August 9, 2014

Some thoughts about the suicide of Yoshiki Sasai - Scientific American ( Doing Good Science )

In the previous post I suggested that it’s a mistake to try to understand scientific activity (including misconduct and culpable mistakes) by focusing on individual scientists, individual choices, and individual responsibility without also considering the larger community of scientists and the social structures it creates and maintains. That post was where I landed after thinking about what was bugging me about the news coverage and discussions about recent suicide of Yoshiki Sasai, deputy director of the Riken Center for Developmental Biology in Kobe, Japan, and coauthor of retracted papers on STAP cells.
I went toward teasing out the larger, unproductive pattern I saw, on the theory that trying a more productive pattern might help scientific communities do better going forward.
But this also means I didn’t say much about my particular response to Sasai’s suicide and the circumstances around it. I’m going to try to do that here, and I’m not going to try to fit every piece of my response into a larger pattern or path forward.
The situation in a nutshell:
Yoshiki Sasai worked with Haruko Obokata at the Riken Center on “stimulus-triggered acquisition of pluripotency”, a method by which exposing normal cells to a stress (like a mild acid) supposedly gave rise to pluripotent stem cells. It’s hard to know how closely they worked together on this; in the papers published on STAP. Obokata was the lead-author and Sasai was a coauthor. It’s worth noting that Obokata was some 20 years younger than Sasai, an up-and-coming researcher. Sasai was a more senior scientist, serving in a leadership position at the Riken Center and as Obokata’s supervisor there.
The papers were published in a high impact journal (Nature) and got quite a lot of attention. But then the findings came into question. Other researchers trying to reproduce the findings that had been reported in the papers couldn’t reproduce them. One of the images in the papers seemed to be a duplicate of another, which was fishy. Nature investigated, Riken investigated, the papers were retracted, Obokata continued to defend the papers and to deny any wrongdoing.
Meanwhile, a Riken investigation committee said “Sasai bore heavy responsibility for not confirming data for the STAP study and for Obokata’s misconduct”. This apparently had a heavy impact on Sasai:
Sasai’s colleagues at Riken said he had been receiving mental counseling since the scandal surrounding papers on STAP, or stimulus-triggered acquisition of pluripotency, cells, which was lead-authored by Obokata, came to light earlier this year.
Kagaya [head of public relations at Riken] added that Sasai was hospitalized for nearly a month in March due to psychological stress related to the scandal, but that he “recovered and had not been hospitalized since.”
Finally, Sasai hanged himself in a Riken stairwell. One of the notes he left, addressed to Obokata, urged her to reproduce the STAP findings.
So, what is my response to all this?
I think it’s good when scientists take their responsibilities seriously, including the responsibility to provide good advice to junior colleagues.
I also think it’s good when scientists can recognize the limits. You can give very, very good advice — and explain with great clarity why it’s good advice — but the person you’re giving it to may still choose to do something else. It can’t be your responsibility to control another autonomous person’s actions.
I think trust is a crucial part of any supervisory or collaborative relationship. I think it’s good to be able to interact with coworkers with the presumption of trust.
I think it’s awful that it’s so hard to tell which people are not worthy of our trust before they’ve taken advantage of our trust to do something bad.
Finding the right balance between being hands-on and giving space is a challenge in the best of supervisory or mentoring relationships.
Bringing an important discovery with the potential to enable lots of research that could ultimately help lots of people to one’s scientific peers — and to the public — must feel amazing. Even if there weren’t a harsh judgment from the scientific community for retraction, I imagine that having to say, “We jumped the gun on the ‘discovery’ we told you about” would not feel good.
The danger of having your research center’s reputation tied to an important discovery is what happens if that discovery doesn’t hold up, whether because of misconduct or mistakes. And either way, this means that lots of hard work that is important in the building of the shared body of scientific knowledge (and lots of people doing that hard work) can become invisible.
Maybe it would be good to value that work on its own merits, independent of whether anyone else judged it important or newsworthy. Maybe we need to rethink the “big discoveries” and “important discoverers” way of thinking about what makes scientific work or a research center good.
Figuring out why something went wrong is important. When the something that went wrong includes people making choices, though, this always seems to come down to assigning blame. I feel like that’s the wrong place to stop.
I feel like investigations of results that don’t hold up, including investigations that turn up misconduct, should grapple with the question of how can we use what we found here to fix what went wrong? Instead of just asking, “Whose fault was this?” why not ask, “How can we address the harm? What can we learn that will help us avoid this problem in the future?”
I think it’s a problem when a particular work environment makes the people in it anxious all the time.
I think it’s a problem when being careful feels like an unacceptable risk because it slows you down. I think it’s a problem when being first feels more important than being sure.
I think it’s a problem when a mistake of judgment feels so big that you can’t imagine a way forward from it. So disastrous that you can’t learn something useful from it. So monumental that it makes you feel like not existing.
I feel like those of us who are still here have a responsibility to pay attention.
We have a responsibility to think about the impacts of the ways science is done, valued, celebrated, on the human beings who are doing science — and not just on the strongest of those human beings, but also on the ones who may be more vulnerable.
We have a responsibility to try to learn something from this.
I don’t think what we should learn is not to trust, but how to be better at balancing trust and accountability.
I don’t think what we should learn is not to take the responsibilities of oversight seriously, but to put them in perspective and to mobilize more people in the community to provide more support in oversight and mentoring.
Can we learn enough to shift away from the Important New Discovery model of how we value scientific contributions? Can we learn enough that cooperation overtakes competition, that building the new knowledge together and making sure it holds up is more important than slapping someone’s name on it? I don’t know.
I do know that, if the pressures of the scientific career landscape are harder to navigate for people with consciences and easier to navigate for people without consciences, it will be a problem for all of us.

August 8, 2014

Yoshiki Sasai: A tribute to an outstanding scientist - The Guardian

The scientific community was shocked to hear of the death earlier this week of stem cell researcher Yoshiki Sasai, who apparently committed suicide in the wake of a high profile case of scientific fraud at the RIKEN Center for Developmental Biology (CDB) in Kobe, Japan, where he had worked.
Two papers from the RIKEN CDB, co-authored by Sasai and published in the journal Nature in late January, described a simple method for converting mature cells into embryonic stem cells, called stimulus-triggered acquisition of pluripotency (STAP).
It seemed to good to be true – and it was. The findings were challenged and other labs tried but failed to replicate the method. Lead researcher Haruko Obokata was found guilty of scientific misconduct and in July both of the papers were retracted. Sasai himself was cleared of any involvement in the misconduct, but Obokata did the work under his supervision, and so he was criticised for oversights while the papers were being written up.
I had been working on a feature article about Sasai’s own work for Mosaic, and travelled to Japan earlier this year to visit his lab, as part of my reporting for the article. By coincidence, I arrived the day the STAP method hit the news - the Daily Telegraph had accidentally published their story about it too early - and so found myself competing with several film crews for his attention.
As a result, my visit to the lab was cut short, and I spent far less time there than had been planned, but nevertheless I managed to interview Sasai and two of his colleagues and take a look around.
The story was originally scheduled for publication on 26th August, and my editors at the Wellcome Trust have decided to go ahead and publish it on the scheduled date. They felt that it should mention of these tragic events, without letting them overshadow the real focus of the story, and so, apart from several small changes to the main story, and the addition of a brief epilogue, it is unchanged.
I spent very little time with Sasai but he struck me as a very proud man, and the remarkable work being done in his lab gave him every reason to be, so I do not doubt reports that he had felt “deeply ashamed” about the STAP cell papers and the disrepute they had brought to RIKEN, in the weeks leading up to his death. During this time, an independent committee had recommended that the CDB be dismantled, and Sasai’s mental and physical health had by then suffered considerably, so I feel doubly honoured to have visited him there when I did.
Sadly, many of the news stories about his death have focused on the unfortunate circumstances that mired the last few months of his life. We would like to send our deepest condolences to Sasai’s family and friends and hope that that the Mosaic story will serve as a sensitive and timely tribute to the pioneering work of an outstanding scientist.
This is an unedited version of an article I wrote for the Mosaic blog.

August 5, 2014

Researcher’s death shocks Japan - NATURE News

Yoshiki Sasai, one of Japan’s top stem-cell researchers, died this morning (5 August) in an apparent suicide. He was 52.
Sasai, who worked at the RIKEN Center for Developmental Biology (CDB) in Kobe, Japan, was famous for his ability to coax embryonic stem cells to differentiate into other cell types. In 2011, he stunned the world by mimicking an early stage in the development of the eye — a three-dimensional structure called an optical cupin vitro, using embryonic stem cells.
But lately he had been immersed in controversy over two papers, published in Nature in January, that claimed a simple method of creating embryonic-like cells, called stimulus-triggered acquisition of pluripotency (STAP). Various problems in the papers led to a judgement of scientific misconduct for their lead author, Haruko Obokata, also of the CDB. The papers were retracted on 2 July.
Sasai, who was a co-author of both papers, was cleared of any direct involvement in the misconduct. But he has been harshly criticized for failure of oversight in helping to draft the paper. Some critics, often on the basis of unsupported conjecture, alleged deeper involvement of  the CDB. An independent committee recommended on 12 June that the CDB, where Sasai was a vice-director, be dismantled. Sasai had been instrumental in launching the CDB and helped it to develop into one of the world’s premier research centres.
Just after 9 a.m., Sasai was found hanging in a stairwell of the Institute of Biomedical Research and Innovation, next to the CDB, where he also had a laboratory. He was pronounced dead just after 11 a.m., according to reports by Japanese media.  A bag found at the scene contained three letters: one addressed to CDB management, one to his laboratory members and one to Obokata.
In a brief statement released this morning, RIKEN president Ryoji Noyori mourned the death of the pioneering researcher. “The world scientific community has lost an irreplaceable scientist,” he said.

July 15, 2014

Taiwan’s education minister resigns in wake of SAGE peer review scandal - Retraction Watch

Taiwan’s education minister, Chiang Wei-ling, whose name appeared on several of 60 retracted articles by Peter Chen — apparently the architect of a peer review and citation syndicate we were first to report on last week — has resigned over the publishing scandal.
According to the University World News:
Chiang said in a statement that the decision to resign was made to uphold his own reputation and avoid unnecessary disturbance of the work of the education ministry, after the incident ignited a wave of public criticism.
The UWN reports that Chaing’s resignation on Monday came after Taiwan’s premier, Jiang Yi-huah, instructed the Ministry of Science and Technology to investigate the Chen case.
What’s more, according to the UWN — in news that, we humbly submit, hammers home the point of our New York Times op-ed last Friday:
The Ministry of Science said this week that it may have funded the research for 40 of Peter Chen’s questionable papers amounting to some NT$5.08 million (US$169,164), according to Lin Yi-Bing, vice-minister of science and technology.
He said in remarks released last Sunday that if Chen was found to have violated academic ethics, the science ministry would demand a return of any research funds awarded to him and bar him for life from applying for such funding.
The relationship between Chiang and Peter Chen is a bit complicated, but may hinge on the researcher’s twin brother C.W. Chen, the UWN reports.
Five of the 60 papers, written by CW Chen – Peter’s twin brother – bore Chiang’s name as a co-writer but also listed Peter Chen as one of the writers.
Chiang was CW Chen’s former thesis advisor. In a statement issued this week CW Chen acknowledged that the papers in question bore Chiang’s name without Chiang having been informed in advance because they were a continuation of research on subjects related to his thesis. “It was my decision,” CW Chen said.
He said he had also sought the opinion of his twin brother on some of the papers and therefore had listed him as a co-author but had not informed Chiang. His academic advisor and his brother had never met to discuss the papers, CW Chen said.
At an earlier press conference, CW Chen insisted that the minister did not have any links to his brother. Peter Chen and the minister had met on only two occasions, once in 2004 when CW Chen graduated from the doctoral programme at National Central University where the minister was teaching, and at a science forum.

July 10, 2014

Scholarly journal retracts 60 articles, smashes ‘peer review ring’ - The Washington Post

Every now and then a scholarly journal retracts an article because of errors or outright fraud. In academic circles, and sometimes beyond, each retraction is a big deal.
Now comes word of a journal retracting 60 articles at once.
The reason for the mass retraction is mind-blowing: A “peer review and citation ring” was apparently rigging the review process to get articles published.
You’ve heard of prostitution rings, gambling rings and extortion rings. Now there’s a “peer review ring.”
The publication is the Journal of Vibration and Control (JVC). It publishes papers with names like “Hydraulic engine mounts: a survey” and “Reduction of wheel force variations with magnetorheological devices.”
The field of acoustics covered by the journal is highly technical:
Analytical, computational and experimental studies of vibration phenomena and their control. The scope encompasses all linear and nonlinear vibration phenomena and covers topics such as: vibration and control of structures and machinery, signal analysis, aeroelasticity, neural networks, structural control and acoustics, noise and noise control, waves in solids and fluids and shock waves.
JVC is part of the SAGE group of academic publications.
Here’s how it describes its peer review process:
[The journal] operates under a conventional single-blind reviewing policy in which the reviewer’s name is always concealed from the submitting author.
All manuscripts are reviewed initially by one of the Editors and only those papers that meet the scientific and editorial standards of the journal, and fit within the aims and scope of the journal, will be sent for peer review.  Generally, reviews from two independent referees are required.
An announcement from SAGE published July 8 explained what happened, albeit somewhat opaquely.
In 2013, the editor of JVC, Ali H. Nayfeh, became aware of people using “fabricated identities” to manipulate an online system called SAGE Track by which scholars review the work of other scholars prior to publication.
Attention focused on a researcher named Peter Chen of the National Pingtung University of Education (NPUE) in Taiwan and “possibly other authors at this institution.”
After a 14-month investigation, JVC determined the ring involved “aliases” and fake e-mail addresses of reviewers — up to 130 of them — in an apparently successful effort to get friendly reviews of submissions and as many articles published as possible by Chen and his friends. “On at least one occasion, the author Peter Chen reviewed his own paper under one of the aliases he created,” according to the SAGE announcement.
The statement does not explain how something like this happens. Did the ring invent names and say they were scholars? Did they use real names and pretend to be other scholars? Doesn’t anyone check on these things by, say, picking up the phone and calling the reviewer?
In any case, SAGE and Nayfeh confronted Chen to give him an “opportunity to address the accusations of misconduct,” the statement said, but were not satisfied with his responses.
In May, “NPUE informed SAGE and JVC that Peter Chen had resigned from his post on 2 February 2014.”
Each of the 60 retracted articles had at least one author and/or one reviewer “who has been implicated in the peer review” ring, said a separate notice issued by JVC.
Efforts by The Washington Post to locate and contact Chen for comment were unsuccessful.
The whole story is described in a publication called Retraction Watch” under the headline: “SAGE Publications busts ‘peer review and citation ring.’”
“This one,” it said, “deserves a ‘wow.’”
Update: Some additional information from the SAGE statement: “As the SAGE investigation drew to a close, in May 2014 Professor Nayfeh’s retirement was announced and he resigned his position as Editor-in-Chief of JVC….Three senior editors and an additional 27 associate editors with expertise and prestige in the field have been appointed to assist with the day-to-day running of the JVC peer review process. Following Professor Nayfeh’s retirement announcement, the external senior editorial team will be responsible for independent editorial control for JVC.”
Note to readers: Thanks for pointing out my grammatical error. No excuses.
There’s a follow to this story here.

July 3, 2014

Research integrity: Cell-induced stress - NATURE News

As a much-hailed breakthrough in stem-cell science unravelled this year, many have been asking: ‘Where were the safeguards?’
It seemed almost too good to be true — and it was. Two papers1, 2 that offered a major breakthrough in stem-cell biology were retracted on 2 July, mired in a controversy that has damaged the reputation of several Japanese researchers. >>>
Haruko Obokata tearfully faces the media after she was found guilty of misconduct in April.

January 4, 2014

Guest Post: Plagiarism has been left unpunished - Copy, Shake & Paste

This guest post is from Kayhan Kantarlı, a retired professor of physics from the University of Ege in Turkey. He published a first version of the article on his blog on December 10. I edited the article somewhat and am publishing this version here with his permission, as I do not read Turkish and am unable to verify the sources. -- dww >>>

December 7, 2013

Plagiarism has been legalized !

Translated from Gazete soL 
State Council Committee for Administrative Cases in Turkey has ruled that banishment of faculty members who has been involved in plagiarism cases is not based on legislation, in other words, they have legalized plagiarism. 
Especially in the last few years, there has been a rise in plagiarism cases in Turkish Universities. State Council’s verdict, on the other hand, will encourage those who are involved in plagiarism. State Council Committee for Administrative Cases has decided that banishment of faculty members from their universities is unjust. 
Higher Educational Council (YÖK) of Turkey did not waste any time to put the decree in action by issuing a directive to obey the State Council’s decision.
According to the 3rd  paragraph of 11th article in Faculty Members Discipline Bylaw of YÖK’s Legislature, “using other’s work or study as one’s own without any reference” is a basis for banishment of the faculty member from the university or civil service, however, according to a State Council Decision issued in 2012, this deed has been dropped from being a crime.
There is no Legal basis
The 15 month old decision of State Council Committee for Administrative Cases has rendered the crime of plagiarism sanctionless. Council’s Decision, dating September 2012, states that “there are no regulations for punishment of faculty member, which is established by Faculty Member Discipline Bylaw as banishment, in the YÖK Legislature no. 2547 and State Officer Legislature no. 657” the penalty has no legal basis. As a result, Council has ruled that the disgraceful act of plagiarism /scientific rip off is not a crime.
YÖK: Do not punish
Faculty Members Discipline Bylaw was issued according to the YÖK Legislature no. 547, thus, after the decision of State Council Committee for Administrative Cases regarding the legality of the punishment, YÖK did not attempt to remove the legal void by National Education Ministry and Grand Turkish Assembly; furthermore, it has issued an invoice to rectorates. YÖK’s notice petitioned “to act according to the civil jurisdiction in cases initiated for plagiarism charges”. This official notice directly means to do nothing against faculty members that commit plagiarism.
YÖK’s notice has been imparted to corresponding units in 19 November 2013 by Yunus Söylet, Rector of İstanbul University.
Old penalties rendered void 
On the other hand, according to the Council’s rule, bygone penalties given to the faculty members regarding the plagiarism has “rendered void due to legality”. This opened up the channel for all faculty members who have been banished for committing plagiarism to return to their old posts and demand all of the salaries and monetary entitlements.
‘This will encourage plagiarism’
Prof. Dr. Kayhan Kantarlı, a retired faculty member of Ege University of İzmir, Turkey, stated that Council’s rule will encourage those who intend to do plagiarism. Kantarlı invited all authorities to act against the President of Higher Education Council who breached his duty by letting this scandalous thing to happen which will pave the way for collapse of ethical perception. Kantarlı also called attention of legislative bodies to close this legal void immediately.
‘There is no corresponding crime or act’
Lawsuit was filed by Kamil Can Bulut who was a faculty member at Department of Literature in Ege University, was found to plagiarize in one of his books. In the decree of State Council Committee for Administrative Cases it has been stated that “there is also no corresponding penalty that requires banishment of the faculty member of the university in Legislature no. 2547. In this case, since there are no legal decrees that require the penalty of banishment and there is no legal basis for the act that require this penalty, there is no illegality according to the regulations that is the case before the court and the act that is based on this regulation.” Decision has passed with unanimity of 15 members of the Council except Halide Ayfer Özdemir, including the vice chairman.

December 1, 2013

Peer Review, Impact Factors, and the Decline of Science -Copy Shake and Paste

The Economist reported on October 19, 2013 (pp. 21-24) that there is "Trouble at the lab". Indeed. And trouble has been brewing for quite some time without a single identifiable culprit or an easy way to solve the problem. This problem is concerned with predatory publishing, irreproducibility of scientific results, and the use of quantitative data as an attempt to judge quality.

University administrations, search and tenure committees, governments, funding associations, and other bodies need some way of judging people they don't know in order to decide whether to offer them jobs or promotions or funding. This has often boiled down to counting the number of publications, or the impact factors of the journals in which their articles are published. Coupled with the crisis in publishing, with the subscription price of subscription journals exploding, an unhealthy mix is brewing.

Predatory publishers promise quick publication in good-sounding "international" journals, using the Open Access "golden road" to extract fees from authors. They promise peer review, but if at all they only seem to look at the formatting. Established publishers trying to keep up their profits have incorporated more and more journals into their portfolios without keeping a watchful eye on quality control.

Enter John Bohannon. In October 2013 Bohannon published an article in Science, Who's Afraid of Peer Review? He details a sting operation that he conducted between January and August 2013, submitting 304 papers with extremely obvious deficiencies to journals that he chose both from Lund University's "Directory of Open Access Journals" as well as from Jeffrey Beall's list of predatory publishers.

Bohannon has put his data online, showing that 82% of the journals chosen from Beale's list accepted the fabricated paper, as well as 45% of the journals on the DOAJ list. Predictably, DOAJ is not amused and accusing Bohannon of, among other things, racism because he chose African-sounding names for the authors (1 - 2).

In August 2013, Nature journalist Richard van Noorden detailed a scheme by publishers called "citation stacking" in which a group of publishers collude to quote extensively from each other's journals in order to avoid being sanctioned for coercive citation. This activity was described in Science in 2012 by Allen W. Wilhite and Eric A. Fong as a process by which authors are instructed to quote from a publisher's own journals in order to increase the so-called impact factor. van Noorden's article focused on a group of Brazilian journals, so he, too, was accused of racism. This is unfortunate, as it detracts from a very serious problem.

We find ourselves today in a rapidly expanding world with scientific research being conducted in many different places and much money being invested in producing results. People need publications, and have little time for doing peer review, a job that is generally not paid for and performed as a service to the community. Universities in countries without a tradition of rigorous scientific practice have researchers who need publications, and there are people out to make money any way they can. Researchers competing for scarce jobs in countries that are trying to spend less on science and education than they have in the past are also sometimes tempted to follow the path of less resistance and publish with such journals. And some are not aware that they have just selected a publication that sounds like one that is well respected, as Beall has noted.

I don't have a solution to offer, other than boycotting the use of quantitative data about publications and getting people to be aware of the scams going on. We need to get serious about peer review, embracing such concepts as open access pre- and post-publication peer review in order to get more rigor into the publication process. I realize that people have been complaining about the decline of science since at least Charles Babbage (Reflections on the Decline of Science in England, And on Some of Its Causes, 1830). But we are in grave danger of letting bad science get the upper hand.

And what happens to those who try and point out some of the dicier parts of science? Nature just published another article by van Noorden, together with Ed Yong and Heidi Ledford, Research ethics:  3 ways to blow the whistle.