Academic papers yanked after authors found to have used unlicensed software An academic journal has retracted two papers because it determined their authors used unlicensed software. As noted by Retraction Watch, Elsevier's Ain Shams Engineering Journal withdrew two papers exploring dam failures after complaints from Flow Science, the Santa Fe, New Mexico-based maker of a computational fluid dynamics …
This is a very strange article. The offence is abuse of a software licence - in particular not obtaining one to use the software. This is an important issue, and IMO the world in general and academia in particular has got to learn that software doesn't just come out of thin air, if you want high quality and especially if you want maintenance you will have to pay for or contribute to it in some way. But then the article goes off talking about access to academic publications, a totally separate issue. It's of definite importance but I fail to see how retracting a paper due to breaking the law connects with it.
Companies like Elsevier take tax-funded resaerch results, tack on their own copyright and make a living off selling access to that content.
So they have a conflict of interest with regard to copyright law, where they promote a very strict interpretation, basically to protect their own revenue stream.
In addition, not having "a license" to base a paper on can be anything from having no license at all, only having a personal license instead of a team license, up to not having bought additional rights to publish results/screenshots/logos/etc.
Companies like Elsevier take tax-funded resaerch results, tack on their own copyright and make a living off selling access to that content.
The problem is two fold: The publishers won't allow libraries to only buy the journals they want and force them to buy way more than they want. Second, the researchers could stop publishing papers in pay-to-view journals.
I believe some funding bodies (e.g Welcome Trust) now mandate that any papers must be published in free-to-read locations.
I'm surprised that America allows tax-funded research to be kept behind paywalls. Isn't this why so much of NASA's work in freely available?
There is another aspect to this.
Not all research in academic institutions is totally funded through public grant schemes.
There is research done at academic institutions that is funded either fully or in part by commercial entities, so there may actually be reasons why the distribution of a paper has more interested parties than just the author, the academic institution and the publishers.
But I wonder how nuanced academic licensing is for commercial software. It may be that there are additional license clauses in software being used for commercially funded research over and above the normal academic license. So the authors may have been free to use software as a go-to tool, and publish the results for purely publicly funded academic research, to support and develop their expert knowledge, but would have needed additional licenses for a commercially funded research project. If they hadn't realised this, it is possible that they just fell into this hole.
But I'm speculating here. It would be good to get more information of exactly how they were unlicensed, but it wouldn't surprise me if we never find out.
But I wonder how nuanced academic licensing is for commercial software. It may be that there are additional license clauses in software being used for commercially funded research over and above the normal academic license.
I work in Higher Education IT and get to see some of the work of the software licensing team. Typicaly software is either only allowed for non-profit work (i.e. allowed for research but not for use in spin-off companies) or it's only allowed for teaching/education: Use for research is forbidden unless you pay for a different (i.e. much more expensive) license. Hence you always get academics trying to use weasle words to claim their work is vitial to teaching/education and not for their for-profit side hustle.
I receive copies of a highly ranked quarterly journal for one of my personal interests, and the most recent edition there was an article by an employee of the US government. The article noted that the journal didn't own the copyright as that wasn't allowed by the US government etc so i'm fairly sure that particular part is not so much an issue as might be assumed.
The main problem with the free to view journals is actually a somewhat circular one; the reputable ones are reputable because they have all of the experts doing peer review and thus only print high quality stuff. The free ones don't have the experts and print everything, with no filtering via expert peer review, and so your work would appear alongside an argument with the academic rigour of claiming that the world is really actually flat, which encourages crazies who end up being filtered out of the reputable journals and discourages non crazy people from submitting reputable articles to them.
>” The main problem with the free to view journals is…”
For some reason Xwitter came to mind, troubling as I suspect some may actually regard it as a journal, with an open peer review process…
Challenge post a full scientific paper to Xwitter… whilst I regard this as a joke, I suspect someone will do actually do this.
"Challenge post a full scientific paper to Xwitter… whilst I regard this as a joke, I suspect someone will do actually do this."
and it will mean nothing.
When I comment on something I know very well and somebody tells me I'm wrong, nobody on the outside can form a correct opinion based on those two comments unless they also know the subject well. Peer review is supposed to have an assemblage of people knowledgeable in the thing being reviewed that a reader can have some assurance that the thing is correct or at least doesn't have any glaring errors.
But the "reputable" journals don't pay for peer review either!
Elsevier gets to charge for the "reputable" journals simply because they are reputable. The costs of running an editorial team required to keep it "reputable" is far lower than the amount charged by Elsevier.
But the "reputable" journals don't pay for peer review either!
They don't pay cash, but a reviewer for Elsevier gets free access to all Elsevier journals for a period of 30 days, which could be regarded as payment in kind. This isn't a particularly good payment, as many reviewers will have institutional access anyway, but it helps for independent researchers.
"This isn't a particularly good payment, as many reviewers will have institutional access anyway"
Perhaps not full time, but it will give access to work in advance of everybody else. Even when a paper doesn't get approved, it might still contain some really valuable research. It might also show yet another way to not make a light bulb so the reviewer won't go down that blind alley and waste time/money.
The point was not that they were compensating peer review in a deserved way or that they weren't making massive profits off others' work. The point was that, in comparison to one that doesn't do those things at all, they can still be more respected. Reputation can be an important thing to researchers and those looking for other research to build from. Although a lot of journals have a long history of allowing bad papers in and taking too long to remove them, the reputation of those who filter a lot of them out at source and do retract them when they're found faulty is higher than ones that don't filter much at all and retract only after something egregious.
"Reputation can be an important thing to researchers and those looking for other research to build from."
Accord reputation on the basis of openness to solve that problem. In fact, natural selection may eventually help. As Universities get more an more strapped for cash and cut down on library subscriptions it will be articles in open on-line journals that get cited more and the less open ones become backwaters to avoid.
" The article noted that the journal didn't own the copyright as that wasn't allowed by the US government etc so i'm fairly sure that particular part is not so much an issue as might be assumed."
The journal would hold a compilation copyright which muddies things. It's like a classic story that's in the public domain, but the artwork for a particular edition is still under copyright so one can't duplicate the book without a license from the artist (or their assigns).
@Peter2
Peer Review in journals - don't necessarily get too excited by it.
Typically reviewers unpaid, so no monetary motivation to do a thorough / diligent review. There is a potential advantage in being a reviewer as journal more likely to initially accept your submissions because you are on their review team. Can also get reviewers treating submission by a fellow reviewer more favourably. Reviewers are not necessarily 100% fair and objective*, they typically come with their own prejudices, be that being more favourable to friends, less favourable to competitors, less (or more, tends to vary on reviewers approach to the general consensus) favourable to articles that go against current "received wisdom" in that area.
*You'll find a few stereotypical super honest & objective (often autistic) scientists around, but because much of academia is "publish or perish" then gaming the system from all sides**
** Some of which is bad, often journals are not keen on publishing research that does not show "positive" results (which is an issue, as if someone independently fails to reproduce something published then that is definitely something that merits publication*** )
*** Wheher that means initial paper did not fully explain procedures used (& so reproduction would fail), the results seen were a statistical fluke****, original researchers had made an error somewhere, replication team made an error etc..
**** or fraud
USA Federal law mandates that government entity publications must not be restricted (no copyright)
UK law puts "crown copyright" on all government sourced publications
Elsvier's predecessors got in deep trouble for paywalling access to various "freely available" items but ended up in more trouble over the UK "crown copyright" breaches than the "open copyright" of USA federal stuff
Essentially the Crown could mandate free access as part of the copyright even when bundled. The USA government lost out on "compilation copyright" matters
This is WHY Elsvier et al bundle all that crap into the subscription. It gives them a compilation copyright (and the ability - like mapmakers of old - to slip in few red herrings into the bundles to facilitate breach tracking)
USA Federal law mandates that government entity publications must not be restricted (no copyright)
Work product of US Federal government employees is paid for with tax dollars, so it is in the public domain. But there is a loophole so big you can fly a Boeing plane through it. If the government hires a private company to produce it, then that private company can own the rights to it. They also make it difficult for the average citizen to access public information, allowing special APIs for aggregators so that they can easily access, manipulate, and claim copyright. Weather data, flight info, public records, etc.
"This is WHY Elsvier et al bundle all that crap into the subscription."
Compilations of factual data isn't eligible for copyright so some yellow pages publishers started salting their directories with fake entities so there was enough "creativity" to qualify. If you ever wondered why there was the odd advert with no contact information, there ya go. If you don't what a "yellow pages directory" is, don't say anything, I feel old enough as it is.
I'm surprised that America allows tax-funded research to be kept behind paywalls. Isn't this why so much of NASA's work in freely available?
With the rise of corporatism in the US government from around Reagan's terms, I would not be surprised if the air itself will be regulated and sold. Any El Reg readers in other countries want to sponsor an old Assembler-language programmer and his wife? We're quiet and have the means to support ourselves, promise.
"Isn't this why so much of NASA's work in freely available?"
Yes. If you want photos of space stuff, NASA is awesome. There are very few images they have that would have to be licensed from the original creator that weren't funded with taxpayer money. Some of NASA's technical work is covered under patent, but a free license for much of it can be had on application. A foreign entity might need to pay.
Work funded with tax money is supposed to be available to US citizens and domestic corporations. I think the publishers are getting around some of that by "not charging" for the works, but for a subscription to their service. It's very dodgy and if a judge signs off on it once, there's precedent set. That would mean somebody has to bring suit which is monstrously expensive.
Agee. It is odd as a quick visit to the Flow-3D website, indicates, subject to a few conditions, free academic licenses are available.
Also whilst the paper has been “retracted”, a version is still available, albeit with “RETRACTED” stamped in red across every page. So it should be possible to attempt to contact the authors.
Because is this a case of the authors using a free research licence beyond the 4-month limit, or the university department not maintaining a subscription, or something more deliberate.
A software vendor has had a researcher's work withdrawn from publication because of a claim that their software was not validly licensed. The merits of the research remain unchanged. The ethics of the authors have been impugned and we don't have enough information to judge, because of the opacity of supposedly authoritative journals.
How do we know the software author's claim is valid, or straight defamation? Did the authors believe their own or their institution's licence was valid when they published? Has the publisher been threatened with legal action if they failed to impose the withdrawal? Is this a case of "nice research you're doing there, it would be a shame if anything happened to it"? Software vendors would have an interest in the chilling effect this would have on other authors, to make sure they pay, probably the expensive "you can be sure you publish academically if you've bought our premium edition" route.
I have to disagree. Yes the research may be done in breach of the software copyright. And the IP holders of that software have a right of redress.Against the research team and their institution. But that doesn't invalidate the results- the knowledge added to the human store. IP holder should sue the pants off institution, but the information should be left alone.
This post has been deleted by its author
Well of course it is. They don't want any random person reading it. After all, they may not be qualified.
(I'm firmly in the camp that says if it's a publicly funded body - say, a university - that has provided the paper, it should be easily available free of charge, or for at most a minimal charge. The problem with information like this is that you don't know if it's of any use to your immediate problem without actually reading it.)
Yes, I totally agree - in principle, but those Open Access journals are even more expensive to publish in than Evilsvier journals. Unless you have the grants to actually pay for that on top of the ridicolous publication charges you just don't do it. The science publishing world is completely f'd up: you do your reasearch, some of it on your own time (because, hey, it's interesting, and the 40 hours or so you get paid for are taken up with teaching or faculty stuff, or writing grant proposals, etc.). You write the paper, send it off to a publisher. Then it gets sent to your peers for review (who do that in their own time, for free, see above), and then you pay for it to be published. And then you pay to access your own bloody article you just wrote and paid to get published. It is a f'ing mess, and even ten years ago (when I quit academia) you could easily by a grand for a medium sized paper with a couple of colour pictures (those cost extra, because of... dunno, they say so, used to be that printing colour was expensive, but nowadays this is all "online only") - without it being open access. So... yeah. There's that.
And a software license for a couple grand per year and probably person (and those are "academia rates")? You got to be joking! There's no way small groups in underfunded basic research have that kind of cash.
You'd be surprised what you get for if you ask. We get requests from Academia for our software, and if it's research focused will often give a free license for a year or so.
That is very true. One numerical algebra/optimisation library package with a fairly expensive commercial license is/was available gratis to academic institutions for noncommercial or teaching use with the requirement that credit was given in any publication. For the BOFH the only hassle was renewing the licence every 12 to 18 months.
Most software had fairly reasonable academic licenses in terms of cost and restrictions but notably computational fluid dynamics packages basically ranged from eye watering (academic) to being flayed (commercial.)
Another peculiarity was the more expensive and restrictive licenses used flexlm (lmgrd+vendor daemon) (mis)configured in ways that made circumvention under *ix fairly straightforward. Have to wonder about the quality of the software if their developers couldn't secure their license enforcement. ;)
In reality no one begrudges the vendor of decent software their license fee if only for the support and maintenance (updates, patches.) Unfortunately there is also a fair amount of expensive, crappy software out there (generally true.)
I guess the issue there is even if the research was paid for the publishing wasn't. How significant the costs of publishing are I don't know, storing a few bits on a web server is trivial and the peer reviewers do it for free, though there will be some admin to that. Can anyone explain what else there is, if anything?
Perhaps though we should be putting more effort in to resolving the more fundamental issues, like the positive result bias in getting published in the first place. I know Ben Goldacre has some ideas, is there a movement we can get behind?
I'm inside the paywall so I can tell you that "the study" was all their own work, though using publically available data, so as far as I can see they are perfectly entitled to keep it behind a paywall just like the FT or other newspapers. The principal points made are that the retraction rate is going up faster than the publication rate and the retractions are associated more strongly with certain geographical areas and certain types of journal, implying that there are people exploiting the system to generate publication records without decent science behind them. (Why? Well in the academic world, papers get you points in most performance evaluation systems, and as we all know "points mean prizes", but that's a different debate.) There's nothing really relating to the specific retraction in the Reg article.
As to those calling for everything to be made publically accessible at no cost, well somebody's got to pay for the costs of integrity checking, we can argue about who and how, but we can all see where that's gone with social media. You-tube Science anyone? X-periments?
Somebody has to pay for which costs exactly? As a peer reviewer I work for free....
Yes, there's typesetting and general manuscript wrangling, and I really enjoyed the times when I got some motivated typesetter who did actually catch an inconsistent notation in the maths (vectors should look like this, tensors should be that, use upper case greek for these things... ). We had some disagreement about points, but in the end it was a good process. So there (an open access journal) things went very well. The university did cough up the publication costs, they had a special grant to make things open access. So, yes, there are some costs, and those need to be covered somehow.
I'm firmly in the camp that says if it's a publicly funded body - say, a university - that has provided the paper, it should be easily available free of charge, or for at most a minimal charge.
I agree, but you can usually find an online draft (basically the final paper without the publisher's logos) or simply ask the authors for a copy. Generally authors love to find out that someone is interested in their work.
Generally, if the author of an academic article is still around, requesting a copy of that article by emailing them works 99% of the time. This doesn't make it "easy access", but at least still mostly "free-ish".
Which makes the desire of most publishers to request around $30 per copy of the exact same article a bit strange, but ... welcome to research economics, I guess. None of that $30 goes back to the original researcher(s), either.
It seems rather stupid to use unlicensed software if you intend to publish an article on a site that specifically states that you need to have all your ducks in a row.
That's kind of like a training course in Excel where none of the computers have an official license and you see the red banner at the top stating that this version is unlicensed.
Not very professional.
"It seems rather stupid to use unlicensed software if you intend to publish an article on a site that specifically states that you need to have all your ducks in a row."
There's a difference between pirated software and using software with a restricted license. The fine print might have stated that the particular license can't be used to submit an academic paper. If you look at the normal license for many CAD software packages, they aren't licensed for use with anything nuclear, weapons design, etc. I'm always reading stuff but most people already "know" what's in the EULA so they don't bother.
I laugh we I see people that get a huge bill after renting a car when they take it outside the contract area. Most car hire firms limit how far from where you rented the car you can go unless you have made prior arrangements. It used to be easy to get away with, but those cars now have GPS tracking and remote kill switches. Get within certain distance of the border and the car will shut off. The cops know why the rented car quit and it was in the agreement that the person didn't read. While they often give you "unlimited miles", they define what unlimited really means and it blows their cost calculations out of the window if people were taking cars across the US on a regular basis. If I were going to do a super long driving trip, I'd rent something. The cars are much newer than mine and will have a service network if something goes wrong including a replacement car if repairs can't be made right away. If I get a puncture in my car, I'm the one that has to pay to get it fixed.
Trouble is it leaves you a complete hostage to others. Imagine, you have just finished 5 years of seminal work on spermiferous tubules. It is your lifetime achievement and your doctoral thesis. You submit it for publication and... The publication notices that your uni's subscription to Word is 6 days out of date - the work is withdrawn and your doctorate viva canceled. All for want of a horseshoe.
>a secondary publishing right should be established to ensure that researchers themselves can distribute their work without permission from their publisher<
I'd rather have a law saying any reasearch paper fundet by public money has to be published on the universities web server without a paywall or other access restrictions (and before any 3rd party like Elsevier may publish the same article).
I'm currently studying at a university, and i get access to all of Elsevier's articles, and some other major publishers. Every time i need to access the uni proxy to gain access, it think to myself "this is ridiculous". I can't imagine having to pay insane amounts to access these articles.
Even worse: these publishers don't do jack shit. You need to pay to submit a paper, then the peer review is done by unpaid academics (of course they could refuse, but expect a "the publisher will remember that" popup). Then they publish it, take most of the money instead of giving it to the researchers, and pretend it's all for protecting academic integrity. The only thing they are protecting is their bottom line and their circlejirk system called impact score.
I firmly believe that scientific publishing should be non-profit, or even better, community run. Especially research done with public grants. What pisses me off even more, is when they sell the research data to commercial entities and AI companies.
Not sure what is going on here. Flow-3D has a large and free academic program and according to they website currently supports four universities in Egypt. So why go after this paper and not reach out to the university concerned and sort out a valid license agreement. Are they pissed off with universities using hacked licenses, this particular piece of research or what. And why has the university not got a valid licence have they just not bothered. Did the researcher even know the licence was invalid? Note the paper is still available for download, just with Retracted across every page. There appears to be a completely different and possible more parochial story here than that implied in the article.
Quite odd indeed! The (retracted) paper concludes positively on the software:
"The experimental results are utilized to evaluate the performance of the Flow 3D software in replicating the erosion process. The numerical model successfully simulates the erosion process of non-cohesive earth dams."
... and so one imagines some use-agreement might be beneficial to everyone involved ... something else could be wrong though (eg. Repeat offenses from the institution or research team? Alexandria University not supporting women first authors? ...).
Then there's JStor. I did a quick check and they have papers I wrote long ago on there. I can pay to download a copy of my own work. Did they ever ask for permission to take money for them? Of course not. The really annoying thing was that at least one of them was in a free publication at the time.
"so the university probably has it on a shared computer rather than each researcher having a personal copy, which is probably a licence breech…"
Many expensive pieces of software have a license manager so somebody can "check out" a copy from a pool of seats. They can then check that seat back in or the loan might expire after a period of time.
Licenses can get very complex. My license for photos I create for a customer excludes submitting the images to a magazine or entering contests. In both of those cases, too many times those entities are insisting on having unrestricted rights to images that are submitted including the right to resell them. A customer can buy-out the images so they own the copyright if they like. It's not inexpensive. If the publication or contest don't have those insane clauses and only needs limited rights so they can use the images for the intended purpose, I'm fine with that and will happily send my customer written permission for free.
Setting aside the fuss over who owns what, does the work, now retracted, stand in its own right as a worthy contribution to engineering pertaining to fluid flow? If so, the work must remain as part of citable literature.
The interposition of factors irrelevant to academic worth is easily taken to other ridiculous lengths. Just suppose the authors of a paper refer to other published works not subscribed to by their own institution's library. Further, suppose that rather than messing around with inter-library loan services, the authors read copies of the papers obtained via the esteemable unofficial Sci-Hub service. Under the extremely unlikely circumstance of the authors being found out as having wickedly undermined 'property rights', should their work be binned lest their example encourages other people to stray from the path of rectitude?
It's a simple fact that almost all proprietary software an academic could need is available from reliable unofficial sources. Ditto for academic papers and books. Moreover, these resources can easily be acquired whilst sitting in an armchair at home, and without jumping through hoops imposed at the behest of copyright rentiers upon institutions.
Globally, the bottle of knowledge (and broader culture too) has been uncorked. The genie is out. There is desperate rearguard action by discommoded believers in nebulous property rights. Disobedience is rampant and growing in extent. The Internet, together with its unstoppable darknets, is emancipating creative thinking. So-called AI looks set to be the final straw: properly constructed, AI offers the prospect of well annotated and cross-referenced stores of knowldge presided over by an articial entity acting as curator and subject-matter librarian.
Shifts in the focii of global economic power (e.g. towards BRICS) will enable questioning of ownership assumptions (physical and intellectual) nowadays in the West fossilised. A pragmatically decided accord will arise: one recognising creative prowess (thereby supporting and, when necessary, enforcing attribution), and simulatneously asserting citizens' 'rights' to freely access digitally encoded knowledge/culture, to apply knowldge garnered by others, and to derive from work by others.
In my experience, when I can't find a copy of a paper lying around on the interwebs, I tend to find that if you email the author directly they are more than happy to send you a PDF of their work, the publishing contract allows them to do this, and I suspect they hate the pay-to-play pay-to-read academic journals more than most.
I have also found the “same” paper listed with slightly different titles. Ie. The authors have prepared slightly different versions for different journals and conferences and may even have a version available from their published work on their university’s micro site…
> slightly different versions for different journals
That's skating on thin ice if they all get published*. There is generally a condition that a paper should be "original research not previously published elsewhere", excepting review articles. Stir in too much refried beans and your journal will be kicked off the subscription list. (That was one of the issues brought up in the Nature study). Though everyone seems to have a rival who's getting away with it.
* It is common for authors to have multiple versions if the first choice journal rejects it, then it gets rewritten for another, and so on.
Research was published in 2022, it has been out there for two years. A little late to claim a piracy violation. Unless the main subject of the article, the accuracy of Flow 3D, got their nose out of joint by the results.
This actually speaks poorly of Flow 3D. It is a classic case of a losing argument. If you cannot win the debate, then attack the opposing party.
It would have been much better for Flow 3D to issue a press release stating "We disagree with the results of the research done over two years ago, and we invite the authors to re-visit their analysis. This time using up-to-date, supported, & fully licensed software."
I once read about a Kickstarter-funded game which ran into serious legal trouble when it was discovered a freelance artist had been using a Maya student (or similar trial) licence, which you are not allowed to profit from. Settling the legal matters was a five figure sum of money.
This kind of thing is potentially a major issue.
Can't comment about the software licensing as it's up to authors to provide evidence to publisher that the software used is not unlicensed. As to the pay per view publication, most authors prefer to publish in established journals to gain widespread recognition. Yes they are limited to the copyright distribution of the work by the publisher. However if the study is of utmost important, most authors or part of the main author group will write another article based on the study of the first publication and publish it on a free site and referencing the content to the first publication. The second article is then freely & legally available for distribution without infringing on the copyright of the first publish article but still provide enough information on the study.
It would be nice if in 1,000 years this article and comment thread were included in a textbook for a course about how 21st century western civilization collapsed under the tremendous weight of its own bullshit.
I won't hold my breath though. It will all burn like the libraries of Alexandria and technochitlan and cuzco and the compendium of all the world's recorded audio that was Napster, and who knows how many others that came before all of those. Insert clever Latin phrase here.
"Right now Flow-3D's sales and marketing department should be giving their legal advisers a good kicking. Why? Well, what's the message from this? That publishing a paper based on use of their product is a reputational risk."
If I have a friend that works at a cinema and they let me in to see a feature film that I go on to write a review about, am I a pirate for not having purchased a ticket? Is my review not valid since I hadn't paid?
If somebody wrote a paper about using a particular piece of software for something, why would they need to have a license for that software or for a particular version? The heart of the paper is not actual results from the software but the suitability for a particular purpose. Me thinks there's a touch of Streisand Effect here.
A reminder to those who may be unaware of the role played by "Captain Bob" (AKA Robert Maxwell) in terms of changing academic publishing (I'll leave whether change was positive or negative as an exercise for the reader) - quite a good old article
https://www.theguardian.com/science/2017/jun/27/profitable-business-scientific-publishing-bad-for-science
It does make sense to have a hierarchy of prestige, where a trusted company controls prestigious, academic journals, and the peer review process.
Kind of like the hierarchy of certificate authorities.
It is, however, a single point of failure.
I wonder how reproduction, or better yet, failure to reproduce, feeds into this system.
https://xkcd.com/583/
The Register 
Biting the hand that feeds IT
Copyright. All rights reserved © 1998–2025
