Why did I choose those journals to publish in?

So regular readers of this blog will know that I’m a pretty big fan of open access (OA) publishing. I wouldn’t call myself a “self-proclaimed OA advocate” as some seem to use pejoratively against me, but I support the principles of OA: free, unrestricted access to research for everyone. To that end, during my PhD I promised that every paper I published would be made OA. As a NERC funded student in the UK, this means I was in the fortunate position that the government had given the Research Councils UK (RCUK, which NERC is part of) millions to cover the ‘transitional costs to OA’, thereby alleviating any personal financial burden I might have had in pursuing OA.

What I want to provide here are reasons for the choices I made of where to publish in order of time throughout my PhD, and the associated costs with that. Indicated costs are the APCs, or article processing charges, unless stated otherwise.

Justification, or not..

  1. PLOS ONE. When I first heard about OA during my second Masters, it seemed absurd to me the way the current system worked. Why would I *not* want my research to be available to be read by anyone? PLOS ONE was the first OA journal I heard about, and I pledged that my first paper would be with them. And it was! Some of the work from my Masters thesis. Cost: $1350. Paid by: Imperial College London (via NERC). Also available via my institutional repo. Almost two years later, this paper is still getting media coverage!
  2. PeerJ: At this time, PeerJ didn’t have an impact factor. I wanted to show that it was risk free for junior researchers to publish here and explore new publishing models, so I did! Despite one colleague saying that “It doesn’t count” because it didn’t have an IF (what a lovely sentiment..), I still think it’s a good piece of work. Cost: free. Both me and my co-author got fee waivers; him for peer reviewing for PeerJ, me for commenting on another article. Also available via my institutional repo.
  3. Biological Journal of the Linnean Society. I was brought on last minute during the review process for this one as a croc specialist (note that at this time I hadn’t actually published on crocs, and this was known purely through Twitter!), and had no influence over the publishing venue. This paper formed part of a special volume, and I thought it was OA (it seems to be free at least from time to time), but I think is now only freely available via ResearchGate, Academia.eduand I thought it was available through my repo but apparently is not, which I will fix as soon as the system doesn’t return errors. Cost: free (not free at source) [edit: fixed now, took about ten minutes tops].
  4. Zoological Journal of the Linnean Society. This was a joint choice between myself and the co-authors based on the suitability of the research. Cost: $3600. Paid by: Imperial College London (via NERC). Thoughts? I have no idea what that APC went on. The type-setting and minor copy-editing were no different than at PeerJ, and the process was considerably slower. Also available via my institutional repo.
  5. Nature Communications. A choice beyond my control by the lead authors of the study. Originally submitted to Nature, and rejected without review. Cost: $6000. Paid by: Imperial College London (maybe through a dedicated library fund). Again, the actual publishing process to me did not seem any different from any of the other journals. The peer review quality was also about the same, with a high level of constructive feedback from referees. Also available via my institutional repo.
  6. Biological Reviews. A review paper. The only other journals which accept review papers in my field are operated by Elsevier, a publisher I have personally been boycotting since around 2011 along with more than 15,000 other researchers. This paper originally got rejected based on some very poor reviews (as in, very low quality), a decision which we appealed and was overturned (thanks to the Editors!), and subsequently the paper was handled much better by the referees and Editorial team, and was accepted with minor revisions. Cost: $3600. Paid for by: Imperial College London (via NERC). Available via my institutional repo.
  7. Proceedings of the Royal Society B. I went for a ‘mid-tier’ journal with an OA option as the research was firstly pretty cool, and secondly intensively analytical. Cost: £1700. Paid by: Imperial College London (via NERC). The payment for this was a mess. I got invoiced by both the Royal Society and Imperial College, who kept adding VAT even though that had already been included. Eventually resolved, but I kept thinking, why do they both keep asking me?! The only communication needed to be between the publisher and the payer. Again, production no different from any other journal. Faster process than Wiley. Available via my institutional repo.
  8. Zoological Journal of the Linnean Society. In press. A highly specialised article about fossil crocodilian taxonomy (atoposaurids, for regular readers!). This journal also has unlimited page lengths for submissions. Why did I choose this instead of PeerJ? The subject speciality, I think. Was it worth it? Nope. Especially as Imperial College have a deal with PeerJ for free publications. Seeing as I knew how much it would cost, this was a bad choice. Available via my institutional repo, but embargoed until the year 10000 (not even kidding..). Cost: $3600. Paid by: Imperial College (via NERC).
  9. F1000 Research. In press. Written using Overleaf. Submission took about 10 minutes. First decision took about 36 hours (acceptance). Currently being typeset about 3 days after submission. I cannot think of any reason why not to pursue this system more in future, except for limitations on venue choice (but you can directly submit to pre-print servers, PeerJ, etc). Cost: Free! (part of a special themed collection).
  10. Nature Communications. In review. Because this is the pinnacle of my PhD research, and my supervisor decided a ‘high impact’ journal would be best, given that the work is pretty awesome 😉 I originally wanted to go for PeerJ, to not be constrained by word count. Decided in the end to compromise by having a lengthy supplementary methods section. Potential cost if accepted: $6000.

One thing I don’t get either is how there can be a fixed price for highly variable items. Why is a 10 page paper the same cost or higher than one with 100 pages? What is the difference in the actual cost of production? APCs seem to be almost arbitrarily drawn out of a hat, and in every case it is extremely unclear what is being paid for in terms of services provided. Note also that costs advertised on publishers websites do not include VAT, so for UK researchers whack an extra 20% onto those APCs.

Does open access just create another form of inequality?

In the UK at least, we’ve created a system of ‘OA privilege’ now, where a cohort of junior researchers such as myself are in fortunate positions to publish OA almost wherever we want. Students not in such a fortunate position with less or zero funding will find themselves either constrained in where they can publish OA, or finding that their wish to publish OA is impossible based on the available options. While most major funders, especially those in the UK, now have funds to support OA publishing, this does not extend to all researchers (for example, those who are self-funded, or from foreign organisations), and we have now allowed publishers to replace one unbalanced system (only the privileged can read), with a different one, in which only those with appropriate funds can publish. While there are many waivers in place to reduce this imbalance, it is clearly far from a perfect system.

This of course all refers to ‘gold OA’, where papers are made freely available at the point and time of publication. While statistically around 70% of journals do not charge an APC for this service according to the DOAJ (Directory of Open Access Journals), almost all of the big publishers and journals do, and those are the ones junior researchers will usually be more compelled to publish in. What is important is not that there are options available, but that those options are constrained based on financial privilege.

No one has ever said publishing should be free, it is clear that costs are involved. But the question is how much should we pay. It is everyone’s responsibility to make sure that we get the best value for money in publishing, especially when we’re talking about using taxpayers money. The lack of transparency in APCs, and the total lack of control over how much can be charged and who is willing to pay, or who has to pay, for them does little to resolve this.

Accountability in open access publishing

Those numbers up there are firstly quite variable, and secondly extremely high. However, not a single penny of it was paid from myself. As a government funded student, almost every APC here was paid for by the taxpayer. Did I give them the best value for their money with each of my choices? No. Were the choices I made a compromise between wanting to have career success (by publishing in ‘well recognised’ journals) and wanting to publish OA. Yes.

So I think this is a problem for two reasons. Firstly, it means there is zero accountability for researchers in what they spend on OA, as the money is only being indirectly channeled through them. And secondly, we’re putting researchers in a position where if they want to publish OA, and publish in well-established journals in the hope this will influence their careers (which strong evidence indicates it will), then they have to find often large amounts of cash to fund this.

Now, this isn’t a problem with OA itself. This is the problem of treating something that started off with an idealogical basis, that research should be freely available to all without restrictions on re-use, as a service that many publishers leverage a fee for. And I’m not picking on any publisher here, although it is clear that there are some who are exploiting this financially. I’m saying this is a problem with the system we have allowed to be created around OA. As others like Bjoern Brembs have pointed out, we could publish the entire research outputs of the world OA for a fraction of the present cost we pay, but for some reason we don’t. And I think one of the main reasons for this is because no one is accepting responsibility, or being held accountable, for letting this system perpetuate. It’s no longer a ‘publish or perish’ culture. It’s a ‘publish, pay, and perish’ culture.

But the responsibility to initiate and fight for change shouldn’t be on researchers like myself and my junior colleagues, those in the most risky position at the beginning of their careers, with the most to lose and the least to gain. I take full responsibility for my choices, including the bad ones, but I feel that we shouldn’t have allowed a system like this be created in the first place. In light of this, coordinated change should be coming from the top of academia. From the tenured professors, from the senior admin positions. But nonetheless, I think all researchers need to have a look at how they can improve the system of scholarly communications and OA, and also how they have contributed to it reaching the broken state it’s in.

We need to take responsibility for our publishing decisions, and question what the motivations behind them were, and whether this is in line with the goal of research: to increase global knowledge, and maximise accessibility and re-use of information.

I broke the system.

46 thoughts on “Why did I choose those journals to publish in?

  1. You asked how the publishers choose their prices. One publisher at least let us now:
    “based on market and competitor analysis, will bring […] APC pricing in line with the wider market, taking a mid-point position amongst its competitors.”

    In other words: whatever we can squeeze out of the market.

    Ironically, given that a subscription article costs the taxpayer US$5k on average, each published Nature Communications paper (with 6k) helps raise the price line of the market even above subscription levels, at a time when publisher costs have never been lower. Mind you, I’m not accusing you of anything here, early career researchers need to do what they can to stay afloat!

  2. As you know, this is something that annoys me a lot. As a non-RCUK funded PhD student in the UK (I’m funded partially by my university via a partial fee waiver, and partially by the Canadian government and still not completely funded), I cannot access the funds that most students can in order to publish Open Access. I really would prefer that all of my papers are published in OA journals, but I’m limited in my options. I’ve published 2 papers in PLoS One, successfully getting fee waivers for each, but this is not something I’m particularly keen in continuing as I don’t want all of my papers published in the same journal. This leaves PeerJ, which in comparison to other journals is substantially cheaper for OA, but I don’t have a membership (I’d have to pay out of pocket, something I’m not currently able to do), and most of my coauthors don’t either, meaning it’s a bit tough to do. I’d like to be able to publish in some of the better OA journals like Nature Communications or Scientific Reports, but there is no possible way I can pay $6000 to publish.

    This leaves me with the (less ideal in my opinion) option of posting manuscript drafts or “in press” versions in online repositories, which is not allowed by all journals and can be difficult to navigate if you’re not used to it.

    Universities are starting to say that their research must be OA, but they won’t pay for it to be unless you’re funded, so how am I supposed to pay these fees? There needs to be some kind of change so that students without funding (or in this case, without the “correct” funding) can still publish OA without paying out of pocket. Not all students publish during their PhD, so why not allocate some of that funding to those of us without it?

    1. Liz, on a practical level, don’t forget Acta Palaeontologica Polonica, Palaeontologia Electronica and PalArch’s Journal of Vertebrae Paleontology.

      And as for PeerJ: just spring for that membership. You won’t regret it. Or if you’re really, really short of cash, write to Pete Binfield and ask for quid pro quo arrangement where you get a membership in exchange for performing reviews or something. PeerJ has been by far my best publishing experience, as well as having the cheapest of the non-zero prices.

      1. You can comment on an article and get a free APC for it, if that’s still policy. Recent authors will also have free publishing codes, if that’s still policy too.

        But yeah, Pete and Jason will never charge authors if they can’t afford it.

        The fact still remains though that we have allowed a system of financial inequality to be established, which puts students like Liz at an unfair advantage against students like me, assuming both of our research is of equal quality (note: Liz’ is way more awesome than mine XD)

      2. Acta Pal Pol has long been on my radar of a possibility, but somehow it slipped my mind when I was writing this post! Thanks for reminding me of it and others, Mike. I don’t know anything about the PalArch one… might have to look that up.

        I might try to spring for a membership next time I have a paper that is ready to submit that I think would be good though. The thing I do find frustrating is that all authors need to have a membership, so for some of my papers you’re looking at 6-7 people who need a membership as well. I have a few paper ideas that only have 1-3, and that might be an idea.

          1. Jon – So if the corresponding author is at an institution that covers it, they can pay the $695? I always just assumed it was lead author, not corresponding. Good to know.

            Mike – I’ve heard of PalArch’s JVP, but don’t really know anything about it. I’ll take a look!

    2. Relevant to this thread: I mostly don’t have research grants, either, but I published a lot of papers open access over the last few years. Here’s how: http://neurodojo.blogspot.com/2015/01/who-paid-for-my-open-access-articles.html

      Now, I know that I’m in a different position in my career, and my situation is different than Liz’s situation. What worked for me may not be available for Liz.

      But I put this here because my experience has been that a lot of people look at one open access journal (usually PLOS ONE), think, “I can’t pay that,” and stop. They don’t know about fee waivers. They don’t look around for other journal options. They don’t approach their department chair or administration to help. And then they say that open access is not feasible, despite that they have barely scratched the surface of their publishing options.

      1. For the journals that did not charge you APCs, do they have fee waivers available that you can apply for? Or did you just write to them and ask? I know of at least 2 journals that are new and currently waiving their APC, which I am planning on submitting at least one paper to ASAP. Unfortunately, these “limited time only” offers are not always well timed for when I have a paper ready to submit.

        Definitely some of what you said isn’t possible for me, but it’s interesting to see some other ways you’ve managed. I wish that more OA journals (or journals that offered OA) would offer fee waivers if you could show that you don’t have funding. Not only am I not RCUK funded, but I’m not even fully funded, so paying OA out of pocket is hard.

        1. Liz,

          I am 100% unfunded, and I have yet to pay an APC. I think nearly every OA journal editor is aware of the financial issues different people face, and the great majority will be sympathetic to a simple request to waive the APC. There is certainly no downside in asking!

        2. In general, 70% of ‘gold’ OA journals do not even charge any APCs… Varies from field to field and of course journal reputation (whenever that matters).

        3. “For the journals that did not charge you APCs, do they have fee waivers available that you can apply for? Or did you just write to them and ask?”

          In most cases, it was just the way the journal ran. A couple of journals had their costs picked up by the scientific society that ran them (e.g., Knowledge and Management of Aquatic Ecosystems, Crustacean Research). Some were very small niche journals (Invertebrate Rearing, Global Virtue Ethics Review). One, as mentioned in post, was an introductory offer.

          In no cases did I write and ask for a waiver.

    3. Liz, most Gold OA publishers have waiver schemes regardless of where you are based, so you just need to ask on submission.

  3. I wouldn’t call myself a “self-proclaimed OA advocate”

    Whyever not? That’s what I call myself, and proudly. Anyone who thinks that is a pejorative term is simply mistaken. Fly your flag with pride!

    1. More the ‘self-proclaimed’ part. I’ve never stated that, but still (Angela Cochran, among others) use it pejoratively against me as if it’s a bad thing, so I’d rather not have it attached as a label. As I said, I overwhelmingly support the principles of OA; whether that makes me an advocate or not, I’m not really bothered.

  4. Pathetic that you were duped into spending an additional $5901 for the privilege of having Nature Communications slow down your publication and relegate significant material to an Online Supplement which everyone will ignore and which NPG will inevitable lose after a few years. Shame on your supervisor.

    1. This is exactly the problem though. There is no accountability as the author didn’t pay. I don’t blame Phil for this choice (or Nature for original submission), as at the time he was still a Junior Research Fellow (I think), in a position/institute where the IF still means everything. He made a compromise between OA and ‘high impact’, and someone else paid the price for it. The same for everyone else who ever published there.

  5. “if they want to […] publish in well-established journals in the hope this will influence their careers (which strong evidence indicates it will)” <– [citation needed]

      1. The last postdoc I applied to wanted evidence of publishing in “High impact, international peer reviewed journals”. While the majority of applications still demand this, it will be important.

      2. Thanks for this link, very interesting (and new to me).

        “The actual number of citations is less predictive of becoming a PI than journal impact factor (Figure 1B), suggesting that currently, the perceived quality of a publication (i.e., journal impact factor) is given more weight than its actual quality (i.e., number of citations).”

        Jesus wept.

      3. The one mitigating factor worth mentioning here is while this study does a good job of showing correlation between high-IF publications and “success” (i.e. becoming a PI), it says nothing about causation. Mike Eisen has argued that people whose work ends up in high-IF journals may do so because it’s good work, and the goodness of the work is also the reason they get PI jobs. If he’s right, then the two correlated measures are both dependent on the third. (I don’t know how to test that possibility, though — does anyone see a way?)

        BTW., the article itself is a fine advert for what a completely craptastic process glam-mag publishing is. The whole thing is compressed nearly to the point of unreadability, key information is relegated to the SI, and the single figure is in fact eight or at most five quite separate figures wedged together in super-tiny size to fit some arbitrary and pointless limit imposed by Cell. The authors work would have been far more clear, persuasive and useful if they’d published it at its natural length in a proper journal.

        1. You are correct about causation, of course. However, see this case study for an example of how virtually all decisions about people (tenure, promotion hiring) are made these days (with direct reference to Mike):


          In any meeting where someone wants to describe any other person, the first or second thing they mention is where they publish and how many papers.

  6. “But the responsibility to initiate and fight for change shouldn’t be on researchers like myself and my junior colleagues” <– Funny how every group says that the responsibility shouldn’t be on them, isn’t it?

  7. Well, I made it to the end of this post, despite all my digressions to comment along the way 🙂 What did you mean by “I broke the system” right at the end?

    I think this was a fascinating exercise and very well worth doing. If I get around to it, I hope to do the same thing on SV-POW! for my own choices.

    One thing that’s become apparent from reading this is that you’ve built up a really nice body of work. Congratulations! Let’s hope it lands you the job you deserve — and on the basis of the science, not the the brand-labels attached to it.

    1. That’s me taking responsibility. Even though as I say before, the impetus shouldn’t be on PhD students to drive change, I still contributed towards a broken system by chasing journal prestige (to a degree).

      And that would be great, would love to see others replicate this exercise! And thank you, I have tried 🙂 Why would I bother spending 3.5 years researching stuff no one could read about?!

  8. Thanks for an interesting post. I quite agree that fees are too high, too decoupled from actual costs/services, and not subject to meaningful market forces because funders seem happy to pay any amount.

    Regarding article number 8 above, if NERC paid, shouldn’t the final published version be CC-BY, in which case you can put that in the repository without any embargo, right?

    Regarding VAT, I’d originally thought most universities were exempt, but it sounds like that’s not the case, though I find the information here a little unclear:

    It also sounds like there is a VAT peculiarity about online vs print journals:

    1. It will be CC-BY when it has been published. The article is being typeset now, and as soon as it’s published, the embargo will drop for my IR, and I’ll also upload the final version there too. At the moment, it’s just the accepted manuscript in the IR.

      I have no idea what the policies are regarding VAT, but all I know is that I’ve (my funder) been paying it!

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