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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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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Retraction Watch, Clare Francis, the Mockery of the First Amendment and a Recent Court Order

The blog Retraction Watch plays a game both dangerous and revolting. By making a travesty of the First Amendment to the US Constitution, Retraction Watch has allegedly managed to generate and propagate slander while protecting the anonymity of their tipsters. A recent Court order indicates that this allegedly venal practice will eventually come to an end, possibly making Retraction Watch the target of massive lawsuits.

On the surface, Retraction Watch appears to be a broadcaster of post publication “peer reviews” (whose peers?) that prompt a reaction in scientific journals, motivating the publication of a note, expression of concern or even a retraction notice in case of invalid data. In reality, Retraction Watch is served by what allegedly constitutes a serial defamation ring. The ring often (not always) feeds on comments from angry people with no verifiable credentials, who are typically not the peers of any reputable scientist. These people hide in anonymity to launch their attacks. This modus operandi is of course the despicable way of cowards and is usually fuelled by sheer career frustration: “I am failing, so those who succeed must be phonies, etc.” The angry individuals publish their comments in tributary blogs like PubPeer or simply convey their “critiques” to Ivan Oransky or Adam Marcus, founders of Retraction Watch. These comments are then conveyed to the journals usually in coercive defamatory terms and often under the pseudonym Clare Francis. Clare Francis, or others serving directly the interests of Retraction Watch, allegedly threaten and intimidate the journals and institutions and use words highly reminiscent of Oransky’s style, such as: “many think of this as scientific misconduct”. This wording is naively intended to avoid the defamation lawsuit (not for long). Once Clare Francis or others allegedly on behalf of Oransky manage to elicit a reaction from the journal or institution allegedly under duress, Retraction Watch immediately jumps in and broadcasts the published note, expression of concern or retraction usually in defamatory terms. This leaves us wondering why Retraction Watch founder Ivan Oransky has been named Science’s Garbage Man by the Swiss Radio and Television (Muellsammler der Wissenschaft).

Oransky

Ivan Oransky portrayed at Yale Medicine.

As they allegedly intimidate journals and institutions, Clare Francis or Oransky, or a person on his behalf, brings up PubPeer “investigations”, as if PubPeer were reporting investigations carried out by scientific peers. This in itself constitutes a gross distortion of reality. Thus, the Oransky clique allegedly intimidates the journals within a defamatory context that includes wording like “many people believe this constitutes misconduct”. Not surprisingly, many of these accusations prove to be incorrect, as PubPeer contributors are usually not scientific peers. Yet, a damage is done to the scientist reputation as Retraction Watch hastily publishes the journal reaction it has allegedly elicited through intimidation and coercion.

Most of the time (not always), the Retraction Watch tipsters only have a vested interest in harming the person they target. A case in point is Joshua L. Cherry, a presumed NIH software contractor embarked in a crusade against a specific researcher. The dishonesty of these tipsters is evidenced by the fact that they operate hiding in anonymity as they seek to destroy careers by feeding into Oransky’s blog. Joshua Cherry and others go even further: They seek institutional involvement and immediately inform Retraction Watch on any reaction. Oransky or his cohort of angry people (including the tipsters) then allegedly coerce the journals and institutions seeking to elicit a quick reaction which Oransky (Clare Francis, etc.) demands must be published. Once this is done, the note (expression of concern, correction request, etc.) is immediately disseminated to the general public by the blog Retraction Watch sometimes within a libelous context. This is done even before the results of a formal investigation are known or the validity of the accusations is scientifically established. The alleged slandering is serially committed by Retraction Watch and its associated ring and pipelined along the PubPeer – Oransky axis.

Recent developments, specifically, a court order, suggest that this alleged venality may soon come to an end, with dire consequences for Retraction Watch and its cohort. Prof. Fazlul Sarkar is a professor at Wayne State University who may have lost a generous job offer because of scathing comments about his research posted on PubPeer and channeled into the Retraction Watch defamatory apparatus. His attorney has asked a judge to reconsider last month’s decision not to release information about the site’s anonymous commenters. The brief introducing that motion identifies the PubPeer commenter with the pseudonym Clare Francis.

On March 19, a Michigan court ruled that PubPeer had to disclose identifying information about the PubPeer commenter, identified as the author of the second of the comments below:

Unregistered Submission:
(June 18th, 2014 4:51pm UTC)
Has anybody reported this to the institute?

Unregistered Submission:
(June 18th, 2014 5:43pm UTC)
Yes, in September and October 2013 the president of Wayne State University was informed several times. The Secretary to the Board of Governors wrote back on the 11th of November 2013:  “Thank you for your e-mail, which I have forwarded to the appropriate individual within Wayne State University. As you are aware, scientific misconduct investigations are by their nature confidential, and Wayne would not be able to comment on whether an inquiry into your allegations is under way, or if so, what its status might be. Thank you for bringing this matter to our attention”

In a supplemental brief filed on April 9, Sarkar’s attorney Nicholas Roumel informs the court that Wayne State provided the email exchanges quoted in the comment, and that they were between “Clare Francis” and Julie H. Miller, secretary to Wayne State’s Board of Governors. Thus, the court learned that on November 10, 2013 Clare Francis wrote:

“I am writing to you about multiple scientific concerns about the published work of Fazlul H Sarkar which have been aired on Pubpeer.”

“You can find the entries on Pubpeer here: …”

“Many of the entries mention things which amount to what many think of as scientific misconduct….”

Following the supplemental brief and after spotting the libel, the court ruled that PubPeer must provide the IP for Clare Francis to Roumel.

The blog Retraction Watch offered PubPeer’s attorneys the opportunity to comment, and they had this to say:

We are deeply troubled that a scientist who exercised his or her right to anonymously report anomalies in scientific research is being threatened with possible liability. The First Amendment protects the right to speak anonymously precisely so that, in circumstances like this one, individuals can report on matters of public interest without fear of retribution. This case is especially troubling because it threatens to weaken the foundation of scientific research, which relies on honest feedback and criticism from one’s peers.”

No kidding! This statement cannot pass even the most basic scrutiny! Let’s see:

a)      Where is the proof that Clare Francis is the pseudonym for “a scientist who exercised his or her right to anonymously report anomalies in scientific research”? Clare Francis may just be the pseudonym for an angry person who hates Fazlul Sarkar or someone with a vested interest in his downfall (like the Retraction Watchers). There is not a shred of evidence that the reported anomalies were detected by a competent scholar, that they are scientifically sound or that they were generated by anybody even coming close to be named a peer of Fazlul Sarkar.

b)      Where is the proof that Clare Francis is reporting on a matter of public interest? It could just be that Clare Francis is simply the pseudonym of someone who hates Sarkar, envies his success, or has a vested interest in his downfall (to increase the readership of his blog), and this is surely a personal matter, not a matter of public interest.

c)       How do we know the slanderer of Prof. Sarkar is being honest? He is most likely dishonest. In fact, everything suggests the latter to be the case: honest people who do the right thing do not usually hide, they don’t need to, at least in countries under the rule of law like the US.

d)      How do the PubPeer attorneys know that Sarkar’s attacker is one of Sarkar’s peers? In fact, how do they know anybody at PubPeer is actually a peer of the scientists they are attacking? Clare Francis is not revealing his scientific credentials! Strikingly some journals took him seriously and a few still do.

e)      Given that the person using Clare Francis pseudonym is most likely dishonest, and not a scientific peer of Dr. Sarkar, we obviously cannot assert that the case weakens the foundation of scientific research in any way.

We remain hopeful that the alleged serial defamation ring and venal operation described in this post will soon be brought to justice. With the help of the journals that have been contacted by Clare Francis (or others serving the interests of Retraction Watch) we would be in an ideal position to recruit the necessary elements for formidable lawsuits that will bring to a halt this abominable practice.

RECENT COMMENT

LIPING XIE says:

First and foremost, who says PubPeer contributors are scientific peers of anyone??? Nobody has verified whether they really are!!! This is complete nonsense and the way Retraction Watch harvests and uses the PubPeer feedback is absolutely revolting!

UPDATE FROM MAY 24, 2015

It is odd that we continue to have this discussion on these nobodies taking shots at people doing research, Cardiff University in the UK already led the way and did the right thing. Its policy now in place as described here enables automatic dismissal of all the incognito attacks from PubPeer, Clare Francis, Ivan Oransky and their associated haters!

 

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Retraction Watch: Money Can’t Buy You Class

It is hard to justify the sheer existence of Retraction Watch, a blog run by people with no visible credentials in the sciences who are seeking notoriety in a context where anybody is basically allowed to say anything. The information that Retraction Watch provides is redundant at best. And this redundancy will now be multiplied, we are being told, by a “repository of retractions”, an idiocy akin to a “repository of obituaries”. But the worst side of Retraction Watch is its tendency to ruthlessly prey on career mistakes to destroy people and to do it in the most undignified manner.

The most recent illustration of this appalling behavior is the post by Cat Ferguson, the Retraction Watch intern and a figure in the field of retractions, who wrote the masterpiece entitled: Anyone want to hire an economist who retracted 16 papers for fake peer reviews?

   This piece reports on the efforts by Retraction Watch to destroy the career of Khalid Zaman, a Pakistani economist who retracted several papers on account of allegedly fake peer reviews. Retraction Watch was not satisfied with merely reporting on the case, they went after his life and career, investigating whether he had filed job applications (in Pakistan!), and even got hold of one such application (we of course cannot verify this). This is none of your business, Retraction Watch!

Zaman may have committed fraud, but perhaps his results are still valid and could withstand a real peer review upon resubmission. This is, of course, a futile reflection, Retraction Watch never takes the high ground but instead keeps indulging in the petty smearing of scientists’ reputations. Here is another example of their reported efforts to destroy people from the pen of Adam Marcus and Ivan Oransky, the Retraction Watch founders, from their contribution to The Scientist (the last sentence is particularly revolting and much resembling the vilification of Khalid Zaman):

“…we recommend reading about the case of Michael W. Miller, who faked data on his federal grant applications and had several papers retracted in 2012. This year, however, Miller bounced back, landing a job as, you guessed it, a consultant for grant applications! (He lost that gig after we called his employers to ask if they knew about his past.)”

There are plenty of illustrations of these indignities, where Retraction Watch, not content with having report the case, goes after the person and curtails his/her opportunities to find jobs taking decisive cavalier steps in the most revolting manner imaginable to destroy the person. One is reminded of the case of Diederik Stapel, the Dutch professor who allegedly admitted to fraudulent activity, and was reported by Retraction Watch to have landed on a job in the Netherlands. As expected, the angry commenters poured their vitriol in outrage as they kept vilifying Dr. Stapel, while the blog took all necessary steps to prevent him from getting hired. Again, none of your business, Retraction Watch!

I guess it is a matter of class, some have it, some don’t, and if you, like Retraction Watch, don’t have it, all the money in the world cannot buy it for you.

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Retraction Watch: Toxic Scientific Journalism for the Wild Web

We are often forced to highlight the toxicity of Retraction Watch, a blog that professes to cover scientific mishaps. Retraction Watch has turned into a beacon of junk scientific journalism, fit for the Wild Web. At Retraction Watch there is no publication barrier but there surely is an agenda: anybody says whatever he/she wants and gets published provided that what is said fits the agenda of RW founders Adam Marcus and Ivan Oransky. In Ivan Oransky’s own words, “we hold firm to the notion that the more robust the conversation, the better the science”. Huh? Sure, but the validity of this utterance hinges crucially on what Oransky means by “robust conversation”. I, for one, have never seen a robust conversation leading to the betterment of science at Retraction Watch. Furthermore, I have never seen a conversation at Retraction Watch that is even relevant to science. When I find such utterances by Oransky I ask myself: How can he say this with a straight face? Do we really need to deal with this level of absurdity? I would have hoped not, but I guess we need to. We’ll come back to the “robust conversations” at Retraction Watch in a while.

Oransky
The source of the picture is this article at Yale Medicince.

Ivan Oransky brags about many things, his long list of affiliations always featuring prominently, and he often insists on the large number of hits at Retraction Watch, as if the large number of hits were a measure or indicator of content quality. By that token, “Gangnam Style” would surely surpass Bach’s St. Matthew Passion. We all know that vulgarization of science, and especially of science mishaps, will always sell far better than science itself. That does not make science vulgarization any better than science as a generator of meaning or content. Not surprisingly, Retraction Watch founder Ivan Oransky has been named Science’s Garbage Man (Muellsammler der Wissenschaft) by the Swiss Radio and Television.

Perhaps nowhere is the toxicity of Retraction Watch more apparent than in the words of its own founder Ivan Oransky as he discusses the tragic loss of Japanese scientist Yoshiki Sasai to suicide. Sasai, as we recall, was a major player in the team who worked on the now-discredited STAP stem cell work. By all accounts, Sasai was an honest man but had the misfortune of working with an allegedly dishonest colleague, and his choice of suicide as a form of atonement proved to be one the most tragic turns of science in the Retraction Watch era.

This tragedy has drawn Berkeley biologist Michael Eisen into the debate, as he lost his own father, a notable NIH scientist, to a similar tragic turn. In this case, as in the Sasai case, someone not directly involved in misconduct got the cold shoulder of the scientific community for being associated with an alleged fraudster.

There is hardly any doubt that Retraction Watch, with its undignified opportunistic style of coverage of scientific mishaps, has substantively contributed to this toxic environment. I would not be surprised if the ruthless exposure of the STAP stem cell mishap by Retraction Watch, with its significant traction on the web, contributed in some way to trigger the tragic demise of Yoshiki Sasai. It is obviously up to Sasai’s family and to the incumbent Japanese authorities to take this case to Court if they see fit.

In addressing the accusations that Retraction Watch is poisoning the scientific environment, Ivan Oransky had this to say:

“But we firmly believe that cataloging and probing the symptoms of some of these problems — in our case, that means retractions — is a good way to check the health of transparency in science.
What goes along with that is our belief that a vigorous and open debate is crucial to science. For that reason, we allow our thousands of commenters substantial latitude in their posted opinions.”

Oransky’s idea is, in my opinion, perplexingly stupid. It opens the gates for a flood of nonsense poured into the web with no restraint. Can you imagine bringing anybody into a “vigorous open debate for the benefit of science”? What kind of outcome would you expect from having a bunch of nobodies and angry people opine often anonymously on scientific matters? And who conducts this debate? Ivan Oransky? Adam Marcus? or perhaps the Retraction Watch intern Cat Ferguson? What kind of scientific credentials do these people have to conduct any form of scientific debate? None whatsoever, as far as we can tell.

Along the same crassness, Ivan Oransky carries on:

“We can always do better in our comment moderation. But we hold firm to the notion that the more robust the conversation, the better the science.”

Sure, Mr. Oransky, but the catch here is the competence and intellectual acumen of the people that Retraction Watch allows to be involved in what you call “the robust conversation”! By “robust conversation” do you mean the kind of absurd and often malicious drifting that you and your commenters engage in at Retraction Watch? Contrasting Oransky’s statement with the grotesque reality of Retraction Watch makes me wonder if Oransky is being serious or sardonically factitious. Tragically, I think he really meant what he said, as he repeated the same statement twice in the same post.

The kind of journalism embodied by Retraction Watch, with no publication barriers and with thousands of unqualified people allowed to freely comment on any scientific controversy, is actually very dangerous and very demeaning to science.

RELATED READING:
Ivan Oransky at Yale Medicine.
Sasai’s suicide covered by The Boston Globe
Stem cell work is allegedly fraudulent (The Boston Globe)

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Adam Marcus, Argentina, Ariel Fernandez, Ariel Fernandez Publications, Ariel Fernandez Research, Ariel Fernandez ResearcherID, Buenos Aires, Cat Ferguson, 阿列尔·费尔南德斯, Ivan Oransky, Joshua Cherry, Joshua L. Cherry, Michael Lynch, Nature, Nature Addenda, NCBI, NIH, Peer Review, Post publication peer review, PubMed, Scientific publication, Scientific Research, Swiss Radio and Television, Weishi Meng on Ariel Fernandez

Post Publication: Interview with Dr. Ariel Fernandez on a Nature Paper Controversy (Ten more minutes added on 12/2)

As a glance at his CV reveals, Dr. Ariel Fernandez (阿列尔·费尔南德斯), the discoverer of the dehydron (脱水元), is a very creative physical chemist and mathematician, a key player in the recent biotechnology transformation. His research has been heralded in auspicious terms, as illustrated for example in this review published in Scientific American. The breadth of research accomplishments of Ariel Fernandez, ranging from abstract algebra to drug design is breathtaking and probably unheard of in science (see a linked version of his publication record). In his ResearcherID page, Thomson/Reuters estimated that Ariel Fernandez has published 485 professional articles, book chapters included. His innovative drug designs were enthusiastically received by eminent doctors such as Thomas Force (Vanderbilt University) and were also reported in laudatory terms, as shown for example in this review by legendary Harvard oncologist George Demetri. Quoting Dr. Demetri:

“The first generation of kinase-inhibitory drugs such as imatinib and sunitinib have already provided patients with life-saving therapeutic options, and with tools such as those described by Fernández et al., the future certainly looks bright for constructing ever-better agents that can be combined safely and effectively to manage, and eventually cure, many forms of human cancer”.

Dr. Ariel Fernandez

Dr. Ariel Fernandez

In a recent collaboration with eminent cardiologist Richard L. Moss, Dr. Ariel Fernandez came up with a potential treatment of heart failure by disrupting a myosin association with a myosin-regulatory protein, a novel invention recently awarded the US patent 9,051,387. You may find descriptions of this invention at: US Patent and Trademark Office page, Espacenet page, University of Wisconsin-Madison, Ariel Fernandez Consultancy, Academia.edu, Ariel Fernandez’s professional page.

In spite of this stellar career and in spite of his efforts to fight cancer and heart failure, Dr. Ariel Fernandez is not impervious to slander. In the new era of post publication peer review, where anybody says whatever they like without even revealing his identity or his credentials, Dr. Ariel Fernandez has been the target of libel. In this note, Dr. Ariel Fernandez reflects on post-publication peer review in light of a recent attack by journalist Ivan Oransky, the self-proclaimed champion of scientific transparency, who has been recently named Science’s Garbage Man (Muellsammler der Wissenschaft) by the Swiss Radio and Television. In his post, Oransky mentions a Note that Nature Editors appended as Addendum to a Nature paper by Ariel Fernandez.

oransky fernandez
The source of the picture on the left is this article at Yale Medicince.

WM: Thank you doctor for agreeing to talk to us on such short notice. What was your reaction to the recent post by Ivan Oransky (and Adam Marcus) published in their blog in regards to your Nature paper?

Ariel Fernandez: It is hard for me to understand the motivation for such posts by Ivan Oransky and Adam Marcus and for some of the comments in their blog. The story is thin on reality. It reads like an attack. These people seem angry (they surely sound angry) and probably think they will get some credit for doing what they do. Meanwhile, the science establishment is not taking the needed leadership in regards to post-publication assessment and in regards to fixing the peer review system.

WM: Why do you think Oransky dislikes you?

Ariel Fernandez: I don’t think our paths ever crossed, I don’t even know him. I heard he is a doctor, and that he is smart. There are many wonderful things that a smart doctor can do, what Oransky is doing is not one of them.

WM: Can you tell us what are the news exactly?

Ariel Fernandez: The Addendum published by the Nature Editors on my paper [Ariel Fernandez, Nature 474, pages 502-5 (2011)] exposes a controversy between the two authors of the paper, former author Michael Lynch and me. This is hardly a news item. Lynch and I have a disagreement on the data and what it means. The Nature addendum is appended to the paper at the url:

http://www.nature.com/nature/journal/v474/n7352/full/nature09992.html

I posted my own tutorial on the Nature paper, including the code, raw data and statistical analysis in compliance with the open data mandate. Anybody interested can help clarify the matter if he/she so choses.

WM: How did this problem originate?

Ariel Fernandez: As I recall, in November of 2011, a Joshua Cherry, a sort of contractor (?) at NIH/NCBI first contacted me indicating that he wanted to reproduce my data in the Nature paper. After exchanging dozens of mails, I offered him a tutorial, because I realized he had little or no background in biophysics. He rejected my tutorial and from then on began challenging my papers. Now, why would a person with no background in my field decide to challenge my papers is a mystery to me. This fellow Joshua Cherry is behind the attacks on my work and my person. He seems somewhat obsessed (?) with me for some reason. Now, from what I can see, Cherry has authored some reasonable papers on population dynamics, yet he invests heavily on the downfall of someone working in a field he knows nothing about?

WM: That is odd.

Ariel Fernandez: The most important lesson to be drawn from this incident requires that we all take the high ground and ask ourselves: How should post-publication peer review be conducted? I believe there is only one way which has been the way of science for centuries: If anyone feels the need to challenge a published paper, the person should send the comments to the journal where the original work was published, request that his/her comments be subject to peer review and if they pass peer review, the objections should be published side by side with the response by the original author for everybody to examine and draw conclusions. The rest, including Oransky’s blog, is just noise.

WM: Doctor, I heard rumors that you and I are the same person.

Ariel Fernandez: Well, let’s see. You surely sound quite different from me and I don’t have any Chinese ancestry to speak of…

WM: Thank you doctor, have a good evening.

Ten more minutes on the phone with Dr. Ariel Fernandez (12/2/2014)

07

WM: Did you read the comments at the blog run by Ivan Oransky and Adam Marcus?

Ariel Fernandez: I read a bunch, then it got too silly with the Meng-Fernandez duality and I took my dog for a walk. It made me sad that these people cannot seem to be able to take the high ground on the broad issues at stake.

WM: Yes, they seem to dwell on whether I am a real person or whether you are actually me, or dual realities, or God knows what. Totally immaterial, like asking whether the characters in Plato’s dialogues are real or fake and take away merit if the latter were the case (I prepared that one beforehand, by the way). So, what are the issues at stake?

Ariel Fernandez: As I see it, the only thing worth focusing on is the failure of the peer review system. If the system were water- tight, there would be no need for PPPR [post publication peer review], of course. There are core issues worth focusing on: lobbying, editor courtship, fake reviewers, and cronyism in the peer review system.

WM: Well, so what do we do then?

Ariel Fernandez: Many journals are simply too amateurish to lead in this crisis, and the absence of leadership in times of crisis, often leads to bad things as we all know too well. Opportunists take over, as history has shown time and again. A leadership void has been created concurrently with the peer review crisis and, quite opportunistically, the blog by Ivan Oransky and the other fellow fills in that void. It is a bad thing but it has managed to parasite over the space available, fits right in there. Tragically, everybody watches in complete stupor while these people run the agenda.

WM: OK, so what do we (you and me) do?

Ariel Fernandez: Well, we keep it up. We help them realize that there is a loftier pursuit than indulging in the trigger-happy nonsense of the blog. We try to educate the bloggers and commenters because we believe that there is a higher ground and that they can truly contribute. Oransky, for one, is possibly a very smart person and could do plenty of good.

WM: And the lofty pursuit is…

Ariel Fernandez: Help the establishment fix the peer review system by showing concrete failures of peer review and how we can learn from the mistakes to make improvements, how we can introduce better ways to safeguard the integrity of reported work with concrete working examples while fighting the problems alluded to previously. Above all, ensure that if and when PPPR becomes an absolute necessity, it is subject to the standards that science has upheld for centuries, since professional journals came into existence. In this pursuit there is no room for Ivan Oransky or the other fellow, or the commenters, unless they choose to get serious about fixing the system and stop being silly. Vulgarization of career mistakes and tragic turns of fortune is not going to get them anywhere (except in the eyes of the angry mob of losers in science who invest in the downfall of the winners). They need to help device clever ways to deal with and combat scientific corruption at its root.

WM: My pleasure again doctor, enjoy the rest of the day.

RELATED READING:

Ariel Fernandez and Michael Lynch (2011) Nature 474, 502-505

Disclaimer by Ariel Fernandez

Ariel Fernandez complete CV updated May 18, 2015

Ariel Fernandez featured in Baidu Encyclopedia (Mandarin)

Books by Ariel Fernandez

Ariel Fernandez at ResearchGate

Curriculum Vitae for Ariel Fernandez

The Peer Review Crisis by Ariel Fernandez

Rice University Faculty Catalogue

Ariel Fernandez Consultancy

Transformative Concepts for Drug Design: Target Wrapping, Book by Ariel Fernandez, Springer, 2010

Ariel Fernandez Professional Website

Biomedical Research by Ariel Fernandez, NIH

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Adam Marcus, Anonymous Commenter, Cat Ferguson, Character Assassination, Corruption, Data Fabrication, Data Falsification, Hilda Bastian, Ivan Oransky, JATdS, Joshua Cherry, Leonid Schneider, Mass hysteria, Misconduct, NCBI, NIH, Peer Review, Post publication peer review, PubMed, PubMed Commons, Reporting Retractions, Reporting Science Retractions, Research Integrity, Retraction Watch, Retractions, Science, Scientific corruption, Scientific Misconduct, Scientific publication, Scientific Research, Suicide, Transparency

Retraction Watch tracks down scientific corruption. Huh?

We would like to believe that people associated with the practice of science regard the process of tracking down corruption in research as a worthy undertaking. We better be careful with what exactly we wish for because the emerging picture, as it stands today, is looking ugly and getting uglier: Corruption is far more frequent than we would like to admit and, depending on where you draw the line, the indicators show that it is probably rampant. In this regard, a great piece on reproducibility by science writer Philip Ball is particularly enlightening.

Be as it may, efforts to track down corruption appear to be ill fated, poorly conceived, with some of the players even more corrupt than the subjects they choose to condemn. In principle, post-publication peer review (PPPR) is a plausible vehicle to track down corruption when the latter is detectable in published research. In practice, PPPR has turned into a rogue operation driven by losers seeking to elevate themselves by bringing down established figures while creating the perception they are doing something useful. Unfortunately, the scientific establishment will need to get out of its lethargy and, until that happens, PPPR will remain mostly in the hands of blogs run by nobodies seeking notoriety.

Perhaps the most grotesque of these blogs – and by far the loudest – is the self-published Retraction Watch. This blog is run by Ivan Oransky and Adam Marcus, two self-proclaimed experts on retractions, science reporting complications, career-related suicides and other tragedies associated with corruption. These towering figures are assisted by Cat Ferguson, a formidable writer whose ability to report on corruption tragedies earned her an internship at Retraction Watch (they even got a bit of money contributed by their commenters).

Oransky
The source of the picture is this article at Yale Medicince.

A beacon of decorum and noblesse, Retraction Watch does not simply broadcast journal notifications, they distort the findings to a grotesque degree in order to smear or destroy reputations and take active steps single-handedly to ruin the careers of those that they find guilty of having committed some form of misconduct. Not surprisingly, Retraction Watch founder Ivan Oransky has been named Science’s Garbage Man (Muellsammler der Wissenschaft) by the Swiss Radio and Television. The agenda of Retraction Watch is pretty much dictated by the hysteria of its commenters, veritable nobodies seeking attention and hoping to be rewarded for “tracking down the phonies”, to paraphrase the assassin of John Lennon. Some of these commenters such as JATdS, Leonid Schneider, Neuroskeptic, etc. opine on most notifications, regardless of the subject matter (that is irrelevant to them) contributing veritable manifestos. Some of these manifestos are inflammatory, while others take a more sober tone, but all seem supremely irrelevant. In these harangues the commenters demand that the suspected wrong-doers be sent straight to the scaffolds, repudiating the tendency of the defendants to defend themselves or get “lawyered up”. In his blog, Ivan Oransky himself frequently laments the fact that people accused of misconduct often try to defend themselves and that the lawyers they engage are responsible for belated and opaque post-publication notifications. In his world, only the hysteria of his commenters should prevail as justice is delivered.

Ivan Oransky, the self-proclaimed champion of science transparency, has been a staunch protector of the anonymity of his Retraction Watch commenters. He advocates that they are entitled to anonymity invoking the protection of the information source in reporting. This is crass to the point where I find it difficult to imagine a worst aberration. Is he saying that he actually draws information from the hysterical frustration-triggered manifestos of the nobodies that comment on his blog?

A different model for PPPR was recently adopted by PubMed Commons, which is an NCBI/NIH-sponsored forum for post-publication discussion. To state that it is a vehicle for PPPR is actually misleading since the comments at PubMed Commons are NOT subject to peer review. At least the fact that the authors are required to disclose their identity makes PubMed Commons more moderate and balanced than the atrocious Retraction Watch. There is one thing that Retraction Watch and PubMed Commons have in common and that is that they are both irrelevant and inconsequential to science precisely because their contributions are not peer reviewed and would not pass the acid test of science. The most avid contributor to PubMed Commons is… -you guessed it!- Ivan Oransky, who constantly needs to boost his internet presence and affirm his reputation and probably sees his blog Retraction Watch driven to oblivion by PubMed Commons. Other avid contributors are Hilda Bastian a science writer and editor for PubMed Health, who like most science writers, needs to aggrandize her presence on the web, and Joshua Cherry, a scientist? (contractor?) of unverifiable employment at NCBI/NIH who seems to find plenty of time to harangue other scientists with his meta-arguments.

It is hard to imagine that Joshua Cherry or the other individuals mentioned in this post truly believe that their comments constructively enrich the post-publication record. They simply cannot be that delusional.

Things must change with PPPR but this is unlikely to happen unless the science establishment recovers from its lethargic state and begins to act responsibly in the face of corruption.

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