Showing posts with label open access. Show all posts
Showing posts with label open access. Show all posts

29 April 2024

Open access: What is a paper for, anyway?

Brian McGill at Dynamic Ecology blog has an interesting overview of publishing trends. The paragraph that seems to have gotten the most traction is this one: 

Open access has been a disaster. Scientists never really wanted it. We have ended up here for two reasons. First, pipe dreaming academics who believed in the mirage of “Diamond OA” (nobody pays and it is free to publish). Guess what – publishing a paper costs money – $500-$2000 depending on how much it is subsidized by volunteer scientists. We don’t really want Bill Gates etc. to pay for diamond OA. And universities and especially libraries are already overextended. There is no free publishing. The second and, in my opinion most to blame, are the European science grant funders who banded together and came up with Plan S and other schemes to force their scientists to only publish OA. At least in Europe the funding agencies mostly held scientists harmless by paying, and because of the captive audience, publishers went to European countries first for Read and Publish agreements. So European scientists haven’t been hurt too badly. But North America has so far refused to go down the same path, leaving North American scientists without grants (a majority of them) with an ever shrinking pool of subscription-based journals to publish in. And scientists from less rich countries are hurt even worse. Let’s get honest. How long before every university in Africa is covered by a Read and Publish agreement from the for profit companies?

What is interesting about this assessment is that he calls the open access situation a “disaster” on the basis of one very narrow measure: “How does it affect writing scientists?” By “writing scientists,” I mean what are usually called “principle investigators” (PIs), faculty who are busy running a lab and need publications for career advancement.

Two things.

First, most of the paragraph is concerned about how article processing charges affect scientists without grants who need to publish. I emphasize “charges” because, as I have said before, we need to separate open access – a description of who can read scientific articles – from the business models used to support open access. McGill is complaining about the latter, and isn’t addressing the former.

I do agree that many researchers have unrealistic expectations about the costs of publication. I agree that there has not been enough discussion about alternative business models for open access.

Second, journal articles do not just exist merely for the benefit of scientists who need publications to get promotion or tenure. There are not only people who write articles, there are people who read journal articles. You should consider the sizable benefits of more people being able to read scientific papers before judging the success of open access.

Article processing charges do create barriers for researchers with limited resources. But the research of hypothetical African scientists is impeded by not being able to read the scientific literature, not just by being unable to publish in the scientific literature.

If we are concerned about African researcher not being able to pay article processing charges, should we not also be concerned about African researchers being able to buy journal articles or African research libraries being able to buy journal subscriptions?

I see increased ability to read the world’s scholarly literature as a good thing. I don’t see it as an unalloyed good that must be pursued above all else. But it should be in the mix as we’re taking stock of open access.

14 January 2023

Publisher bans: A repeating pattern of attack on academic freedom

Last week, a couple of websites reported that a couple of departments at Zhejiang Gongshang University were not going to count publications appearing in three large open access publishers: MDPI, Frontiers, and Hindawi.

The policy appears to be leaked from internal memos. I searched the university site for the memo, and Google reports a result, but it is hidden behind an institutional login, so I can’t see the rationale behind this move.

This is the third attempt I know of to stop researchers from using certain publishers. I say again, publishers. And this doesn’t include the Chinese Academy of Sciences flagging dozens of journals as “risky.” 

You know, back when European funding agencies were announcing so-called “Plan S” to promote open access publication, some folks got all huffy 😤 about how vital it was to academic freedom that researchers be able to exercise choice in where they chose to publish their results. How dare a funding agency tell a researcher that they can’t publish in journals like Nature or Science, just because they are not open access! 

If that principle of researchers being able to choose their journal is important, then we are seeing a lot of attacks on academic freedom. But not many people seem to care. Far from being concerned, a lot of researchers seem to think banning researchers from using particular publishers is a great idea. That’s kind of blowing my mind. 🤯

Have these people not heard of the Declaration on Research Assessment (DORA)? It says, we “need to assess research on its own merits rather than on the basis of the journal in which the research is published.” The same principle should extend to publishers. If we shouldn’t judge research based on the journal it is in, we shouldn’t judge research based on the publisher of the journal, either.

For what it’s worth, I’ve tracked a lot of the criticism of MDPI in particular here on the blog. There are valid reasons to be concerned about editorial practices. But on the other hand, I’ve read a lot of useful papers in journals from all three of the publishers that Zhejiang Gongshang University are trying to blacklist.

Hat tip to Mario Barbatti and Richard Sever.

P.S.—Weirdly, when I searched the university for references to this new policy, one of the hits was to an open access library that said, “Most of these papers come from internationally renowned publishing institutions, including Hindawi, PlosOne, MDPI, Scientific Research Publishing and some high-quality articles from Biomed.” (Emphasis added.) So the library knows not what administrators are doing?

Update, 18 January 2023: I ran a couple of polls asking if people considered being able to choose their publication venue to be important to their academic freedom.

People on Twitter voted “Yes” more than twice as much as “No.” The vote on Mastadon was smaller but even more lopsided.

External links

Related posts

University tells scholars what journals to publish in

09 August 2022

What happened to Matters?

Logo for journal Matters
A few years ago, a journal launched called Matters. The interesting thing about this journal was that it was devoted to single observations. Science magazine saw fit to write about Matters, so it’s not like it was hidden in a dark hole under the stairs somewhere.

The journal homepage is now offline.

The journal’s Twitter account hasn’t sent tweeted since 2019. The person behind the journal, Lawrence Rajendran, is still active on Twitter, however.

Worst of all, I can’t find articles published in Matters using the DOI. They seem to have completely vanished into the ether. (There was a cool one about hermit crabs.)

I’d noticed that Matters vanished a while ago, but couldn’t tell you when. But I was reminded because I learned of MicroPublication Biology. It seems to be trying the exact same thing Matters did: offer per reviewed publication for single short papers that don’t fit into some larger narrative.

I’m skeptical of MicroPublication Biology because nobody’s name appears anywhere in the journal’s website that I can find. Who is the editor? Are there associate editors? 

But I’m also skeptical because, well, we had Matters. And it tanked. It would be nice to know the full backstory of the journal, but even without that, I think it’s fair to say Matters didn’t take the academic publishing world by storm. It may be that this is a service that people say they want, but when push comes to shove, their actions don’t back up their words. Maybe researcher would rather publish “complete stories” – with all the ambiguity and frustration of what that phrase means.

External links

Got just a single observation? New journal will publish it

Matters description on PubLons

09 December 2021

University tells scholars what journals to publish in

University of SOuth Bohemia logo and MDPI logo

The latest news around the controversial publisher MDPI, from Katarina Sam on Twitter:

Our uni made official statement about publications in MDPI journals: Such papers will not be funded, supported, and considered as a valid scientific result. We were also recommended not to do any services for them.

From her Google Scholar page,  Katarina appears to be at the University of South Bohemia (which is an awesome name, incidentally). When I search for “University of South Bohemia MDPI,” I can’t find any official statement. The first page of hits is a list of MDPI articles where one or more authors have an affiliation with the University of South Bohemia. Searching the university website also returns no policy statement, but a few articles publihsed in MDPI journals.

I am interested in the policy statement because this seems to me to be very weird and very bad.

I was under the impression that the ability to choose which journals to publish in was part and parcel of academic freedom. Indeed, one of the arguments against open access mandates from funding agencies and others was that it compromised academic freedom. But I think people made a fuss there because such mandates meant they wouldn’t be able to publish in glamour mags like Nature and Science

Here, I am less sure people are going to make a fuss because a lot of people... dislike MDPI. 

I am very, very nervous about an institution trying to ban its faculty from using, not a single journal, but an entire publishing company.

I think MDPI will be outraged because the people in charge seem to have thin skins, but I don’t think they will be harmed much. MDPI clearly has authors who value their services.

I’m more concerned by the harm this precedent sets.

Update: Charles University has a vice-dean writing blog posts about MDPI. Not so much policy, but an expression of concern, I suppose.

But what’s the point of noting that MDPI is a “Chinese company (with a postal address in Basel, of course).” How is national origin relevant to the quality of an academic publisher? What is being implied here?

More edits: The National Publications Committee of Norway (they have one of those?) announced a new listing for dubious journals: “level X.” The article begins by singling out an MDPI journal that got added to the list.

I was about to tweet earlier today that “I wonder if the push against MDPI was because an institution was unhappy about paying open access fees.” And sure enough:

The phenomenon Røeggen refers to is open publishing with author payment. - Many are worried about the phenomenon. Not for open publishing, which I experience that there is great support for in Norwegian research, but the solution we have received in open publishing where the institutions have to pay when the authors publish, says Røeggen. ...

In recent years, the requirement for open publication, through national guidelines and the so-called Plan S, has created a significant shift. Now more and more money is being paid for publishing, instead of paying to be able to read the magazines.

Emphasis added. 

And I’ve said it before, but I’ll say it again: It is weird to me that academics will bitch and moan about how long journal reviews take (“Careers are on the line here! People’s lives are put on hold because reviews take so long!”), but then consistent and prompt review is used as a reason to suspect a journal.

Questions have been asked about the rapid pace from submission of manuscripts to publication and that this is in line with research quality.

MDPI is not alone here, though. Frontiers publishing and more traditional publisher Taylor & Francis also have journals making the “level X” status. Norway is also avoiding the “carpet bombing” approach taken by the University of South Bohemia.

Still. This is not a great week for MDPI specifically and perhaps for open access more generally.

Related posts

The paradox of MDPI

My resolve not to shoot the hostage is tested

External links

The same week that the researchers' article was published, the journal ended up on the gray zone list (Automatic translation of Norwegian title; article in Norwegian, naturally)

27 June 2021

The paradox of MDPI

One of the most puzzling trends in scientific publishing for the last couple of years has been the status of the open access publisher MDPI.

On the one hand, some people I know and respect have published their papers there. I’ve reviewed for some journals, and have seen that authors do make requested changes and there is some real peer review going on.

On the other hand, few other publishers today seem so actively engaged in pissing off the people they work with. Scientists complain about constant requests to review, particularly in areas far outside their domain expertise – an easily avoided and amateurish mistake. 

And MDPI’s boss seems like a dick.

A few people have been trying to make sense of this paradox. Dan Brockington wrote a couple of analyses over the last two years (here, here) that were broadly supportive of what MDPI has done.

Today, I stumbled across this post by Paolo Crosetto that takes a long view of MDPI’s record. It prompted another analysis by Brockington here.

Both are longish reads, but are informed by lots of data, and both are nuanced, avoiding simple “good or bad” narratives. I think one of the most interesting graphs is this one in Crosetto’s post on processing turnarounds:

Graph of time from submission to acceptance at MDPI journals.  2016 shows wide variation from journal to journal; 2020 data shows little variation.

There used to be variation in how long it took to get a paper accepted in am MDPI journal. Now there is almost no smear how long it takes to get a paper accepted in an MDPI journal. That sort of change seems highly unlikely to happen just by accident. It looks a lot like a top down directive coming from the publisher, putting a thumb on the decision making process, not a result of editors running their journals independently.

Both Crosetto and Brockington acknowledge that there is good research in some journals. 

The questions seems to be whether the good reputation is getting thrown away by the publisher’s pursuit of more articles, particularly in “Special Issues.” Crosetto suspects the MDPI is scared and wants to extract as much money (or “rent” as he calls it) from as many people as fast as possible. Brockington says that this may or may not be a problem. It all depends on something rather unpredictable: scientists’ reactions. 

Scientists may be super annoyed by the spammy emails, but they might be happier about fast turn around times (which people want to an unrealistic degree) with high chance of acceptance. 

If the last decade or so in academic publishing has taught us anything, it’s that there seems to be no upper limit for scientists’ desire for venues in which to publish their work.

PLOS ONE blew open the doors and quickly became the world’s biggest journal by a long ways. But even though it published tens of thousands of papers in a single year, PLOS ONE clones cropped up and even managed to surpass it in the number of papers published per year. 

MDPI is hardly alone in presenting bigger menus for researchers to choose where to publish. Practically every publisher is expanding its list of journals at a decent clip. I remember when Nature was one journal, not a brand that slapped across the titles of over 50 journals.

MDPI is becoming a case study in graylisting. As much as we crave clear categories for journals as “real” (whitelists) or “predatory” (blacklists), the reality can be complicated.

Update, 1 July 2021: A poll I ran on Twitter indicates deep skepticism of MDPI, with lots of people saying they would not publish there.

Would you submit an article to an MDPI journal?

I have done: 9.4%
I would do: 3.9%
I would not: 50%
Show results: 36.7%

Update, 21 August 2021: A new paper by Oviedo-García analyzes MDPI’s publishing practices. It makes note of many of the features in the blog posts above: the burgeoning number of special issues, the consistently short review times across all journals. Oviedo-García basically calls MDPI a predatory publisher.

This earned a response from MDPI, which unsurprisingly disagrees.

Update, 7 March 2022: Mark Hanson lays out more issues with MDPI in this Twitter thread. A few point that he brings forth that I have not seen before:

Articles in MDPI journals have unusually high numbers of self-citations.

His blog post is also worth checking out.

Update, 13 October 2023https://twitter.com/eggersnsf/status/1557273726571487232 shows data that shows MDPI is shooting ahead of Frontiers, PLOS, and Hindawi in terms of articles published. So clearly they are offering some sort of service that people want.

Update, 10 November 2022: Dan Brockington has an updated analysis of MDPI journals.

External links

An open letter to MDPI publishing

MDPI journals: 2015 to 2019

Is MDPI a predatory publisher?

MDPI journals: 2015 to 2020 

Oviedo-García MÁ. 2021. Journal citation reports and the definition of a predatory journal: The case of the Multidisciplinary Digital Publishing Institute (MDPI). Research Evaluation: in press. https://doi.org/10.1093/reseval/rvab020

Comment on: 'Journal citation reports and the definition of a predatory journal: The case of the Multidisciplinary Digital Publishing Institute (MDPI)' from Oviedo-García

Related posts 

My resolve not to shoot the hostage is tested

Graylists for academic publishing

08 December 2020

My resolve not to shoot the hostage is tested

I’ve written before about how refusing to review a paper because you don’t like a journal hurts authors more than editors or publishers. I called refusing to review “shooting the hostage.”

I am being sorely tested in my resolve not to shoot the hostage.

MDPI is a publisher already short of good will for their amateurish practices. Their president last week seems intend in burning any remaining good will by spouting pretty fascist-sounding rhetoric.

When I got an invitation to review yesterday, I legitimately couldn’t do it because I’m moving. But it was a lot easier to say “No” than it would have been otherwise.

24 October 2019

How academic publishing is like a really nice bra

In my jackdaw meanderings around the internet, I stumbled on this thread from Cora Harrington.

Sometimes I like to look at lace prices on sites like Sophie Hallette. It’s good for giving perspective on how, even if the cost of lingerie was just fabrics (and it’s not because people should be paid for their labor), many items would still be expensive.

She gives many examples, of which I will show just one (emphasis added):

The Chloris reembroidered lace is around $1600/meter.


And that isn’t the most expensive one. Cora concludes:

When someone says “There’s no way x could cost that much,” keep in mind that there are fabrics - literally just the fabrics - that can cost 4 figures per meter.

And the labor - the expertise - involved in knowing how to handle these fabrics is worth many, many times more.

This made me think a lot about academic publishing. Because I am always fascinated by people who say something like undergraduate textbooks or journal subscriptions or article processing fees for open access publishing costs “too much.” When someone says something costs “Too much,” that means they have some notion in their head of what the “right” price is.

But as this example shows, people don’t always have a clear conception of the costs involved. And people complaining about costs sometimes tend to assume that the labour involved is simple, quick, and not worth paying a decent wage for.

This is not to say prices can’t be too high. But at least as far as academic publishing goes, I’ve only seen one attempt to work out what costs are. That is, apart from publishers themselves, who have conflicts of interest in calculating and disclosing costs.

11 May 2019

A pre-print experiment, part 3: Someone did notice

In 2016, I wrote a grumpy blog post about my worries that posting preprints is probably strongly subject to the Matthew effect. It was a reaction to Twitter anecdotes about researchers (usually famous) posting preprints and immediately getting lots of attention and feedback on their work. I wanted to see if someone less famous (i.e., me) could get attention for a preprint without personally spruiking it extensively on social media.

I felt my preprint was ignored (until I wrote aforementioned grumpy blog post). But here we are a few years later, and I’m re-evaluating that conclusion.

A new article about bioRxiv is out (Abdill and Blekman 2019), and it includes Rxivist, a website that tracks data about manuscripts in bioRvix. Having posted a paper in BioRvix, that means that my paper is tracked in Rxivist.

It’s always interesting to be a data point in someone else’s paper.

The search function is a little wonky,but I did find my paper, and was surprised (click to enlarge).


Rxivist showed that there has been a small but consistent number of downloads (Downloaded 421 times). Not only that, but the paper is faring pretty well compared to others on the site.
  • Download rankings, all-time:
    • Site-wide: 17,413 out of 49,290
    • In ecology: 542 out of 2,046
  • Since beginning of last month:
    • Site-wide: 19,899 out of 49,290
My little sand crab natural history paper is in the top half of papers in bioRxiv?

I did not expect that. Not at all.

I know there is an initial spike because I wrote my grumpy blog post and did an interview about preprints that got some attention, but even so. I know there aren’t hundreds of people doing research on sand crabs around the word, so hundreds of downloads is a much wider reach than I expected.

And some of the biggest months (October 2018) are after the final, official paper was published in Journal of Coastal Research. The final paper is open access on the journal website, too, so it’s not as though people are downloading the preprint because they are circimventing paywalls. (Though in researching this blog post, I learned a secondary site, BioOne, is not treating the paper as open access. Sigh.) (Update, 14 May 2019: BioOne fixed the open access problem!)

I am feeling much better about those numbers now than in the first few months after I posted the paper. I never would have anticipated that long tail of downloads years after the final paper is out.

And Rxivist certainly does a better job of providing metrics than the journal article does:


There’s an Altmetric score but nothing else. It’s nice that the Altmetric score for the preprint and published paper are directly comparable (and I’m happy to see the score of 24 for the paper is a little higher than the preprint at 13!), but I miss the data that Rxivist provides.

Other journals provide top 10 lists (and I’ve been happy to be on those a couple of times), but they tend to be very minimal. You often don’t know the underlying formula for how they generate those lists. The Journal of Coastal Research has a top 50 articles page that shows raw download numbers for those articles, and if you are not in that list, you have no idea how your article is doing.

While I still never got any feedback on my article before publication, I don’t feel like posting that preprint was a waste of time like I once did.

References

Abdill RJ, Blekhman R. 2019. Tracking the popularity and outcomes of all bioRxiv preprints. eLife 8: e45133. https://doi.org/10.7554/eLife.45133

Faulkes Z. 2016. The long-term sand crab study: phenology, geographic size variation, and a rare new colour morph in Lepidopa benedicti (Decapoda: Albuneidae). BioRXiv https://doi.org/10.1101/041376

Faulkes Z. 2017. The phenology of sand crabs, Lepidopa benedicti (Decapoda: Albuneidae). Journal of Coastal Research 33(5): 1095-1101. https://doi.org/10.2112/JCOASTRES-D-16-00125.1 (BioOne site is paywalled; open access at https://www.jcronline.org/doi/full/10.2112/JCOASTRES-D-16-00125.1)

Related posts

A pre-print experiment: will anyone notice?
A pre-print experiment, continued

Fiddly bits and increments

External links

Sand crab paper on Rxivist

12 April 2019

“Open access” is not synonymous with “author pays”

Wingfield and Millar have a well-meaning but misleading article, “The open access research model is hurting academics in poorer countries.” They say:

The open access model merely changes who pays. So rather than individuals or institutions paying to have access to publications, increasingly, academics are expected to pay for publishing their research in these “open access” journals. ... The bottom line is that payment has been transferred from institutions and individuals paying to have access to researchers having to pay to have their work published.

The first sentence is correct. The second is even correct. It is true that there are now more journals that require article processing charges than their used to be. Importantly, though, the phenomenon of authors paying is not new. “Pages charges” existed long before open access.

But they lose all nuance in the third sentence and commit a category error. They are confusing “freedom to read” with “business model.” These two things are not the same.

There are many counter examples to their central premise. SciELO journals are open access, but have no article processing fees. I could go on.

I am not saying that there is not a concern about the effects of article processing charges. It isn’t even restricted to scientists in “poorer countries.” Michael Hendricks, a biologist at one of Canada’s major research universities (hardly a “poorer country” by any measure, and not even a “poorer institution” by any measure) is concerned about the cost of article processing charges. He wrote:

US$2500 is 1% of an R01 modular budget. It is 2.5% of the average CIHR Project grant. It’s 10% of the average NSERC grant.

Add to that the vastly differing support across universities for article processing charges (ours is $0). There is no way around that fact that shifting publication costs from libraries to PIs imposes a massively different burden according to PI, field of science, nation, and institution.

The solution is that universities should pay article processing charges by cancelling subscriptions (with huge $ savings). But they generally aren’t. The only way I see to force the issue is for funders to make article processing charges ineligible, which will be seen as an attack on open access.

It’s real problem: library subscription costs are staying the same or going up. At the same time, more and more grant money is being spent on article processing charges. The public paying even more for science dissemination than they were is not what we want. Funders and/or universities have to stop this.

But looking back up to the counter-example, SciELO, shows something important. It shows that you can create open access journals with alternative business models that are not “author pays.” It’s unusual, maybe even difficult, but it’s not impossible.

That’s a line we should be pursuing. Not dumping on open access because people can’t distinguish between “common” and “necessary.”

External links

The open access research model is hurting academics in poorer countries

28 March 2018

Innovation must be accompanied by education


When Apple launched the iPod, the company had to put a lot of effort into educating people about digital music.

Mr. Jobs pulled the white, rectangular device out of the front pocket of his jeans and held it up for the audience. Polite applause. Many looked like they didn’t get it.

That was just fine with Mr. Jobs. They’d understand soon enough.

Apple had to inform the mass market that digital downloads could be legal (remember Napster?). They had to let people know how much music you could have with you. They had to let people know about the iTunes store. Without all those pieces of the puzzle, the iPod would have tanked.

I was reminded of these scene when Timothy Verstynan asked:

Why can’t we have a scientific journal where, instead of PDFs, papers are published as @ProjectJupyter notebooks (say using Binders), with full access to the data & code used to generate the figures/main results? What current barriers are preventing that?

I follow scientific publishing at a moderate level. I write about it. I’m generally interested in it. And I have no idea what Jupyter notebooks and binders are. If I don’t know about it, I can guarantee that nobody else in my department will have the foggiest idea.

This is a recurring problem with discussions around reforming or innovating in scientific publishing. The level of interest and innovation and passion around new publication ideas just doesn’t reach a wide community.

I think that this is because those people interested might undervalue the importance of educating other scientists about their ideas. Randy Olson talks a lot about how scientists are cheapskates with their communications budgets. They just don’t think it¤s important, and assume the superiority of the ideas will carry the day.

I’ve talked with colleagues about open access many times, and discover over and over that people have huge misconceptions about what open access is and how it works. And open access is something that has been around for a decade and has been written about a lot.

Publishing reformers drop the iPod, but don’t do the legwork to tell people how the iPod works.

So to answer Timothy’s initial question: the current barrier is ignorance.

29 January 2018

Goodbye, Storify


Storify is shutting down soon. Which is a shame. There was a point where I, and others, were using is a lot. It was a nice way to compile lots of internet resources into a single coherent timeline.

This has some relevance to matters of scientific publishing. On lots of sites like Quora, I see variations of, “Why can’t scientific articles be free to read?” Heck, here are some:


Online services — like Storify — may contribute to the lack of understanding that publishing is not free, regardless of whether the reader pays or not. They make stories, it costs them only a sign-up information, and they wonder why scientific publishing can’t be the same.


People do not understand that services that are called “free” are only free to them, not free across the board. Someone is paying bills. Preprint servers get millions of dollars in support to keep them running.
 
Or, you have operations that are not able to make a go of it, and close up shop, like Storify is now doing. Or like Google Reader did. (That one still makes me sad.)

The closing of Storify shows one of the reasons “free” is not a good way to think about scientific publishing. “Free to read,” sure. But as much as I love me some free to user online services (like Blogger, which has powered my writing here for over a decade and a half), they’re not a good model for scholarly publication.

I am playing with Wakelet as a replacement for Storify.

Hat tip to Carl Zimmer for the news about Storify.

24 September 2017

Paying to publish and Poynder

Richard Poynder and Michael Eisen got into it on Twitter over the weekend over open access publishing. Poynder wrote:


My view is that PLOS legitimised a deeply-flawed business model: pay-to-publish.

Hm. The problem is that many journals used “pay to publish” before PLOS journals came along. They were called “page charges.” You can still find many journals with page charges that are not open access. Cofactor has a list here.

These seem to indicate that asking scientists to bear some of the cost of publication is not inherently problematic. At least, I certainly don’t recall any serious discussion about them as deeply flawed. There probably should have been. But people accepted page charges as a normal, routine part of some corners of academic publishing. Saying PLOS legitimized that model is questionable.

PLOS ONE revolutionized academic publishing. But what was revolutionary was its editorial policy of not screening for “importance.” That lead to it publishing a lot of papers and generating a lot of money. It was through that combination that PLOS ONE paved the way for many imitators, including bad journals (documented in Stinging the Predators).

To me, the bigger problem is that “pay to publish” is very often equated – wrongly – with “open access.” The business model used to support publishing is not closely related to whether people can freely read the paper.

External links

Journals that charge authors (and not for open access publication)

18 September 2017

A pre-print experiment, continued


Over a year ago, I uploaded a preprint into bioRxiv. When people upload preprints, bioRxiv sensible puts on a disclaimer that, “This article is a preprint and has not been peer-reviewed.”

A little over a week ago, the final, paginated version of the paper that arose from the preprint was published. Now, bioRxiv is supposed to update its notice automatically to say, “Now published in (journal name and DOI).”

Perhaps because the final paper was substantially different than the preprint – in particular, the title changed – bioRxiv didn’t catch it. I had to email bioRxiv’s moderators through the contact form asking them to make the update.

The preprint was making more work for me. Again. It wasn’t a lot of work, I admit, but people advocating preprints often talk about them as though they take effectively zero time. They don’t. You have to pay attention to them to ensure things are being done properly. I want people to cite the final paper when it’s available, not the preprint.

Some journals are talking about using bioRxiv as their submission platform. This would be a good step, because it would remove work duplication.

I’m glad I’ve been through the preprint experience. But I am still not sold on its benefits to me as a routine part of my workflow. It seems all the advantages that I might gain from preprints can be achieved by other methods, notably publishing in open access journals with a good history of good peer review and production time.

Related posts

A pre-print experiment: will anyone notice?

26 July 2017

World’s worst... scientific papers


I have a new project to share! Just for fun, I spent the last few days making another little ebook, similar to what I did with Presentation Tips.

Stinging the Predators is a collection of deliberately horrible papers that were created to punk predatory journals. There have been six such pranks in the last two years. The most recent, which sort of triggered this project, was on Neuroskeptic’s blog last Saturday. Thinking about all the “sting” papers I’d seen over the years, it occurred to me that fake papers were practically their own emerging genre. And what better way to draw attention to a genre than with a curated anthology?

I collected all the sting papers I knew about. There turned out to be thirteen, and collecting them convinced me that it was useful to have all these examples in one place. Each paper has a short new introduction, and links to articles about it. I rounded off the collection with some short essays, some of which appeared here on the blog before, and a couple of which were new.

Once I got started with this project, I couldn’t let it go. I promised myself I would only let myself work on it for a few days, and then get back to work on writing that could be published by other people.

The ebook is available on figshare and on DoctorZen.net.

Update, 28 July 2017: After I posted the first version, I was reminded of another sting paper on Google Plus (see? It’s not a ghost town). I found another abstract after that. I decided to make a quick turnaround from version 1 to 2. There are now fifteen entries in this anthology.

The easy to remember link is http://bit.ly/StingPred. (Capitalization matters! “stingpred” will not work.)

Update, 31 July 2017: I know, two revisions in less than a week? I learned of another sting paper, and another conference abstract, bringing the total number of entries to 169 pages of mostly rubbish. (Some will probably say all is rubbish.)

Update, 7 August 2017: This little project is featured in Times Higher Education today and the Improbable Research blog!

External links

Stinging the Predators on Figshare
Predatory Journals Hit By ‘Star Wars’ Sting
Worst ever research papers revealed
“All these papers were deliberately bad”

03 July 2017

American Society of Parasitologists, Day 5

For the last day at the Parasitologists conference, I mostly sat in on taxonomy talks. Now, I love taxonomists and admire the work that they do to no end, but I think it’s fair to say that their talks do not always have the most compelling narratives. So most of my notes for talks I saw were very short.

Sara Brandt: Schistosome taxonomy. Thinks snail ecology plays the biggest role in determining the schistosome relationships.

Santos Portugal (@jsportugal3): Tick phylogeny.

Tim Ruhnke: Cestode tapeworm phylogeny.

Veronica Mantovani Bueno: More cestode tapeworm phylogeny. The revision the taxonomy of host skates and rays led to big changes in interpretation of the taxonomy and ecology of their cestode parasites. There seems to be very relaxed associations between host and parasite. Some of the cestodes she studies have very similar DNA sequences, but dramatically different morphology.

Anna Phillips: new medicinal leech. #CollectionsAreEssential

Carlos Ruiz: I came in late and missed the start of this talk, but it involved possible new copepod species.

Jackson Roberts: Turtle blood flukes, of which he described one new species. A bunch of stuff is coming about flukes in South American turtles.

Bret Warren: Looking at flukes in sturgeon. I learned that Lake Winnebago has a sturgeon fishery, which is spearfishing in winter, through holes in ice. That alone was worth the price of admission. Here’s a video of this great tradition:


Carlos Ruiz again (this was sprung on him about 10 minutes before the talk): Myxozoans are parasitic jellyfish. In this case, they cause “whirling disease” in fish. Very tough to get rid of. Started with reports from anglers noticing strange fish. State natural resources came on board to get samples.

After the contributed talks, the moment I had been waiting for: poster session! I had a poster that I was very happy with. I’ll show it on the Better Posters blog after the paper is published. (I’m writing it now!)


I was also super pleased to be reunited with my SICB symposium partner in crime, Kelly Weinersmith, who had new progeny with her.


Because the diversity of parasite research is so wide, it can be hard to detect commonalities across a conference (which I saw less than half of, at best). But there were a recurring theme from this meeting.

Parasitology, like much of biology, has been transformed by molecular biology. The techniques are making it possible to answer questions that would have been very difficult to answer without them. For instance, “Is this species of parasite in this intermediate host the same species in this definitive host?”

But parasitologists emphatically do not want molecular biology to take over their field.

Several speakers referenced the #CollectionsAreEssential hashtag on Twitter, which was prompted by the possible loss of NSF funding supporting museum collections. Museum collections are constantly under threat, and constantly proving useful to current science.

Several people noted that DNA sequence data needs to be connected to “ground truths”: you have to be able to see the organism whose DNA you are sequencing.

The recurring theme of this meeting was that for parasitology to remain a viable field, never mind a vibrant one, organismal biology has to remain strong. This is going to be a challenge, because many people find the “Sequence it all and let algorithms sort it out” approach enticing and alluring.

One last note that is tangential to the conference, but relevant to a recent post on publishing costsThe Journal of Parasitology has very competitive article processing charges, particularly for open access. Even nonmembers can publish open access for $1,000, about the same as PeerJ, which is one of the most cost effective open access megajournals.

Related posts

American Society of Parasitologists, Day 1 and 2
American Society of Parasitologists, Day 3
American Society of Parasitologists, Day 4