Tag Archives: John Bohannon

What’s happening to the scientists in Turkey?

In the wake of the July 15-16, 2016 attempted coup in Turkey, there have been widespread reprisals including one focused on the scientific community. An Aug. 3, 2016 news item on the Al Jazeera website describes a situation at Turkey’s national science research council,

Turkish police have raided the offices of the national science research council, private broadcaster NTV reported.

Many people were detained in the raid on the offices of the Scientific and Technological Research Council of Turkey (Tubitak) in the northwestern province of Kocaeli on Wednesday [Aug. 3, 2016], NTV said.

Tubitak funds science research projects in universities and the private sector and employs more than 1,500 researchers, according to its website.

An Aug. 3, 2016 CBC (Canadian Broadcasting Corporation) news item adds some detail,

… a Tubitak official told Reuters the raid had happened on Sunday [July 31, 2016], adding he did not have any details about the number of detentions. He declined to comment further.

The raid on TÜBİTAK takes place within the context of widespread retaliation. A July 20, 2016 article by John Bohannon for Science magazine describes the situation,

In the wake of a failed coup attempt last weekend, the Turkish government has brought higher education to a grinding halt. It appears to be part of a massive political purge in which the government has arrested and fired thousands of people. And educators across the country are bracing for more bad news after the government this week suspended teachers and academic deans. “They are restructuring academia,” says Caghan Kizil, a Turkish molecular biologist based at the Dresden University of Technology in Germany who has been in close communication with colleagues in Turkey. “People are very scared and not hopeful.”

In the span of a few days, more than 45,000 civil servants in the military and judiciary have been fired or suspended. Although there are ambiguous and conflicting media reports, it appears that some 15,000 staff members of the ministry of education also were fired, 21,000 teachers lost their professional licenses, and more than 1500 university deans were all but ordered to resign.

The latest clampdown took place yesterday [July 19, 2016] when the government ordered universities to call back Turkish academics from abroad. “They want to take the universities under their full control,” says Sinem Arslan, a Turk doing a political science Ph.D. at the University of Essex in the United Kingdom. “Academic freedoms will no longer exist. I don’t think that anybody will be able to work on research areas that are considered taboo by the government or write anything that criticizes the government.”

With its latest raid, the Turkish government has raised concerns about Turkish scientists and the American Association for the Advancement of Science (AAAS) has produced a letter in response. From an Aug. 3, 2016 AAAS news release,

As the Turkish government restores order after the failed coup, the American Association for the Advancement of Science (AAAS) and seven other leading science and engineering societies today expressed concern for the human rights of the Turkish scientific community, which has reportedly been subject to restrictions including travel bans and the ordered return of Turkish academics working abroad.

“The future prosperity and security of any nation depends on its ability to be a knowledge-based, innovative society and to a considerable extent on the work of its scientists, engineers, academics, and researchers,” the science group wrote, in a letter to President Recep Tayyip Erdoğan of Turkey.

They emphasized that the health of the scientific enterprise requires that scientists have freedom to think independently and innovatively and are able to engage with scientists around the world. Noting that the Turkish government had previously stated that “democracy, freedom, and the rule of law are nonnegotiable in Turkey,” the science organizations urged President Erdoğan to “follow through on this pledge to fully respect human rights, the rule of law, and due process” to protect both citizens and the scientific community.

The letter was signed by AAAS CEO Rush Holt, executive publisher of the Science family of journals, as well as the leaders of the American Anthropological Association, the American Association of Geographers, the American Physical Society, the American Sociological Association, the American Statistical Association, Sigma Xi, and the Society for the Psychological Study of Social Issues.

“Reports of forced resignations, suspensions, and travel bans affecting thousands of Turkish scientists and academics are deeply troubling, and deeply problematic for any civil society,” said Rush Holt, CEO of AAAS and executive publisher of the Science family of journals. “We urge President Erdoğan to follow through on his pledge to protect basic human rights, the rule of law, and academic freedoms for citizens and scholars alike.”

This is not the first time in this decade that the Turkish government has ordered repressive measures against scientists. Here’s more from my Sept. 9, 2011 posting, a time when Erdogan was Prime Minister,

Scientists in Turkey are threatening to walk out on the Turkish Academy of Sciences due to some recent government initiatives affecting the academy’s governance. From the Sept.9, 2011 news item on physorg.com,

Members of TÜBA [founded in 1993], the Turkish Academy of Sciences, are threatening to resign en masse in order to fight a decree issued by the government of Turkey that would strip the Academy of its autonomy.

The decree, issued on 27th August, which was just after the start of a nine-day holiday in Turkey, says that one-third of the members of the academy will now be appointed by the government and a further one-third by the Council of Higher Education, which is also a government body. [emphasis mine] Only the remaining one-third will be elected by current members. The president and vice-president of the academy will in future be appointed by the government rather than by sitting members. In addition, honorary members will lose their voting rights and the age at which members are deemed honorary will be reduced from 70 to 67.

A Sept. 7, 2011 editorial in Nature provides a more comprehensive description of what was then occurring,

On the eve of a week-long holiday to celebrate the end of the fasting period of Ramadan, the Turkish government executed an extraordinary scientific coup. On 27 August, it issued a decree with immediate effect, giving itself tighter control of Turkey’s two main scientific organizations: the funding agency TÜBİTAK and the Turkish Academy of Sciences (TÜBA), the governance of which is now so altered that it can no longer be considered an academy at all.

The move has startled and appalled Turkish scientists. It should also sound an alarm bell throughout Turkish society. The government of Prime Minister Recep Tayyip Erdoğan is also taking greater control of other sectors through a series of decrees requiring no parliamentary debate. …

This time scientists are being targeted along with many other groups and, if rumours are even partially correct, government actions are more severe than they were in 2011.

Science (magazine) investigates Sci-Hub (a pirate site for scientific papers)

Sci-Hub, a pirate website for scientific papers, and its progenitor, Alexandra Elbakyan, have generated a couple of articles and an editorial in Science magazine’s latest issue (April 28, 2016?). An April 29, 2016 article by Bob Yirka for phys.org describes one of the articles (Note: Links have been removed),

A correspondent for the Science family of journals has published an investigative piece in Science on Sci-Hub, a website that illegally publishes scholarly literature, i.e. research papers. In his article, John Bohannon describes how he made contact with Alexandra Elbakyan, the founder of what is now the world’s largest site for pirated scholarly articles, data she gave him, and commentary on what was revealed. Bohannon has also published another piece focused exclusively on Elbakyan, describing her as a frustrated science student. Marcia McNutt, Editor-in-Chief of the Science Family also weighs in on her “love-hate” relationship with Sci-Hub, and explains in detail why she believes the site is likely to cause problems for scholarly publishing heading into the future.

An April 28, 2016 American Association for the Advancement of Science (AAAS) news release provides some detail about the number of downloads from the Sci-Hub site,

In this investigative news piece from Science, contributing correspondent John Bohannon dives into data from Sci-Hub, the world’s largest pirate website for scholarly literature. For the first time, basic questions about Sci-Hub’s millions of users can be answered: Where are they and what are they reading? Bohannon’s statistical analysis is based on server log data supplied by Alexandra Elbakyan herself, the neuroscientist who created Sci-Hub in 2011. After establishing contact with her through an encrypted chat system, Bohannon and Elbakyan worked together to create a data set for public release: 28 million Sci-Hub download requests going back to 1 September 2015, including the digital object identifier (DOI) for every paper and the clustered locations of users based on their Internet Protocol address. In his story, Bohannon reveals that Sci-Hub usage is highest in China with 4.4 million download requests over the 6-month period, followed by India and Iran. But Sci-Hub users are not limited to the developing world, he reports; the U.S. is the fifth largest downloader and some of the most intense Sci-Hub activity seems to be happening on US and European university campuses, supporting the claim that many users could be accessing the papers through their libraries, but turn to Sci-Hub for convenience.

Bohanon’s piece appears to be open access. Here’s a link and a citation,

Who’s downloading pirated papers? Everyone by John Bohannon. Science (2016). DOI: 10.1126/science.aaf5664 Published April 28, 2016.


The analysis of the data is fascinating but I’m not sure why this is being billed as an ‘investigative’ piece. Generally speaking I would expect an investigative piece to unearth new information which has likely been hidden. At the very least, I would expect some juicy inside information (i.e., gossip).

Bohannon certainly had no difficulty getting information (from the April 28, 2016 Science article),

For someone denounced as a criminal by powerful corporations and scholarly societies, Elbakyan was surprisingly forthcoming and transparent. After establishing contact through an encrypted chat system, she worked with me over the course of several weeks to create a data set for public release: every download event over the 6-month period starting 1 September 2015, including the digital object identifier (DOI) for every paper. To protect the privacy of Sci-Hub users, we agreed that she would first aggregate users’ geographic locations to the nearest city using data from Google Maps; no identifying internet protocol (IP) addresses were given to me. (The data set and details on how it was analyzed are freely accessible)

Why would it be surprising that someone who has made a point of freeing scientific research and making it accessible also makes the data from her Sci-Hub site freely available? The action certainly seems consistent with her raison d’être.

Bohannon steers away from making any serious criticisms of the current publishing régimes although he does mention a few bones of contention while laying them to rest, more or less. This is no great surprise since he’s writing for one of the ‘big three’, a journal that could be described as having a vested interest in maintaining the status quo. (For those who are unaware, there are three journal considered the most prestigious or high impact for scientific studies: Nature, Cell, and Science.)

Characterizing Elbakyan as a ‘frustrated’ student in an April 28, 2016 profile by John Bohannon (The frustrated science student behind Sci-Hub) seems a bit dismissive. Sci-Hub may have been borne of frustration but it is an extraordinary accomplishment.

The piece has resulted in at least one very irate librarian, John Dupuis, from an April 29, 2016 posting on his Confessions of a Science Librarian blog,

Overall, the articles are pretty good descriptions of the Sci-Hub phenomenon and relatively even-handed [emphasis mine], especially coming from one of the big society publishers like AAAS.

There was one bit in the main article, Who’s downloading pirated papers? Everyone, that really stuck in my craw. Basically, Sci-Hub — and all that article piracy — is librarians’ fault.

And for all the researchers at Western universities who use Sci-Hub instead, the anonymous publisher lays the blame on librarians for not making their online systems easier to use and educating their researchers. “I don’t think the issue is access—it’s the perception that access is difficult,” he says.

Fortunately it was countered, in the true “give both sides of the story” style of mainstream journalism, by another quote, this time from a librarian.

“I don’t agree,” says Ivy Anderson, the director of collections for the California Digital Library in Oakland, which provides journal access to the 240,000 researchers of the University of California system. The authentication systems that university researchers must use to read subscription journals from off campus, and even sometimes on campus with personal computers, “are there to enforce publisher restrictions,” she says.

But of course, I couldn’t let it go. Anderson’s response is perfectly fine but somehow there just wasn’t enough rage and exasperation in it. So I stewed about it over night and tweeted up a tweetstorm of rage this morning, with the idea that if the rant was well-received I would capture the text as part of a blog post.

As you may have guessed by my previous comments, I didn’t find the article quite as even-handed as Dupuis did. As for the offence to librarians, I did notice but it seems in line with the rest of the piece which dismisses, downplays, and offloads a few serious criticisms while ignoring how significant issues (problematic peer review process,  charging exorbitant rates for access to publicly funded research, failure to adequately tag published papers that are under review after serious concerns are raised, failure to respond in a timely fashion when serious concerns are raised about a published paper, positive publication bias, …) have spawned the open access movement and also Sci-Hub. When you consider that governments rely on bibliometric data such as number of papers published and number of papers published in high impact journals (such as one of the ‘big three’), it’s clear there’s a great deal at stake.

Other Sci-Hub pieces here

My last piece about Sci-Hub was a February 25, 2016 posting titled,’ Using copyright to shut down easy access to scientific research‘ featuring some of the discussion around Elsevier and its legal suite against Sci-Hub.

Highlighting the 2011 Dance Your Ph.D. contest

Science magazine (published by the American Association for the Advancement of Science [AAAS]) has been holding a Dance Your PhD contest since 2008* (as best I can determine from a Sept. 17, 2010 posting by Katherine for SciFri). In any case, this year they received a record number of entries (from an Oct. 14, 2011 posting by John Bohannon on Science Now),

Have you ever wondered what nanotube chemistry might look like as a dance? Or fruit fly sex? Or protein x-ray crystallography? Look no further. As part of the 2011 Dance Your Ph.D. contest, scientists who study those phenomena and more have converted their research into dance videos for your enjoyment and edification. And today the 16 finalists of this annual contest are revealed below.

A record 55 dances were created for this year’s contest, submitted by scientists around the globe, from the United States and Canada to Europe, India, and Australia. As the contest rules state, each dance must be based on the scientist’s own Ph.D. research thesis, and that scientist must participate in the dance. For many of the graduate students who danced, the research they depicted is still ongoing. For some of the older contestants, the project is a distant, perhaps harrowing memory from their early days in science. The dances are divided into four categories based on subject: physics, chemistry, biology, and social science. (The criteria for those categories are explained here.)

One of this year’s finalists is from the DeRosa lab at Carleton University in Ottawa, Canada. Titled, “DNA Aptamers as a Tool for Studying Mental Health Disease.” Erin McConnell and her troop are featured in the video below,

DNA Aptamers as a Tool for Studying Mental Health Disease from Erin McConnell on Vimeo.

I haven’t had time to review the other finalists but given this one, I can hardly wait.

The DeRosa lab also had a finalist in last year’s Dance Your PhD contest. It’s not the only reason I contacted the lab’s leader, Maria DeRosa but it did add a piquant flavour to my interview with her, which I will be posting tomorrow (Oct. 25, 2011).

*ETA Oct 24, 2011 1500 hours: There is an Oct. 18, 2011 article by Bob Weber for the Globe and Mail newspaper about the Canadian finalists in the 2011 Dance Your PhD contest. The contest was informally created in 2007 according to its originator John Bohannon.