Corruption, Data Fabrication, Data Falsification, Joshua L. Cherry, Joshua L. Cherry NIH, Meta-Research, Misconduct, Post publication peer review, Post Publication Peer Review Scam, Research Integrity, Research misconduct, Science reproducibility, Science Transparency, Scientific corruption

Reproducibility crisis, sure, but the real crisis is who handles the crisis

The New York Times wants to make us aware there is a reproducibility crisis in science. This is hardly news at all. There surely is a problem and has been there ever since science began to be run like a business, with its system of gratification and punishment, with the explosion in the number of practitioners and the number and size of professional journals, the pressure to excel, the emphasis on quantifying the impact, the system of extramural funding, etc. Take any under-regulated activity, create a system of gratification and you have a problem. It is called human nature.

The real challenge for science today is who is handling the perceived crisis. The science establishment got caught off guard on this one. As it turns out, the ones now handling the crisis are precisely those who installed the perception that there is a crisis in the first place. These are, perhaps with a few exceptions, angry people, science drop-outs and losers who found that science is just too difficult for them. The real problem is that the perception of the crisis has created a void in science governance, i. e. who is going to deal with the problem. Nowadays we have journals of scientific integrity (incredibly boring), world meetings on scientific integrity, not to mention blogs, etc. These are fora designed to channel the voice of those engaged in this second-rate activity.

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Adam Marcus, Anonymous Peer Review, Blog, Character Assassination, Civil Death, Clare Francis, Defamation, Defamation lawsuit, Donald Trump, Expression of concern, Ivan Oransky, John Ioannidis, Joshua Cherry, Joshua L. Cherry, Joshua L. Cherry NIH, Post publication peer review, Post Publication Peer Review Scam, Reporting Retractions, Research Integrity, Retraction Watch, Science, Science blogs, Science Journalism, Science Transparency, Scientific corruption, US President

Anonymous peer review is fine, while anonymous post-publication review is not

When a scientist submits a paper for publication to a journal, he entrusts the journal editor with the task of finding peers would be able to review the paper and are knowledgeable enough to assess its scientific merit. The names of the reviewers are typically concealed to the author. The intent is to grant the reviewer complete freedom in his candid assessment without fear of retaliation. The system is imperfect, very much so, but during the last three centuries scientists have not managed to come up with anything better.

Post-publication peer review (PPPR), on the other hand, cannot be said to be imperfect. It is not even wrong. It is a grotesque aberration. PPPR is usually anonymous but in this case we have absolutely no assurance that the reviewer of the paper is a peer of the author, that is, someone capable of passing serious judgment, or rather someone with an ax to grind launching his or her personal attack. There is simply no editor that arbitrates PPPR, just reporters or science outsiders, like Ivan Oransky, who typically know nothing of the scientific subject of the paper and who merely reproduce a note in a journal or a piece of gossip or an opinion without adding any value. The consequences of this lack of leadership are dire for science: about 90% of the attacks launched by Oransky’s blog Retraction Watch under the pseudonym Clare Francis are either false or lacking merit, even if they manage to elicit an “expression of concern” (an illegality stigmatizing a person presumed innocent unless proven guilty). If US president Donald Trump branded reporters as a pathetic dishonest bunch, just imagine what he would have to say about blogs like Retraction Watch, where the founding reporters usually know nothing about the science related to their mini-scandals.

 

Oransky

This atmosphere of dishonesty provides a fertile soil for PPPR, where a few snipers like Joshua L. Cherry (NIH/NCBI?) strive. As readers may recall, Joshua L. Cherry has been identified by Science Transparency. Cherry is truly obsessed (read Cherry’s exchange with Prof. John Ioannidis), but unfortunately not with producing good science. When he launches personal attacks, Cherry disguises under multiple pseudonyms and e-mails, he cowardly shoots from the shadows, yet his style remains unmistakable: He obsessively insists in performing statistical analysis of large datasets with no scientific understanding of the data, or obsessively tries to reproduce data in a field he knows nothing about, failing miserably. Unfortunately, Joshua L. Cherry is the kind of byproduct that Retraction Watch and other such blogs generate. Were it not for the lack of leadership in PPPR, Cherry would have probably remained a scientist perhaps not incapable of generating interesting ideas. Yet, like many at Retraction Watch, he got trapped in futile battles against windmills.

As the Romans used to say: video meliora proboque, deteriora sequor ( I see the best and verify it, but I follow the worst). Tragic, tragic…

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Adam Marcus, Anonymous Commenter, Character Assassination, Civil Death, Clare Francis, Defamation, Defamation lawsuit, Fake Peer Review, Fazlul Sarkar, First Amendment to US Constitution, Ivan Oransky, Michigan Court of Appeals, Post publication peer review, PubPeer, PubPeer lawsuit, Reporting Retractions, Reporting Science Retractions, Reputation Damage, Research Integrity, Research misconduct, Retraction Watch, Retractions, Science Transparency, Scientific Misconduct, Wayne State University

First Amendment Abuse: Time to Sue Post Publication Reviewers for False Accusations

On Tuesday October 4 at 10AM, a Michigan Court in Detroit conducted a hearing on case 326691 “Fazlul Sarkar vs John Doe”. As you may recall from our coverage at Science Transparency, Prof. Sarkar is a scientist anonymously accused of misconduct through a blog named PubPeer. Whether his data is valid or invalid is something we are not in a position to evaluate or debate. The focus here is the modus operandi of his accusers. The accusations had adverse consequences for his career and so Dr. Sarkar sued PubPeer in Court. The Court requested that the identity of only one of the anonymous accusers be revealed. This has not yet happened. All we know is that the accuser or accusers whose identity is sought by the Court hid under the pseudonym Clare Francis to launch the attacks on Fazlul Sarkar in what constitutes a flagrant abuse of First Amendment rights. The lawyers for the defendants argued that the Constitutional rights bestowed by the First Amendment guarantee the impunity of their clients. That is wrong, very wrong. And whose peers are PubPeers anyway?

To discuss the venal Clare Francis, we need to briefly focus on the blog Retraction Watch (the two are intimately related). This blog is run by two journalists, Ivan Oransky and Adam Marcus. Odd as it sounds, these non-scientists and the anonymous contributors to the blog claim they seek “to increase the transparency of the retraction process in science” (sic), which is an oxymoron. Initially, the founders of Retraction Watch worried they would not get enough stories to cover. So, right around the time the blog came into existence in August 2010, anonymous whistleblowers, including Clare Francis, also surfaced and relentlessly accused scientists of misconduct, allegedly in connivance with Retraction Watch.  The blog harassed, scorned and pilloried anyone immediately after the anonymous whistleblowers managed to elicit some reaction from the journals, be it an expression of concern or a retraction. Obviously, Clare Francis or the cowards that hid in anonymity immediately informed Retraction Watch (or… yes, you are right). The attack then escalated as other journals were contacted once the accusers gained their short-lived credibility with the help of Retraction Watch, and their attacks then spiraled into full defamation cycles.

This seemed like quite an effective strategy to boost the blog, particularly since Clare Francis and other nobodies have been aggressively accusing scientists of fraud and plagiarism. If the anonymous accusers were successful in eliciting damning reactions from the journal editors, Retraction Watch would get a juicy story and a chance to pillory the incriminated scientists. On the other hand, if the cowards were not successful or the accusation proved to be false, there would be no consequence for them or for Retraction Watch since the journals typically do not inform the public or institutions that they have received a false accusation.

The ungainly posts at Retraction Watch elicited by Clare Francis actions contributed to build up a poisonous atmosphere best reflected in Ivan Oransky’s retort to a Nature editorial on retractions. Nature’s cautious reflections contrast starkly with Oransky’s views on the need for immediate condemnation illustrated by the following passage:

“We would argue that journals like Nature actually have a tremendous amount of power. If Nature thinks that they “have neither the authority nor the means to police authors or their institutions,” the editors should sit down with Anesthesia & Analgesia editor in chief Steven Shafer, who gathered a consortium of journal editors that held institutions’ feet to the fire and led to retractions in the Joachim Boldt and Yoshitaka Fujii cases. One can only imagine how quickly a dean would return a call from Nature.”

After this rant, Oransky charged again:

“And why not issue an expression of concern about papers during those years while it’s being investigated? How does Nature justify, for example, leaving the dance symmetry paper in the literature for for five years after authors requested a retraction? Unless, of course, you’re worried about losing those citations, the first two years of which will count toward your impact factor.”

Motivated by recent reports on harassment to scientists and by these troubling views, Science Transparency decided to investigate the matter further. We sought to find out what proportion of accusations by Clare Francis or the cowards operating anonymously allegedly on behalf of the Clare Francis/ Retraction Watch machine had any merit to the point that they would eventually result in retraction. Although editors had not been diligent in collecting statistics, they all pointed to a figure slightly lower than 10%.

In regards to those enduring false accusations of misconduct by Retraction Watch, Paul S. Thaler, one of the most successful lawyer in the field, had this to say:

The first thing to remember is that the federal regulations, as well as the internal policies of most institutions, protect the confidentiality of respondents in research misconduct matters.  Thus, as a matter of federal law, institutions are prohibited from disclosing the identity of an accused scientist, except on a “need to know” basis, for example, to a member of the investigation committee, unless and until a finding of research misconduct is made.  These proceedings are not public as court is in criminal and civil disputes.  It is more comparable to proceedings against other professionals, such as lawyers, who are governed by their licensing organization.  Privacy in these matters is critically important as there is no public need to, or right to know, about professionals simply accused of wrongdoing.  What the public has a right to know about is a professional who has been found responsible for wrongdoing.  At that point, the public is alerted.  But because a professional’s reputation is so important to his or her career, the specter of an accusation can permanently stain that reputation and frequently the accusation is not well founded.  So the confidentiality of the process allows a full examination before the public is made aware.  We certainly do want to know about those scientists who have actually done something wrong that impacts science, but we do not, and should not, be concerned with those who are good scientists but caught up in a sometimes very political, internal dispute.

These remarks by attorney Paul S. Thaler are very much in line with the law (42 C.F.R. § 93.108(b) (2005)), as noted by Nicholas Roumel, the lawyer of plaintiff Dr. Sarkar:

“Because the consequences of a research misconduct proceeding can be dire, the [federal] regulations impose conditions of strict confidentiality on allegations of research misconduct. As section 93.108 of the regulations states: “Disclosure of the identity of respondents and complainants in research misconduct proceedings is limited, to the extent possible, to those who need to know, consistent with a thorough, competent, objective and fair research misconduct proceeding, and as allowed by law.” 42 C.F.R. § 93.108(a) (2005). Disclosure of records or other evidence from which research subjects might be identified is also limited to “those who have a need to know to carry out a research misconduct proceeding.” 42 C.F.R. § 93.108(b) (2005).” [Mauvais-Jarvis v. Wong, 2013 IL App (1st) 120070 (Ill. App. Ct. 1st Dist. 2013)]

It is our expectation that the scientists that have been wrongly accused of wrongdoing and pilloried by Retraction Watch, or by the cowards hiding behind pseudonyms, will now sue those responsible in Court. The writer of this piece may be contacted (weishilaurameng@gmail.com) to help coordinate some of the effort.

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AAAS, Blog, Corruption, Data Falsification, Due process, Internet crank, Marcia McNutt, Mass hysteria, Open research, Post publication peer review, Research Integrity, Retraction Watch, Science, Science blogs, Science Magazine, Science Transparency, Scientific Crisis, Scientific Reproducibility, Scientific Research, Transparency and Openness

TOP: How Science magazine plans to deal with the intrusion of social media

Not long ago Science Editor Marcia McNutt published an appalling editorial entitled “Due process in the twitter age“, where she claimed that social media created an anxiety and added a sense of urgency to the post-publication peer review (PPPR) of reported scientific research. In a post at Science Transparency, we swiftly retorted that if the scientific establishment kept paying attention to blogs like Retraction Watch to conduct their business, they will only have themselves to blame for the current crisis. In our post we felt compelled to quote a Londoner from the Daily Mail (UK) who described the intrusion of social media in the most eloquent terms:

Social Media has turned us all into the baying masses of the medieval witch hunts, with no mediators of our hysterical views, and with the loudest, most ignorant and angry up at the front with their burning tweeting torches.

It would seem that Science magazine has decided to review their own position regarding how they intend to deal with the piracy of PPPR by social media. Marcia McNutt now claims that Science magazine will spearhead the implementation of TOP (Transparency and Openness Promotion), a set of new standards of transparency and reproducibility for the publication of scientific research. This initiative is inspired by the policy forum piece “Promoting an Open Research Culture” published in Science nearly an year ago. In fact, at Science Transparency we argued in support of this policy.

A Friday Evening Discourse at the Royal Institution; Sir James Dewar on Liquid Hydrogen, 1904 (oil on canvas) by Brooks, Henry Jamyn (1865-1925); The Royal Institution, London, UK.

A Friday Evening Discourse at the Royal Institution; Sir James Dewar on Liquid Hydrogen, 1904 (oil on canvas) by Brooks, Henry Jamyn (1865-1925); The Royal Institution, London, UK.

Transparency, availability of raw data, and full disclosure of all tools required by a person skilled in the art to reproduce the work is surely all that is needed to ensure the validity of reported research. This is true today as it was three centuries ago, when scientists were asked to perform their experiments in front of an audience at the Royal Institution. At Science Transparency we welcome the implementation of these TOP protocols as the best route to do away with corruption in science and to end the current hysteria promoted by social media in regards to the reproducibility crisis, real or perceived.

 

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AAAS, Argentina, Ariel Fernandez, Ariel Fernandez Research, Ariel Fernandez Stigliano, Clare Francis, Corruption, 阿列尔·费尔南德斯, Hasselmann Professor at Rice University, Marcia McNutt, Research Integrity, Retraction Watch, Rice University, Science, Science Magazine, Science reproducibility, Science Transparency, Scientific corruption, Scientific Integrity, Scientific Reproducibility, Scientific Research, Weishi Meng on Ariel Fernandez

On “Promoting an Open Research Culture”, Policy Forum, Science Magazine

On 26 June 2015, Science magazine published an article in its section “Policy Forum” entitled “Promoting an Open Research Culture”  (B. A. Nosek et al. Science, Vol. 348, pp. 1422-1425, DOI: 10.1126/science.aab2374). The article and two related pieces (“Self-correction in science at work”, and “Solving reproducibility“) published in the same issue seem to have been inspired by the perception that there is an irreproducibility crisis affecting science. In this regard, this is what Science Transparency has to say:

There is a perceived or real crisis over the reproducibility and transparency of scientific reporting. This crisis is surely being mismanaged by scientists, and they have only themselves to blame. Scientific pursuit requires a highly specialized training, and consequently, so does the assessment of the validity of reported science. Yet, while scientists figure out how to deal with the current crisis, they are allowing journalists like Ivan Oransky (named Science’s Garbage Man by the Swiss Radio and Television), defamation rings, and anonymous nobodies to tell them what to do. This is especially apparent in certain journals that keep listening to Clare Francis, Retraction Watchers or some of the pubpeers, who are in fact nobody’s peers. This nonsense where anyone says whatever they want and pours their anger on the internet, only fuels the current hysteria over fake science. More on this problem has been previously covered in Science Transparency.

As usual, Prof. Ariel Fernandez (阿列尔·费尔南德斯), the discoverer of the dehydron (脱水元), is on the mark in regards to this issue, and his pronouncement featured in Science is reproduced below in accord with Terms and Conditions on User Submissions to Science.

 

Dr. Ariel Fernandez

Dr. Ariel Fernandez . 阿列尔·费尔南德斯

Some journalists and some science outsiders have installed the belief that science is in the midst of a reproducibility crisis. These people are being listened to, at least by some editors, while they feverishly advocate for higher standards of transparency in regards to the way in which scientists conduct and report their findings. The underlying misconception that led to this delusional thinking may well end up sliding into hysteria if scientists keep taking advice from outsiders on how to conduct their business. The misconception sprouts from the odd notion that scientific publications are meant to report monolithic truths that must withstand the acid test of time. Nothing further from the truth, and while scientists comply and try to raise the bar on transparency and accountability, they better take steps to debunk the myth that research papers distill anything other than provisional assertions subject to endless revision.

Much of the science reported is a-priori likely and expected to be faulty merely on statistical grounds. John Ioannidis, a professor of medicine at Stanford University, wrote in 2005 a paper in the journal PLoS Medicine entitled “Why most published research findings are false” (http://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.00…) where, using statistical arguments, he estimated that the likelihood that a scientific paper contains false results is nearly 50%. His analysis reveals that under a great diversity of conditions, most scientific findings are likely to simply represent “measures of prevailing biases”. This statistical study was conducted with the utmost rigor and prompts us scientists to regard research reports with lower expectations, more in the context of a progression of provisional attempts at attaining an independent pristine truth. And please, please, let us focus on running our business ourselves, or we will have no one else to blame for the current crisis, be it real or delusional.

Dr. Ariel Fernandez Stigliano is the former Karl F. Hasselmann Professor of Bioengineering at Rice University (Follow Ariel Fernandez on Twitter).

阿列尔·费尔南德斯(Ariel Fernandez,出生名 阿列尔·费尔南德斯·斯提格里亚诺, 出生于1957年4月18日)是一位阿根廷美国双重国籍的物理化学家[1],1984年在耶鲁大学获化学物理专业博士学位,曾在马克思-普朗克研究所在诺奖得主Manfred Eigen和Robert Huber的指导下从事博士后研究,后在美国莱斯大学任Karl F. Hasselmann讲座讲授,期间曾指导来自两名中国的留学生张曦陈建平的博士学位论文,2011年从莱斯大学退休后开始在瑞士的巴塞尔学院继续从事研究工作,同时创建咨询公司Ariel Fernandez ConsultancyAF Innovation为企业提供咨询服务。

职业生涯

阿列尔•费尔南德斯多个领域的顶级学术期刊上发表文章,包括:代数、动力系统理论、统计力学、化学物理、界面现象、药物设计、癌症治疗和结构生物学视角下的分子进化。他的部分发表成果被收录在Google Scholar CitationsResearchGate。他曾在国际重要期刊上发表过350篇学术论文,包括:Proceedings of the US National Academy of Sciences, Annual Reviews of Genetics, Nature, Physical Review Letters, Genome Research,其科研成果曾被 Nature, Nature Reviews Drug Design, Chemistry World (UK Royal Society), Scientific American等著名期刊评述。阿列尔•费尔南德斯著有一部学术著作,持有两个药物治疗方面的专利。

阿列尔•费尔南德斯在药物设计领域的一部分最重要的研究成果属于转化医学。他建立了被称之为dehydron的物理化学模型用于描述蛋白质分子的一种结构奇点,并将此模型用于进行药物特异性筛选从而设计更为安全的药物。基于dehydron理论,阿列尔•费尔南德斯发明了分子工程中的“包裹技术”(wrapping technology)。“包裹技术”让药物设计人员能够根据蛋白质靶点的dehydron分布特点来设计药物,从而达到更好的特异性。“包裹技术”及其应用在阿列尔•费尔南德斯的著作“Transformative Concepts for Drug Design: Target Wrapping”(Springer-Verlag, Berlin, 2010)中有详细描述。

著作

  • “Transformative Concepts for Drug Design: Target Wrapping”, by Ariel Fernandez (ISBN 978-3642117916, Springer-Verlag, Berlin, Heidelberg, 2010).[2]
  • “Biomolecular Interfaces: Interactions, Functions and Drug Design”, by Ariel Fernandez (ISBN-10: 3319168495, ISBN-13: 978-3319168494, Springer; 2015 edition)..[3]

外部链接

 

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阿列尔·费尔南德斯 – Ariel Fernandez biosketch at Baidu Baike

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