Scrofulous

In my papers I (try to) follow the ethics of a journal such as Physics of Fluids, say. "When an error is discovered in a published work, it is the obligation of all authors to promptly retract the paper or correct the results." and "All coauthors have an obligation to provide prompt retractions or correction of errors in published works. Any individual unwilling or unable to accept appropriate responsibility for a paper should not be a coauthor." Some reflections on disingeneous behavior in science are found here: Hypocratie van alternatieve en voldongen feiten ... (google translate is reasonable except for some subtle errors/word variations) and below.

    In 2007 I developed a marvelous interdisciplinary collaboration on granular flows with Prof Hans Kuipers, who left the University of Twente around 2010 while I left in 2013. Disagreement about the management directions were the main reasons to leave including, for me, scrofulous behavior that continues to date.

    (i) In general, the amount of editting required is underestimated by juniors and some supervisors. E.g. for (I. JFM 2014 paper), there were about 6 to 10 iterations required from the 1st iteration with circa 100 comments on Dec. 12th 2013 till the last iteration on Dec. 23rd 2013 (to be quite honest doing this just before Xmas at a workshop was outrageous but the editor had given us 14 days to resolve matters). Notice how the oscillations in Fig. 2 have disappeared in the final version because the resolution was increased and a computational error was found during the editting process. Making double-resolution runs to verify convergence was dismissed as a time waste and I was asked by the supervising professor to leave as co-author of this paper. That loud request was made before regarding another paper in 2012, another paper in 2013, in 2014 and has recently been made again for yet another paper --see below. [Fixing these errors is not urgent according to some people as the results are "kind of" the same and one can always publish the correct figure in a new publication, thus boosting one's publication and citation records. I don't belong to the group of people advocating that kind of philosophy. The (Dutch) academic system does, however, award this kind of behaviour of quantity above quality. It thrashes people who advocate quality.] One reviewer congratulated us in the end for a well-written and impactful paper. The dean of the said faculty dismissed it all as fixing typos because it delayed the process (by two weeks) and because seniors such as the dean and the prof above, dismiss(ed) careful editting as mistrusting other people (I always triple-check my own work, let it be the work of others, especially juniors who need to learn the trade, and so do my Leeds and Imperial mathematics' colleagues).

    (ia) As said, it is not the first time that sloppy science causes mishaps. In 2012, I turned down authorship of a paper since it contained too many copied sentences of four of our joint papers (four 2012 papers). Such copying first of all leads to a poorly written paper and, second, it is self-plagiarising and after I declined, plagiarism. In addition, I had asked to not mention the specific idea to couple DEM (a package to calculate granular particle trajectories) to hpGEM (a package to solve equations using finite elements), an idea that I had proposed and advocated in the STW-proposal, which I wrote for 95% as PI. Given my move to Leeds and also given the more stringent clamp-down on plagiarism in the UK, as opposed to The Netherlands, and rightly so, I did not want to get involved in self-plagiarising. The authors refused to clean up their act and mentioned ideas I had proposed and advocated without reference to me in relation to the STW-proposal. They also did not acknowledge that I had given them my suggestions for improvement, which they did use. Relative to the first draft the final paper indeed had greatly improved ---they should have asked me to rejoin again as co-author, which they did not, thus plagiarising my ideas without acknowledgment. Such Trumpian-bully style tactics are standard in that university and apparently allowed by the Dutch funding agency STW-NWO. My complaint at STW-NWO was cleverly and incorrectly circumvented and led back to me, thus avoiding STW to take responsibility: as project leader I was forced to sign a STW project-form effectively stating "the project leader confirms that all research complies with the Dutch scientific ethics laws". I refused to do so, as that was not the case, and raised my complaint, in vain. Poor leadership on the part of STW which ultimately led to the approval of a PhD thesis with a provably incorrect chapter, in which calculations need to be redone --see point ii). Apparently, approval of an incorrect PhD thesis (chapter) is allowed in The Netherlands and by funding agency STW-NWO. Given the history, STW could have known that sloppy science was likely to happen again. Hence, they cannot use the "ich-habe-es-nicht-gewusst" excuse as I had flagged the issue with several of their employees including the former director (now an MP on education). [This director/MP abused the complaints procedure by relaying my complaint in confidence to the dean of the faculty, saying that I threatened to also raise a complaint against the dean. The angry dean let this slip in August 2015 during a conversation with also our two lawayers present. That is a formal breach of confidence which undermines the entire complaint procdure. Bankdirecteur Barclays kreeg half miljoen boete toen hij identiteit klager probeerde te achterhalen.] One STW employee supported my complaint but warned me that I was likely to lose since the dean of the faculty was a member of STW's advisory board; he expected my character assassination given that I was not physically present full-time in The Netherlands to defend myself---this is indeed what happened; "group dynamics against the person who cannot defend himself", was a friend's analysis and: "a common trick". It still does not allow STW-NWO or any other management to approve of plagiarism, ghost authorship, and stealing of shared ideas combined with agressive attempts (4x by the same senior prof) to bully a key author in an attempt to make him withdraw as author for the wrong reasons. Apparently in The Netherlands this all is allowed, which is why I defected the country. Organised Dutch science, like organised crime, is at fault here, notwithstanding that I know and collaborate with plenty of bonafide scientists in The Netherlands.

    (ii) On (II JFM manuscript in progress 2016-2018), this manuscript found in the archive here was deposited while neither co-author Thomas Weinhart nor I were given the opportunity to proofread and make corrections. The archive also refused to delete the deposited manuscript given that our names are illegally attached. My comments were finally asked late Nov 2016 and the manuscript (essentially an approved PhD thesis chapter --how on Earth did this pass the PhD committee? --I was not involved) with my 172 minor and major comments is found here; I also rewrote one subsection later (not shown) as it copied a part of the published Akers and Bokhove 2008 article (Phys. Fluids) too much. Some serious corrections are required; attempts to correct came seven months later, see (v) below. These are facts, as you can check yourself given the interim manuscripts, not alt-facts the latter aka typos, errors-declared-no-errors, minor quibbles, etc. My main point of critique was actually raised at the PhD defence, I was told by one of the committee members, but the incorrect write-up was defended as another and apparently acceptable alternative (fact), aka ``Dutch science''. [With minor defensive writing, by admitting the mistake and outlining its correction, the current write-up could have been augmented, so a practical correction would have been trivial way to set matters right.]

    (iii) I have the opinion that the PhD student has been a victim of inadequate supervision and that he therefore should be allowed to correct the erroneous chapter in his online PhD thesis. It is unprofessional (otherwise said simply sickening) that the collective formal supervisory team of this junior researcher at that university was unwilling to provide serious and constructive comments fixing the minor and major errors in the four manuscripts/iterations to date (two archived manuscripts, a thesis chapter and two draft journal articles). This correctional procedure should be checked by an independent, ad-hoc (PhD) committee of two esteemed scientists who should oversee the corrections as (remote) reviewers. Substance should go before old-fashioned Dutch customs. That is unlikely to happen as not loosing face is deemed more important than maintaining quality and substance, a difference of principles that lies at the heart of the matter. Is that Dutch academics in a nutshell? As external I recently proofread a draft thesis in the UK. On page 2 of that UK thesis, now approved by me, the following statement emerges: "I cerify that this thesis is the product of my own work, and that any ideas or quotations from the work of other people, published or otherwise, are properly acknowledged". Regarding the chapter in the approved 2015 PhD thesis on granular flow through a contraction that statement does not apply. That I defined the problem as PI of the proposal, that I set up and shared the detailed calculations with the PhD student and one of the authors in 2010-2012, that I pointed out that the shallow water and DEM calculations could principally not be that different (already pointed out in 2012) and that I pointed out further errors in the 2014 archived manuscript, has not been acknowledged in the PhD thesis. The incorrect reference in the thesis gives the impression that 2 or 4 supervisors are jointly responsible for the intelllectual content of that chapter. The addition of 2 or 3 professors --including me-- afterwards, in the draft article, gives the incorrect impression that I am an add-on, which I am not. Till 2014, I was always last author in the draft article as mentioned in the minutes of many STW meetings. I am not a ghost author, a well-defined phrase in academic publishing, namely an author who should not be co-author on an article because he/she does not satisfy the four rules on authorship below in (vi); quite the contrary, I am one of the lead authors, the one who defined this research before anyone else was involved.

    (iv) Just to be clear why I have taken the unusual step to place matters openly online: I have given university and funding agency ample opportunities (2012-2016) to solve these matters behind closed doors. They refused at all levels. Defending my right and the general scientific principle that errors should be fixed and that all authors should be asked for permission (to submit to a journal or archive), against all odds and certainly when feasible corrections are known, which was the case as I have always provided such corrections promptly, cost me personally 6000 euros in legal fees. It concerned four articles, two of which have been considered for submission as Level 4 Research-Excellence-Framework papers. Without my insistence to correct errors the latter REF-papers would have a lower rating. In addition, ``driemaal is scheeprecht'' (three times is enough --a Dutch saying), a prof for the third time asked me to withdraw as co-author on a third (journal) paper, while criticising my so-called high standards, i.e. the fact that I actually proofread draft work a few times, while he admits to simply ``trust'' the word of juniors that the corrections are done. Well, I am finally and openly fed up with such unprofessional behaviour; it is not happening in my backyard. The cynical question is whether such behaviour is unprofessional or not: from the point of view of maximising the number of PhD theses supervised and the number of journal articles published the said prof is a top professional and my insistence on quality (for corrections feasible within the time span of a few weeks) is simply unprofessional (aka stupid), given that the (Dutch) academic system awards quantity above quality. It thrashes -de facto- people like me, both at the funding agency (NWO/STW) as well as the university levels. Remember Arthur Gotlieb? Apparently, the only defense a scientist has when incomplete and incorrect work based on his input is placed online and cannot be removed, is to place the critical and constructive comments on this research online. Normally such corrections are done behind the scene and that is preferred, of course. But if the scientist is attacked and threatened with being fired, for insisting on sensible and manageable corrections, he or she has no other choice than go public. [Update 28-09: finally one other senior co-author proofread carefully; that took him apparently and unexpectedly 3 weekends; join my UK academic world as proofreading indeed takes time. Update 01-12: after highlighting that matters are still not resolved, I got an update back. TBC.]

    (v) Reading the new draft, page by page. 18-08-2017: on page 8, hitherto 95 comments (as of 19-08: 100 comments); ... I will continue my careful proofreading probably later this autumn (I spent one week proofreading a UK thesis as external reviewer, which should be the normal state of affairs but in an altfacting world of one-liners and quick fixes has become the anti-norm, and had two weeks of holidays in Aug/Sept). Meanwhile I have been accused that my standards are too high by a prof who strongly suggested me to leave as author (for the fourth time since 2012). Whatever my standards are, what is relevant is that the science needs to be fine, that e.g. the following needed and needs to be corrected:
    - The basic mistake in the Dec 2016 draft remains unsolved: a very thin channel has been taken, as thin as the inflowing layer with only a short contraction, and this does violate the shallow flow assumptions made. The issue is not that a junior makes an error, we all make errors, but the issue is the refusal to find these errors by careful proofreading by the official supervisors and the dismissal of obvious errors as "high standards" beyond reach of correction, plus the subsequent attempt to get rid of the person finding the errors and suggesting the corrections to these errors. Instead, I have been asked to withdraw as co-author, whereafter they would undoubtedly fix the errors I pointed out ---this happened with a paper in 2012 in which my contributions were not acknowledged. In this case my contributions are much more profound. The actual corrections are a week to two weeks worth of work --that is all.
    - More technically, the basic scaling error that tan(theta) = [tan(theta)]' times H/W with H a different layer thickness length scale than channel width W is suboptimal to say the least. The prime means that [tan(theta)] was scaled. Well, an angle is dimensionless and so is the tangent so it cannot be made dimensionless as it already is dimensionaless. Now as adviced by me, H=L is taken but the in-plane scale L cannot equal to W otherwise the flow is not shallow (a mistake likely present in this new draft). See expression (2.3) in the 2016 draft with my comments and the thesis, etc.
    - Except that taking the upstream depth scale H also as width and downstream length scales in combination with the shallowness assumption implies that the width of the channel should be "many" depth scales H (e.g, 5H, 10H or more or many more particle diameters?) and that the channel constriction length should be a multiple of the width (e.g., 20H, 40H or more?). After all, the 1D but also 2D models are based on asymptotics. I am doubtful whether the plots displayed take into account this necessity to keep width and downstream scales very long?
    - So despite the correction of the formal scaling, due to the use of a domain that is too narrow and a contraction that is too short, the previous lack of agreement between shallow water theory and discrete particle simulations is still suboptimal, to say the least. Nonetheless, it is ambiguously described in the 2017 draft text to be both as "close agreement could not be reached" as well as "i.e. the flow profiles in the contraction did not completely match the one-dimensional predictions"; as said, there likely still is an issue regarding the shallowness induced by the channel width and downstream contraction length scales used; the problem is that these statements are unclear if not mutually exclusive; "not completely match" meaning that the agreement is close which is not in agreement with the first statement that "close agreement could not be reached"; I prefer precise languange to be used as well as correct shallow flow and DEM simulations to be performed with clear scale markers to be added in the article, to celebrate a possibly joint victory, credited to us all.
    - In the 2017 draft the 2D oblique shocks are described as being smooth. They are not. Shocks are by definition not smooth. The point is that the width-average of these oblique shocks is smooth. Well, then say so. Clarity matters.
    - A hydraulic set-up in another article (Akers and Bokhove 2008) was called the same as these inclined channel calculations while the hydraulic channel was in fact horizontal, meaning not inclined. I know as I did 50% of these experiments. Then say so. Clarity matters.
    I prefer all such things to be presented truthfully and consider it as an integral part of publishing to eliminate nearly all misrepresentations and errors, within the reach of a few careful rounds of proofreading. This is only round two of proofreading of full drafts (of 2016 and 2017 as the 2014 archived draft I just browsed while spotting several mistakes within the span of 15 minutes). Two rounds of proofreading is not very much, by the way. I object to careless or no proofreading. Dutch organised science (as opposed to Dutch scientists) does, apparently and till proven otherwise, not care about careful science but awards sloppy science. That sloppy science and altfacting is likely commonplace in (Dutch) science is argued here by Prof Lex Bouter and in my wordpress blog article Hypocratie van alternatieve en voldongen feiten in de Nederlandse wetenschap.

    (vi) Finally, this is what Springer (first link to this clear set of rules) recommends [I am on the editorial board of a Springer journal so ought to know and follow this]:
    "The ICMJE recommends that authorship be based on the following 4 criteria:
    1. Substantial contributions to the conception or design of the work; or the acquisition, analysis, or interpretation of data for the work; AND
    2. Drafting the work or revising it critically for important intellectual content; AND
    3. Final approval of the version to be published; AND
    4. Agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.
    Contributors who meet fewer than all 4 of the above criteria for authorship should not be listed as authors, but they should be acknowledged. "
    What a relief. I ticked all four boxes, i.e., I should be co-author according to (Springer) standards which nobody is upholding in a world where only the number of papers published and citations count! To wit: 1. The intellectual design is mine since I led and wrote 95% of the STW proposal plus set up/shared my (hand-written and blackboard) calculations; 2. for sure I drafted the work and my standards are not disputed, apparently, instead my standards are deemed too high; 3. my approval is obviously not yet given but matters are coming along; and, 4. for sure, I am clearly accountable as follows from my proofreading and checking, which should be standard practice by any professional academic. Wow, that's great. Tough but fair requirements though. Unfortunately, Springer or publishers in general do not let their editors sign a contract stating explicitly that they will follow these rules in their own scientific practice, all of them, not on a voluntary basis. Only when there is a signature can there be repercussions. My standards are normal by the way: in the above July 2017 draft version reference to the 2015 PhD thesis has been removed since referencing a thesis chapter with errors was deemed unwise, i.e., they implicitly admit themselves that the standard of the thesis chapter was too low. The suggestion by this senior prof that my standards are too high are nothing less than an attempt to claim that the high standards are his and not mine. It is a dirty trick, tried for the fourth time for a fourth article which, my dear friends would say, is apparently perfectly allowable in the Dutch academic setting, unless proven otherwise. "Dutch science", till proven otherwise, a close friend has called it, like "Dutch wife", "Dutch courage" and such.
    Update 02-07-2018: Several rounds of editting further, the main error has finally been resolved but other errors remain including the omission of a very important inference about the model. I have offered the main author to come to Leeds to sort out these remaining issues and the write-up. Another issue is the co-authorship: the four senior Twente authors do not satisfy Springers rules (ie they have niether brought in at least 1 main idea nor proofread the article according to the described Springer standards --which follows by the fact that I found and still fnd a multitude or remaining errros) and the rules of the Dutch chacademic conduct, except possibly one; so I have suggested to reduce the number of authors by three (3 Twente authors go out and are thanked in the acknowledgments). As far as I know this has been refused, including my potential offer to pay the trip, to date. How daft can you be to reject an offer to improve and finish a paper; this is anti-science?

    (vii) The above is a scientific discourse. Recall that I paid a lawyer 6000 euros in the period 2013-2015 to defend my author's rights and my right to do exactly what Springer refers to in the point 4. above: "to be accountable for all aspects of the [ie my] work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved", as well teach junior researchers to do so. Those rights were and probably are still under threat in the current (Dutch) scientific climate. (In 2013 concerning a different junior, after approval of a manuscript by the reviewers of a high-ranking journal, I found a serious error. I asked the editor of that journal whether we could have one extra month and later another month, for us to fix the error. We added an extra appendix with permission of the editor. This was a tough learning experience for the, excellent, junior. When the page proofs of the article arrived, my wife and I took the junior and partner out for dinner in our old home town (Enschede), our treat, of course, to celebrate victory after all this extremely hard work. That was an act of empathy.)

    (viii) Every Thursday (in term time) my research group of PhDs and PDRA's has a group meeting in which we in turn listen to informal research presentations. This also includes try-outs for formal presentations and discussions on research obstacles. Afterwards we go for lunch. Often I don't have to say much as the group has the answers to most questions and the group picks up the weak points in presentations. These are training sessions for all "ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved". Late April 2015, my group picked my draft public outreach presentation which I had prepared completely apart. I had asked them to comment, admitting beforehand that I was stuck in trying to deliver my message to the general public. That must have been amusing for them to pick their supervisor's trial presentation apart. They showed no mercy in a polite but clear manner and, in effect, did show actual as oppposed to surperficial mercy, since the factual public presentation would otherwise have been of lesser quality. Constructive yet firm criticism is crucial for making progress. (A significant subset of the senior co-authors in the above papers on granular flows does understand this very well, of course, but want(ed) to get rid of me as co-author so they can claim my contributions as their own. Recall that one of ``them'' profs actively suggest(ed) I leave the paper on which I should be co-authored according to all Springer authorship's rules cited above. Such agressive attempts to get rid of authors is likely a common tactic in science.) Afterwards we had our (nice) weekly group lunch and the subsequent Sunday in Hebden Bridge I gave a well-received presentation on the science of flooding. The School of Maths has discussed the option to create more of these small-scale group meetings within the School to enhance the research atmosphere. During my PhD study in Toronto under the supervision of FRS Prof Ted Shepherd such informal group meetings, followed by a lunch in China Town (``rice with beef and black bean sauce'' was my favourite), were the norm. The apple does not fall far from the tree.

    (ix) March 2018: the draft JFM paper has been declared ready for submisison by the 4 senior authors from University Twente, backed up in a statement by a senior prof that they all carefully proofread the draft. Since then, I have relayed two rounds of comments back to the junior lead author, including requests to correct: incorrect labels on axes of figures, defined definitions of scalings used, complement lobsided choices of parameters (by references to two classic papers which pdf's I had sent along) and a statement that a small parameter, which should be [much] smaller than 1 in this context, was 1 to the power of minus 10, which is 1/(1*1*1*1*1*1*1*1*1*1)=1 and therefore not small. While the latter is a mere typo, it should be 10^(-10) and not 1^(-10), it nicely illustrate the way (lack of or poor) proofreading has become accepatble. As the above story illustrates poor proofreading has happened since 2012: concerning now a draft of 2012, a thesis of 2015, a draft 2016, a draft 2017 and the latest draft of 2018. In other words, the statement that these 4 senior authors from the University of Twente have carefully proofread the draft papers is at odds with the actual state of the draft paper, unless of course, sloppy supervision is an acceptable modus operandi with UT-management? I have politely suggested the (poor) junior author to update the paper with precise instructions and please send the new draft version back to me for further and, hopefully, only a final inspection. I may soon upload a link with the new draft with my (email) remarks added as pdf-comments. Note that UT-management has still not interferred in a constructive manner (recalling my two rejected requests for moderation).

    (x) June/July 2018: I have offered the junior lead author to come to Leeds to finish the draft paper provided the authorship issues are resolved: 4 senior Twente co-authors should be reduced to only one senior Twente co-author given that they do not satisfy publishing rules on authorship. While the offer has been accepted provided we can find a mutually acceptable time, the authorship issue has been ignored.


    (x) The trick to let someone do the work and then try to get rid of them as co-author, meanwhile profitting from their work without acknowledging their contribution, it is a commmon trick used by Prof XL He phones or skypes or emails you and then starts yelling, writing in capitals letters and such till you buckle and withdraw from the paper just to get rid of the nauseating behaviour. He tried it in 2013 and succeeeded. Het tried it in 2013 and succeeded. He tried it with the JFM paper discussed above in 2014 and failed. With the granular contraction paper he will fail too: that is all my IP from A to T. Prof XL tried it in 2013 with a Phys. of Fluids paper found here, which contained project data and results from a project resulting in the four 2012 papers on granular flows which I had mainly supervised; I refrained from co-authorship because at the time I could not do the proofreading effort required according to the rules above, but given that the rules are not followed by a (very) large group of scientists I should have been co-author according to the actual rules on the workfloor, since the token rules in the ludricous codes of academic conduct don't count for anything. XL's trick was used first on me in 2012 at the first incident by Prof XL and Dr YT. Late 2012, I was given the following draft to proofread. Something felt odd while I was reading it. The report was a mismatch of work and I felt I had seen quite some of the sentences before. I put one sentence in google and it led to one of our jointly published papers. I had in fact editted that particular paper line-by-line myself. It was for say 80% my own sentence. I had written it. [Feel free to put the pdf in Turnitin; I never did that. Curious about the results.] At that moment it was a case of what is called self-plagiarising. I gave my comments back, i.e. the report in the above link, with the remark that it copied too literally from our work and was also too long. I had at that point not heard of the word self-plagirism. I was suggested to leave as author. Okay, I said since in the UK they are more strict on plagiarism, I will withdraw as co-author but then you cannot put in my research ideas without acknowledgments. It was published later here, fully rewritten and all my comments had been taken into account, including the ideas from the granular flow STW proposal I had rewritten without acknowledgment of my role and IP. I.e. the hybrid scaling modelling linking of hpGEM FEM simulations with discrete part DPM simulations. While hybrid multi-scale modelling is not new, the specific finite eement hpGEM and DPM linking proposed, via weak forms, as laid out was new and I had proposed it and partly worked it out. In 2015, I discussed these calculations later with one of the co-authors at Wowlab. My contribution was not mentioned in this paper. My ideas were confiscated without acknowlegdments. My useful comments for the editting for the final version were also not acknowledged.

    That is all academic misconduct according to Rules 1.3 and 1.4 of the Dutch Academic Code of Conduct, which code of conduct is to date false advertising because it misleads junior and senior scientists in behaving according to these rules and thinking that there are any rules in academics while the only valid rule is power and abuse of power.