcosm of the Dunning-Kruger effect, where people overestimate their own intelligence. The researchers found that people who believe in fixed intelligence are prone to working hardest at easy problems, neglecting the hard ones, and that they came away from this experience with an overestimation of their own intelligence.

By contrast, people who believe that intelligence can be trained give priority to hard problems, as a way of training that intelligence.

Interestingly, when the researchers directed subjects to focus their efforts on easy problems at the expense of hard ones, the subjects finished up with overestimations of their own intelligence, regardless of their beliefs about intelligence.

There’s an interesting correlate here with the idea that “Straight White Male: The Lowest Difficulty Setting There Is”: if you only solve easy problems, you overestimate your own problem-solving ability, and also end up believing that problem-solving ability is innate and can’t be changed.

The people who freak out at the idea of class analysis, privilege and affirmative action often espouse the idea that promoting people who haven’t attained the same success markers is anti-meritorcratic, promoting “less qualified” candidates over “better qualified” ones. But if intelligence and capability are trainable, and if starting on an easy setting makes you prone to overestimating your abilities, then promoting people who’ve been solving harder problems will fill your positions with people more likely to believe that they can make themselves smarter by applying themselves to your organization’s hardest problems.

http://boingboing.net/2016/03/17/study-people-who-believe-in-i.html

“Language of Protest” - Inside Higher Ed

by Scott Jaschik:

“All six editors and all 31 editorial board members of Lingua, one of the top journals in linguistics, last week resigned to protest Elsevier’s policies on pricing and its refusal to convert the journal to an open-access publication that would be free online. As soon as January, when the departing editors’ noncompete contracts expire, they plan to start a new open-access journal to be called Glossa.

“The editors and editorial board members quit, they say, after telling Elsevier of the frustrations of libraries reporting that they could not afford to subscribe to the journal and in some cases couldn’t even figure out what it would cost to subscribe. Prices quoted on the Elsevier website suggest that an academic library in the United States with a total student and faculty full-time equivalent number of around 10,000 would pay $2,211 for shared online access, and $1,966 for a print copy.”

Wow.  Mind you, Lingua will still be available only from Elsevier, but with a completely different staff.  I wonder who will be approached by Elsevier to fill in the gaps.

Something startling, also, even though the subscription to Lingua is thousands per year:

“By quitting his position, [Lingua executive editor Johan] Rooryck will give up his current compensation from Elsevier, which he said is about 5,000 euros (about $5,500) a year.“ 

So…if the editors and the contributors aren’t getting rich off of this publishing model, who is?  If no one is, what is this money used for?  Is is really helping the academic publishing world, to have such restricted access when no researchers are paid for it?

Endangered chimpanzees may experience drastic habitat loss within 5 years

The Nigeria-Cameroon Chimpanzee (Pan troglodytes ellioti) is the most endangered of all chimpanzee subspecies in the world, with only about 6,000 individuals estimated in the wild. While their habitats are already threatened by logging, agriculture and illegal hunting, few studies have looked at the possible effects of climate change.

First author Paul Sesink Clee, Graduate Research Fellow at Drexel University, USA, said: “The Nigeria-Cameroon chimpanzee is perhaps the least studied of all chimpanzee subspecies. This is the first time that their distribution and habitat has been studied in such detail, and the data used to predict how their habitats might alter under climate change. We were surprised to see that the Nigeria-Cameroon chimpanzees living in the savanna-woodland habitat of central Cameroon are under the most immediate threat of climate change, and may completely lose their habitat within our lifetime…”

While the team predicted little change in the mountainous rainforest habitat, the ecotone habitat of the second population was predicted to decline quickly under all scenarios by the year 2020 and could disappear almost entirely under the worst case scenario by 2080. With roughly half of the 6,000 Nigeria-Cameroon chimpanzees existing in the ecotone habitat of central Cameroon, the results suggest that this subspecies of chimpanzee is particularly vulnerable to climate change. (continue)

Journal Source:
Paul R Sesink Clee, Ekwoge E Abwe, Ruffin D Ambahe, Nicola M Anthony, Roger Fotso, Sabrina Locatelli, Fiona Maisels, Matthew W Mitchell, Bethan J Morgan, Amy A Pokempner, Mary Katherine Gonder. Chimpanzee population structure in Cameroon and Nigeria is associated with habitat variation that may be lost under climate changeBMC Evolutionary Biology, 2015; 15 (1) DOI:10.1186/s12862-014-0275-z (PDF)

Photo credit: 
“Ngambe”, Limbe Wildlife Center, Cameroon. (Paul Sesnik Clee)

When you support open publishing, you support free access to ideas, innovations, and learning for all.  Universal access to learning makes us all better off; universal access is the power of open.  

Open publishing is exactly opposite of traditional “Big Textbook” publishers that seek to stifle and exclude.  As Mr. Vaughn says in the article, “copyright law and publishers’ business plans are preventing an enormous educational benefit." 

Open textbook publishers’ business plans are centered on enabling and empowering everyone’s ability to learn, share, and grow.  A vibrant community of open publishers will force all publishers to behave in a manner that supports education.

Your voice matters.  Be a rebel.  Sign the petition demanding educators and administrators consider and support open textbook solutions today.  If we join together, our voices will be heard.

Sign the petition here:  http://www.textbookrebellion.org/petition

Some see the discipline of anthropology as being an expert and professional society. They want to share their work with other anthropologists who have the same interests and concerns as themselves. Feedback from random Youtube users, or even people in other disciplines, isn’t very valuable to them. The feedback they can get through peer review in professional anthropology journals is exactly what they want, as is the recognition. … Also, I don’t think every researcher agrees that expensive academic journals fail to disseminate work. They only want to share their work with a select audience, and don’t see the point in making it available free online. In the end they disagree that free access would improve the impact of their work (it comes down to who they are trying to impact).
—  Owen Wiltshire, antropologi.info
youtube

Open Access Published explained by phdcomics. A good overview of the concepts with a bit of personal insight thrown into the mix.

nature.com
Mathematicians aim to take publishers out of publishing

Episciences Project to launch series of community-run, open-access journals.

Mathematicians plan to launch a series of free open-access journals that will host their peer-reviewed articles on the preprint server arXiv. The project was publicly revealed yesterday in a blog post by Tim Gowers, a Fields Medal winner and mathematician at the University of Cambridge, UK.

Nature News. 

Hearts of cows used in ancient cosmetics, claims study

It is said that the average modern woman consumes more than 3 kilograms of lipstick in her lifetime.

Some might find all that wax, oils and emollients a bit hard to digest, but the prehistoric inhabitants of Northwest China’s Xinjiang Uygur autonomous region made their women’s cosmetics sticks out of something a little more edible around 3,500 to 4,000 years ago.

According to the latest archaeological research published on Thursday night in Scientific Reports, an online, open access journal from the publishers of Nature, the red cosmetic sticks buried with women in Xiaohe Cemetery (1980-1450 BC) were made from cow hearts. Read more.

Alzheimer’s culprit causes memory loss even before brain degeneration

A brain protein believed to be a key component in the progress of dementia can cause memory loss in healthy brains even before physical signs of degeneration appear according to new University of Sussex research.

The study, published in the open access Nature Publishing Group journal Scientific Reports, reveals a direct link between the main culprit of Alzheimer’s disease and memory loss.

Alzheimer’s disease is characterized by the formation of amyloid plaques in the brain tissue. These amyloid plaques are made up of an insoluble protein, “Amyloid-beta” (Abeta), which forms small structures called “oligomers” that are important in the disease progression.

Although these proteins are known to be involved in Alzheimer’s, little is understood about how they lead to the memory loss.

Sussex Neuroscience researchers investigated how Abeta affected healthy brains of pond snails (Lymnaea stagnalis) by observing the effect of administering the protein following a food-reward training task.

The results showed that snails treated with Abeta had significantly impaired memories 24 hours later when tested with the food task, even though their brain tissue showed no sign of damage.

Lead author on the study Lenzie Ford said this demonstrated that Abeta alone is enough to lead to the symptoms of memory loss that are well known in Alzheimer’s disease.

She said: “What we observed was that snail brains remained apparently healthy even after the application of the protein. There was no loss of brain tissue, no signs of cell death, no changes in the normal behaviour of the animals, and yet memory was lost.

“This shows that Alzheimer’s amyloid proteins don’t just affect memory by killing neurons of the brain, they seem to be targeting specific molecular pathways necessary for memories to be preserved.”

Professor George Kemenes, a Sussex neuroscientist who pioneered a thorough understanding of the molecular mechanisms of learning and memory in the pond snail’s nervous system, said: “Because we understand the memory pathways so well, the simple snail brain has provided the ideal model system to enable us to link the loss of established memory to pure Abeta.”

The work will provide a platform for a more thorough investigation of the mechanisms and effects on memory pathways that lead to this memory loss.

Professor Serpell, a senior author on the study and co-director of the University of Sussex’s Dementia Research Group, said: “It is absolutely essential that we understand how Alzheimer’s disease develops in order to find specific targets for therapeutics to combat this disease.”

How understanding GPS can help you hit a curveball

Our brains track moving objects by applying one of the algorithms your phone’s GPS uses, according to researchers at the University of Rochester. This same algorithm also explains why we are fooled by several motion-related optical illusions, including the sudden “break” of baseball’s well known “curveball illusion.”

The new open-access study published in PNAS shows that our brains apply an algorithm, known as a Kalman filter, when tracking an object’s position. This algorithm helps the brain process less than perfect visual signals, such as when objects move to the periphery of our visual field where acuity is low.

However, the same algorithm that helps our brain track motion can be tricked by the pattern motion of an object, such as the seams on a spinning baseball, which causes our brain to “see” the ball suddenly drop from its path when, in reality, it curves steadily.

Though we often rely on Global Positioning System (GPS) to get us to our destination, the accuracy of GPS is limited. When the signal is “noisy” or unreliable, your phone’s GPS uses algorithms, including the Kalman filter, to estimate the location of your car based on its past position and speed.

“Like GPS, our visual ability, although quite impressive, has many limitations,” said the study’s coauthor, Duje Tadin, associate professor of brain and cognitive sciences at the University of Rochester.

We see an object’s position with great accuracy when it’s in the center of our visual field. We do poorly, however, at perceiving position when it shifts into our visual periphery; then our estimate of its position becomes unreliable. When that happens, our brain gives greater emphasis to our perception of the object’s motion.

“And, this is where we start seeing fascinating phenomena like the curveball illusion,” said Tadin. “We’ve found that the same algorithm that is used by GPS to track vehicles also explains why we perceive the curveball illusion.”

“A curveball pitch does indeed curve,” said the first author Oh-Sang Kwon, assistant professor at Ulsan National Institute of Science and Technology, South Korea. “But when it is viewed in the visual periphery, the spin of the ball—the motion of the seam pattern—can make it appear to be in a different location than it really is.”

“Here, the brain ‘knows’ that position estimates are unreliable in the periphery, so it relies more on other visual cues, which, in this case, is the motion; the spin of the ball,” said Kwon, who led the study while serving as a research associate in the Center for Visual Science at the University of Rochester.

The perceived motion and position of the curveball depends on where it is in your visual field. So, when the ball enters your periphery, it appears to make an abrupt shift: The infamous and sudden “break” of the curveball as it nears home plate.

The Kalman filter algorithm, named after its coinventor, mathematician Rudolph Kalman, is used to find optimal and integrated solutions from noisy or unreliable data whether in GPS or our brains.

Most of the time our vision does a really good job, but in some cases, such as a breaking curveball, the optimal solution that our brain comes up with belies the actual behavior—and trajectory—of the ball, and the result is an optical illusion.

Therefore, Tadin explained, you have a better chance of hitting a curveball by realizing that our brains, like GPS, can lead us to “see” changes in speed or direction that don’t actually occur when the ball moves from the center of our visual field to the periphery.

These illusions should not be seen as evidence that our brains are poor at perceiving the world around us, though,” explained Tadin. “They are interesting side-effects of neural processes that, in most cases, are extremely efficient at processing ‘noisy’ visual information.“

“This study shows that the solutions that the brain finds for dealing with imperfect information often match optimal solutions that engineers have come up with for similar problems, like your phone’s GPS.”

Metal-eating Plant Discovered in Philippines

Scientists from the Univ. of the Philippines, Los Baños have discovered a new plant species with an unusual lifestyle — it eats nickel for a living — accumulating up to 18,000 ppm of the metal in its leaves without itself being poisoned, says Prof. Edwino Fernando, lead author of the report. Such an amount is 100 to 1,000 times higher than in most other plants. The study was published in Pensoft Publishers’ open access journal PhytoKeys.

The new species is called Rinorea niccolifera, reflecting its ability to absorb nickel in very high amounts. Nickel hyperaccumulation is such a rare phenomenon with only about 0.5–1 percent of plant species native to nickel-rich soils having been recorded to exhibit the ability. Throughout the world, only about 450 species are known with this unusual trait, which is still a small proportion of the estimated 300,000 species of vascular plants.

Read more: http://www.laboratoryequipment.com/news/2014/05/metal-eating-plant-discovered-philippines

THE VORTEX: From Soap Bubble to Jupiter’s Great Red Spot
A report in Nature Scientific Reports 3, Article number: 3455:  “Intensity of vortices: from soap bubbles to hurricanes” by T. Meuel et al.

Open Access || Published 13 December 2013

Vortices are prominent features of fluid flows and span length scales ranging from an insect’s length to planetary sizes. Understanding the displacement of vortices, their structure, and their long time dynamics is crucial for different aspects be they at the level of small engines, turbulent flows, or planetary atmospheres.

Vortices may be found in turbulent flows, where they appear at all scales, in the wake of a bluff body, where they come in pairs, or in atmospheric flows whether on earth or on other planets …

Here we use a half bubble heated from below on which large isolated vortices are observed. …  Read more

THE BUBBLE
(a) The Set Up: a brass disk (1) with a circular groove (3) can be rotated using a continuous motor (6) connected to it by a shaft (5). This disk is heated by the proximity of a hollow annulus (2) connected to a water circulation bath. The bubble is blown using the soap solution in the groove (3). The inner side of the brass disk is covered by a Teflon coating (2 mm thick) to minimize the heating of the air inside the bubble. The temperature at the equator of the bubble is set by the temperature of the water bath.

VISUALIZATIONS
(b) and ©
 show the detachment of thermal plumes from near the equator and rising towards the pole; they were taken using (b) an infrared camera (the temperature scale is in deg °C)  and© a CCD color camera .

(d) The full bubble with a vortex being formed by a large thermal plume.

(e) A zoom on the vortex in which the colors are interference colors of white light being reflected by the thin water layer constituting the bubble.

(f) Numerical simulation of thermal convection on the surface of a sphere of radius 1, where the colors indicate the vorticity field.

(g) A zoom on the single vortex in image (f). The color code indicates the value of the vorticity …