Retraction Watch

Tracking retractions as a window into the scientific process

BMC retracts paper by scientist who banned use of his software by immigrant-friendly countries

with 10 comments

Screen Shot 2015-11-10 at 12.24.42 PMA BioMed Central journal has pulled the paper of a scientist who decided to prohibit countries that are friendly to immigrants from using his software.

Recently, German scientist Gangolf Jobb declared that starting on October 1st scientists working in countries that are, in his opinion, too welcoming to immigrants — including Great Britain, France and Germany — could no longer use his Treefinder software, which creates trees showing potential evolutionary relationships between species. He’d already banned its use by U.S. scientists in February, citing the country’s “imperialism.” Last week, BMC Evolutionary Biology pulled the paper describing the software, noting it now “breaches the journal’s editorial policy on software availability.”

Many scientists have used Jobb’s software: The BMC paper that describes it, “TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics,” has been cited 745 times since it was published in 2004, according to Thomson Scientific’s Web of Knowledge.

Jobb told Retraction Watch that the software is still available to any scientist willing to travel to non-banned countries, and that he does not care about the retraction:

BMC believes that I breached their journal policies by disallowing the use of my software in certain countries. I don’t think so, because still every scientist can use Treefinder, as long as he or she does it in one of the allowed countries and is personally present there. However, having to travel to a neighbouring country is inconvenient, I admit. I don’t care. Retraction of one of their most popular articles is the journals problem, not mine. I am not getting paid for that article, anyway.

Here’s the retraction note:

The editors of BMC Evolutionary Biology retract this article due to the decision by the corresponding author, Gangolf Jobb, to change the license to the software described in the article. The software is no longer available to all scientists wishing to use it in certain territories. This breaches the journal’s editorial policy on software availability which has been in effect since the time of publication. The other authors of the article, Arndt von Haeseler and Korbinian Strimmer, have no control over the licensing of the software and support the retraction of this article.

A spokesperson for BMC declined to comment on how the issues with software availability came to light, and if the journal made any effort to persuade Jobb against his decision. Here’s what the journal’s policy says about availability:

If published, software applications/tools must be freely available to any researcher wishing to use them for non-commercial purposes, without restrictions such as the need for a material transfer agreement.

In February when Jobb banned the use of Treefinder by scientists in the U.S. he noted the reasons on his blog:

My reasons:

(1) I want to protest against American imperialism, which I regard as the cause of most of all evil in the world: wars, tyranny, poverty, migration.

(2) I want to protest against EU tyranny, which is mostly the result of US imperialism.

(3) I want to demonstrate my sovereignty, something I would welcome to see much more often in science and politics.

In particular, I dislike that the USA and the EU aggressively promote a way of life that conflicts with my own way of life. I dislike the flood of immigrants they caused to come here – come here to replace unprofitable Europeans like me.

After so many years of hard work on TREEFINDER, I have still not been paid any reward.

The latest ban in October focused on European countries with immigrant-friendly policies, including Germany, Austria, France, Netherlands, Belgium, Great Britain, Sweden, and Denmark.

Co-author Korbinian Strimmer, a computational biologist at Imperial College London, told Retraction Watch that he has “supported the retraction of the paper” and does not agree with Jobb:

I for one have strongly distanced myself from these views…In addition, in all my own programming since my own Ph.D. project I have always been as strong advocate free and open source software – see http://strimmerlab.org/software.html.

He also told us that he’s going to take steps in the future to prevent co-authors from putting similar restrictions on software:

The present relicensing would not been possible if the software were released under GNU GPL license or similar, in the first place. Thus, in the future I will be ever more strict in enforcing free software licenses when working with collaborators.

In the meantime, scientists in affected countries who are unwilling to buy a plane ticket have the option of similar software, noted Strimmer:

There are many excellent software packages for reconstructing gene trees, so there is no shortage of alternatives.  For example, in the R platform I would recommend using the package “ape”: https://cran.r-project.org/web/packages/ape/index.html

When Jobb changed the software license in September ScienceInsider talked to scientists about the effect it might have on their work. The answer? Not much: 

“I’d say not being able to use Treefinder would be no great loss to anyone,” says Sandra Baldauf, a biologist at Uppsala University in Sweden. A paper co-authored by Baldauf last year in Current Biology used Treefinder primarily because a colleague had long worked with it, she says; now that that researcher has left, Baldauf uses different software, she wrote in an email. And after reading Jobb’s statement, “I would stop using [Treefinder] just on general principle, even if we had to resort to using pencil and paper.”

The ScienceInsider article includes an update, published a day after the article appeared, which notes that a comment was removed:

Comments from Jobb were added to this story after its first publication. Also, a comment about the Treefinder software was removed and the name of the Senckenberg Biodiversity and Climate Research Centre was corrected.

We asked Jobb where he works, and he told us he’s working on repairing a his house.

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Comments
  • Prof. Dr. Alexander Lerchl November 11, 2015 at 2:51 pm

    This is soooo stupid. And embarrassing at the same time. Scientists should NEVER EVER mix science with politics. There is a German word “Fremdschämen” for which I couldn’t find a translation, it means feeling ashamed of someone’s actions. I feel very much ashamed by the behavior of Mr Jobb.

  • homolog.us November 11, 2015 at 3:16 pm

    Springer (owner of BMC) seems to apply their rules arbitrarily. A few months back, we complained about a genome paper, whose authors did not follow BMC’s data submission requirement and did not provide us with the genome sequence despite repeated requests over a year. The senior author was an editor of one of BMC’s flagship journals. We have still not seen the requested sequence.

    In another instance, Berkeley professor Lior Pachter complained about scientific fraud against another paper published by Springer-owned journal, but the journal allowed the author Manolis Kellis (a NIH honcho) to merely change the supplement of paper.

    We outlined those examples in the following blog post.

    http://www.homolog.us/blogs/blog/2015/11/10/bmc-springer-sends-shockwave-through-bioinformatics-community/

  • Stevelaudig November 11, 2015 at 5:27 pm

    A political retraction is just as reprehensible as the political limitation. Perhaps more so.

    • strobi November 12, 2015 at 2:04 pm

      It is a retraction based on a change in the availability of a software, it is not political. Maybe the author didn’t read the terms of the publishing agreement, but one usually has to agree to provide enough information for people to be able to replicate the work. If in a software paper the software is not available, that is in breach of that agreement. It is perfectly justified. This Jobb guy clearly doesn’t understand how science works.

  • goose November 11, 2015 at 5:42 pm

    So you have to emigrate to another country, and of course act as an immigrant while there, to use this software. I wonder if this ironic situation has occurred to the author.

    • Keith DeHavelle November 11, 2015 at 8:18 pm

      Jobb is explicitly against “non European” immigration, and wants refugees to be kept isolated and ultimately returned. And he is vehemently anti-capitalist; among other things, he perceives that immigrants provide cheap labor and consumption that “delays the inevitable collapse” of the free market system. At the same time as he promotes the destruction of the free market, he asserts his own sovereignty. An odd combination, but he seems like an odd Jobb.

      ===|==============/ Keith DeHavelle

    • Bob O'Hara November 12, 2015 at 3:06 am

      Perhaps scientists who do this should claim asylum.

  • PJTV November 13, 2015 at 4:18 am

    Indeed, the behaviour of Dr Jobb is – euphemistically speaking – less than desirable. Is the retraction by the journal editor appropriate? Is it not also a political statement disguised as that Dr Jobb “breaches the journal’s editorial policy on software availability”? The methodology of the work is not in question and should be universally available for all scientists. Also the software implementation is available for scrutiny. Therefore, this work should not have been retracted.

    • Conrad Seitz MD November 14, 2015 at 3:13 pm

      It’s more of an ANTI-political action, and it is because the availability policy breaches the editorial policy, not because the availability policy is a political statement

  • genetics November 13, 2015 at 7:30 am

    Whether or not you agree with Jobb’s points and his actions is irrelevant in the context of Retraction Watch, IMHO. But the whole thing does raise a few interesting questions:

    He could leave the original version (April 2004) as used in the publication still available for everyone and impose the restrictions only on any newer version. The effect would be nearly the same but BMC would not have a formal reason for retraction.

    An interesting aspect: What would happen, if he indeed would do so? Would the retraction be retracted? I would actually urge him to do so, so we can all find out……

    An interesting question the homolog.us blog raises is: What happens to all the bioinformatics papers of past X years where the described software is not available anymore for other reasons? The institution ceasted to exist, the authors have deleted all copies after 10 years and no one else on this planet has retained a copy, the software has been archived in a format or on a storage medium that is not readable anymore, whatever. Do all these papers have to be retracted? After all, these papers all breach the journals policy.
    In more traditional bioscience, authors also usually have to agree to share reagents etc. But to draw an analogy here, should a paper from 2004 be retracted because the authors cannot provide the self-generated polyclonal antibody anymore in the year of the lord 2015?

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