In the last post, I catalogued some of the reasons why Scientific Reports, in its cargo-cult attempts to ape print journals such as its stablemate Nature, is an objectively bad journal that removes value from the papers submitted to it: the unnatural shortening that relagates important material into supplementary information, the downplaying of methods, the tiny figures that ram unrelated illustrations into compound images, the pointless abbreviating of author names and journal titles.

This is particularly odd when you consider the prices of the obvious alternative megajournals:

So to have your paper published in Scientific Reports costs 10% more than in PLOS ONE, or 56% more than in PeerJ; and results in an objectively worse product that slices the paper up and dumps chunks of it in the back lot, compresses and combines the illustrations, and messes up the narrative.

So why would anyone choose to publish in it?

Well, the answer is depressingly obvious. As a colleague once expressed it to me “until I have a more stable job I’ll need the highest IFs I can pull off to secure a position somewhere“.

It’s as simple as that. PeerJ‘s impact factor at the time of writing is 2.353; PLOS ONE‘s is ‎2.776; That of Scientic Reports is ‎4.525. And so, it in the idiotic world we live in, it’s better for an author’s career to pay more for a worse version of his article in Scientific Reports than it is to pay less for a better version in PeerJ or PLOS ONE. Because it looks better to have got into Scientific Reports.

BUT WAIT A MINUTE. These three journals are all “megajournals”. They all have the exact same editorial criteria, which is that they accept any paper that is scientifically sound. They make no judgement about novelty, perceived importance or likely significance of the work. They are all completely up front about this. It’s how they work.

In other words, “getting into” Scientific Reports instead of PeerJ says absolutely nothing about the quality of your work, only that you paid a bigger APC.

Can we agree it’s insane that our system rewards researchers for paying a bigger APC to get a less scientifically useful version of their work?

Let me say in closing that I intend absolutely no criticism of Daniel Vidal or his co-authors for placing their Spinophorosaurus posture paper in Scientific Reports. He is playing the ball where it lies. We live, apparently, in a world where spending an extra $675 and accepting a scientifically worse result is good for your career. I can’t criticise Daniel for doing what it takes to get on in that world.

The situation is in every respect analogous to the following: before you attend a job interview, you are told by a respected senior colleague that your chances of getting the post are higher if you are wearing designer clothing. So you take $675 and buy a super-expensive shirt with a prominent label. If you get the job, you’ll consider it as bargain.

But you will never have much respect for the search committee that judged you on such idiotic criteria.

As I was figuring out what I thought about the new paper on sauropod posture (Vidal et al. 2020) I found the paper uncommonly difficult to parse. And I quickly came to realise that this was not due to any failure on the authors’ part, but on the journal it was published in: Nature’s Scientific Reports.

A catalogue of pointless whining

A big part of the problem is that the journal inexplicably insists on moving important parts of the manuscript out of the main paper and into supplementary information. So for example, as I read the paper, I didn’t really know what Vidal et al. meant by describing a sacrum as wedged: did it mean non-parallel anterior and posterior articular surfaces, or just that those surfaces are not at right angles to the long axis of the sacrum? It turns out to be the former, but I only found that out by reading the supplementary information:

The term describes marked trapezoidal shape in the
centrum of a platycoelous vertebrae in lateral view or in the rims of a condyle-cotyle (procoelous or opisthocoelous) centrum type.

This crucial information is nowhere in the paper itself: you could read the whole thing and not understand what the core point of the paper is due to not understanding the key piece of terminology.

And the relegation of important material to second-class, unformatted, maybe un-reviewed supplementary information doesn’t end there, by a long way. The SI includes crucial information, and a lot of it:

  • A terminology section of which “wedged vertebrae” is just one of ten sub-sections, including a crucial discussion of different interpretation of what ONP means.
  • All the information about the actual specimens the work is based on.
  • All the meat of the methods, including how the specimens were digitized, retro-deformed and digitally separated.
  • How the missing forelimbs, so important to the posture, were interpreted.
  • How the virtual skeleton was assembled.
  • How the range of motion of the neck was assessed.
  • Comparisons of the sacra of different sauropods.

And lots more. All this stuff is essential to properly understanding the work that was done and the conclusions that were reached.

And there’s more: as well as the supplementary information, which contains six supplementary figures and three supplementary tables, there is an additonal supplementary supplementary table, which could quite reasonably have gone into the supplementary information.

In a similar vein, even within the highly compressed actual paper, the Materials and Methods are hidden away at the back, after the Results, Discussion and Conclusion — as though they are something to be ashamed of; or, at best, an unwelcome necessity that can’t quite be omitted altogether, but need not be on display.

Then we have the disappointingly small illustrations: even the “full size” version of the crucial Figure 1 (which contains both the full skeleton and callout illustrations of key bones) is only 1000×871 pixels. (That’s why the illustration of the sacrum that I pulled out of the paper for the previous post, was so inadequate.)

Compare that with, for example, the 3750×3098 Figure 1 of my own recent Xenoposeidon paper in PeerJ (Taylor 2018) — that has more than thirteen times as much visual information. And the thing is, you can bet that Vidal et al. submitted their illustration in much higher resolution that 1000×871. The journal scaled it down to that size. In 2020. That’s just crazy.

And to make things even worse, unrelated images are shoved into multi-part illustrations. Consider the ridiculousness of figure 2:

Vidal et al. (2020: figure 2). The verticalization of sauropod feeding envelopes. (A) Increased neck range of motion in Spinophorosaurus in the dorso-ventral plane, with the first dorsal vertebra as the vertex and 0° marking the ground. Poses shown: (1) maximum dorsiflexion; (2) highest vertical reach of the head (7.16 m from the ground), with the neck 90° deflected; (3) alert pose sensu Taylor Wedel and Naish13; (4) osteological neutral pose sensu Stevens14; (5) lowest vertical reach of the head (0.72 m from the ground at 0°), with the head as close to the ground without flexing the appendicular elements; (6) maximum ventriflexion. Blue indicates the arc described between maximum and minimum head heights. Grey indicates the arc described between maximum dorsiflexion and ventriflexion. (B) Bivariant plot comparing femur/humerus proportion with sacrum angle. The proportion of humerus and femur are compared as a ratio of femur maximum length/humerus maximum length. Sacrum angle measures the angle the presacral vertebral series are deflected from the caudal series by sacrum geometry in osteologically neutral pose. Measurements and taxa on Table 1. Scale = 1000 mm.

It’s perfectly clear that parts A and B of this figure have nothing to do with each other. It would be far more sensible for them to appear as two separate figures — which would allow part B enough space to convey its point much more clearly. (And would save us from a disconcertingly inflated caption).

And there are other, less important irritants. Authors’ given names not divulged, only initials. I happen to know that D. Vidal is Daniel, and that J. L. Sanz is José Luis Sanz; but I have no idea what the P in P. Mocho, the A in A. Aberasturi or the F in F. Ortega stand for. Journal names in the bibliography are abbreviated, in confusing and sometimes ludicrous ways: is there really any point in abbreviating Palaeogeography Palaeoclimatology Palaeoecology to Palaeogeogr. Palaeoclimatol. Palaeoecol?

The common theme

All of these problems — the unnatural shortening that relagates important material into supplementary information, the downplaying of methods, the tiny figures that ram unrelated illustrations into compound images, even the abbreviating of author names and journal titles — have this in common: that they are aping how Science ‘n’ Nature appear in print.

They present a sort of cargo cult: a superstitious belief that extreme space pressures (such as print journals legitimately wrestle with) are somehow an indicator of quality. The assumption that copying the form of prestigious journals will mean that the content is equally revered.

And this is simply idiotic. Scientific Reports is an open-access web-only journal that has no print edition. It has no rational reason to compress space like a print journal does. In omitting the “aniel” from “Daniel Vidal” it is saving nothing. All it’s doing is landing itself with the limitations of print journals in exchange for nothing. Nothing at all.

Why does this matter?

This squeezing of a web-based journal into a print-sized pot matters because it’s apparent that a tremendous amount of brainwork has gone into Vidal et al.’s research; but much of that is obscured by the glam-chasing presentation of Scientific Reports. It reduces a Pinter play to a soap-opera episode. The work deserved better; and so do readers.

References

 

I got back on Tuesday from OpenCon 2015 — the most astonishing conference on open scholarship. Logistically, it works very different from most conferences: students have their expenses paid, but established scholars have to pay a registration fee and cover their own expenses. That inversion of how things are usually done captures much of what’s unique about OpenCon: its focus on the next generation is laser-sharp.

Open-Con-Slider-Attend-a-Satellite-960x540

They say you should never meet your heroes, but OpenCon demonstrated that that’s not always a good rule. Here I am with Erin McKiernan — the epitome of a fully open early-career researcher — and Mike Eisen, who needs no introduction:

CT2Id_YWEAAguOK

(This photo was supposed to be Erin and me posing in our PeerJ T-shirts, but Mike crashed it with his PLOS shirt. Thanks to Geoff Bilder for taking the photo.)

It was striking the opening session, on Saturday morning, consisted of consecutive keynotes from Mike and then Erin. Both are now free to watch, and I can’t overstate how highly I recommend them. Seriously, make time. Next time you’re going to watch a movie, skip it and watch Mike and Erin instead.

Much of Mike’s talk was history: how he and others first became convinced of the importance of openness, how E-biomed nearly happened and then didn’t, how PLOS started with a declaration and became a publisher, and so on. What’s striking about this is just how much brutal opposition and painful discouragement Mike and his colleagues had to go through to get us to where we are now. The E-biomed proposal that would have freed all biomedical papers was opposed powerfully by publishers (big surprise, huh?) and eventually watered down into PubMed Central. The PLOS declaration collected 34,000 signatures, but most signatories didn’t follow through. PLOS as a publisher was met with scepticism; and PLOS ONE with derision. It takes a certain strength of mind and spirit to keep on truckin’ through that kind of setback, and we can all be grateful that Mike’s was one of the hands on the wheel.

At a much earlier stage in her career, Erin’s pledge to extreme openness reflects Mike’s. It’s good to see that so far, it’s helping rather than harming her career.

erin-mckiernen-pledge

(And how is it going? Watch her talk, which follows Mike’s, to find out. You won’t regret it.)

There is so, so much more that I could say about OpenCon. Listing all the inspiring people that I met, alone, would be too much for one blog-post. I will just briefly mention some of those that I have known by email/blog/Twitter for some time, but met in the flesh for the first time: Mike Eisen and Erin McKiernan both fall into that category; so do Björn Brembs, Melissa Hagemann, Geoff Bilder and Danny Kingsley. I could have had an amazing time just talking to people even if I’d missed all the sessions. (Apologies to everyone I’ve not mentioned.)

Oh, and how often do you get to rub shoulders with Jimmy Wales?

CT_UCJFWIAAZKFH

(That’s Jon Tennant in between Jimmy and me, and Mike Eisen trying, but not quite succeeding, to photobomb us from behind.)

And yet, even with global superstars around, the part of the weekend that impressed me the most was a small breakout session where I found myself in a room with a dozen people I’d never met before, didn’t recognise, and hadn’t heard of. As we went around the room and did introductions, every single one of them was doing something awesome. They were helping a scholarly society to switch to OA publishing, or funding open projects in the developing world, or driving a university’s adoption of an OA policy, or creating a new repository for unpublished papers, or something. (I really wish I’d written them all down.)

The sheer amount of innovation and hard work that’s going on just blew me away. So: OpenCon 2015 community, I salute you! May we meet again!

Update (Saturday 21 November 2015)

Here is the conference photo, taken by Slobodan Radicev, CC by:

opencon-team-photo

And here’s a close-up of the bit with me, honoured to be sandwiched between the founders of Public Library of Science and the Open Library of Humanities! (That’s Mike Eisen to the left, and Martin Eve to the right.)

opencon-team-photo-cropped

 

[I am using the term “megajournal” here to mean “journal that practices PLOS ONE-style peer-review for correctness only, ignoring guesses at possible impact”. It’s not a great term for this class of journals, but it seems to be becoming established as the default.]

Bo-Christer Björk​’s (2015) new paper in PeerJ asks the question “Have the “mega-journals” reached the limits to growth?”, and suggests that the answer may be yes. (Although, frustratingly, you can’t tell from the abstract that this is the conclusion.)

I was a bit disappointed that the paper didn’t include a graph showing its conclusion, and asked about this (thanks to PeerJ’s lightweight commenting system). Björk’s response acknowledged that a graph would have been helpful, and invited me to go ahead and make one, since the underlying data is freely available. So using OpenOffice’s cumbersome but adequate graphing facilities, I plotted the numbers from Björk’s table 3.

megajournal-volumes-2010-2015

As we can see, the result for total megajournal publications upholds the conclusion that megajournals have peaked and started to decline. But PLOS ONE (the dark blue line) enormously dominates all the other megajournals, with Nature’s Scientific Reports the only other publication to even be meaningfully visible on the graph. Since Scientific Reports seems to be still in the exponential phase of its growth and everything else is too low-volume to register, what we’re really seeing here is just a decline in PLOS ONE volume.

It’s interesting to think about what the fall-off in PLOS ONE volume means, but it’s certainly not the same thing as megajournals having topped out.

What do we see when we expand the lower part of the graph by taking out PLOS ONE and Scientific Reports?

megajournal-volumes-2010-2015-without-top2-recoloured

Here, the picture is more confused. The numbers are dominated by BMJ Open, which is still growing, but its growth has levelled off. Springer Plus grew quickly, but seems to be falling away — perhaps reflecting an initial push, followed by author apathy for a megajournal run by a legacy publisher. AIP Advances (which I admit I’d not heard of) and SAGE Open both seem to have modest but healthy year-on-year growth. And of course PeerJ is growing fast, but it’s too young for us to have a meaningful sense of the trend.

What does it all mean?

The STM Report for 2015 (Ware and Mabe 2015) estimates that 2.5 million scholarly articles were published in English-language journals in 2014 (page 6). Björk’s data tells us that only 38 thousand of those were in megajournals — that’s less than 1/65th of all the articles. I find it very hard to believe that 1.5% of the total scholarly article market represents saturation for megajournals.

I suspect that what this study really shows us — and I’m sure the PLOS people would be the first to agree with this — is that we need a lot more megajournals out there than just PLOS ONE. Specifically:

  • It’s well established that pure-OA journals offer better value for their APCs than hybrid ones.
  • It’s at least strongly suspected (has there been a study?) that OA megajournals offer better value than selective OA journals.
  • We want to get the APCs of OA megajournals down.
  • PLOS ONE needs competition on price, to force down its increasingly unjustifiable APC of $1350.
  • It’s a real shame that the eLIFE people have fallen into the impact-chasing trap and show no interest in running an eLIFE megajournals.
  • I think the usually reliable Zen Faulks is dead wrong when he writes off what he calls “Zune journals“.

So the establishment of new megajournals is very much a good thing, and their growth is to be encouraged. Many of the newer megajournals may well find (and I hate to admit this) that their submission rates increase when they’re handed their first impact factor, as happened with PLOS ONE.

Onward!

References

Life restoration of Aquilops by Brian Engh. Farke et al. (2014: fig. 6C). CC-BY.

Life restoration of Aquilops by Brian Engh. Farke et al. (2014: fig. 6C). CC-BY.

Today sees the description of Aquilops americanus (“American eagle face”), a new basal neoceratopsian from the Cloverly Formation of Montana, by Andy Farke, Rich Cifelli, Des Maxwell, and myself, with life restorations by Brian Engh. The paper, which has just been published in PLOS ONE, is open access, so you can download it, read it, share it, repost it, remix it, and in general do any of the vast scope of activities allowed under a CC-BY license, as long as we’re credited. Here’s the link – have fun.

Obviously ceratopsians are much more Andy’s bailiwick than mine, and you should go read his intro post here. In fact, you may well be wondering what the heck a guy who normally works on huge sauropod vertebrae is doing on a paper about a tiny ceratopsian skull. The short, short version is that I’m here because I know people.

OMNH 34557, the holotype of Aquilops

OMNH 34557, the holotype of Aquilops

The slightly longer version is that OMNH 34557, the holotype partial skull of Aquilops, was discovered by Scott Madsen back in 1999, on one of the joint Cloverly expeditions that Rich and Des had going on at the time (update: read Scott’s account of the discovery here). That the OMNH had gotten a good ceratopsian skull out of Cloverly has been one of the worst-kept secrets in paleo. But for various complicated reasons, it was still unpublished when I got to Claremont in 2008. Meanwhile, Andy Farke was starting to really rock out on ceratopsians at around that time.

For the record, the light bulb did not immediately go off over my head. In fact, it took a little over a year for me to realize, “Hey, I know two people with a ceratopsian that needs describing, and I also know someone who would really like to head that up. I should put these folks together.” So I proposed it to Rich, Des, and Andy in the spring of 2010, and here we are. My role on the paper was basically social glue and go-fer. And I drew the skull reconstruction – more on that in the next post.

One of the world's smallest ceratopsians meets one of the largest: the reconstructed skull of Aquilops with Rich Cifelli and Pentaceratops for scale.

One of the world’s smallest ceratopsians meets one of the largest: the reconstructed skull of Aquilops with Rich Cifelli and Pentaceratops for scale. Copyright Leah Vanderburg, courtesy of the Sam Noble Oklahoma Museum of Natural History.

Anyway, it’s not my meager contribution that you should care about. I am fairly certain that, just as Brontomerus coasted to global fame on the strength of Paco Gasco’s dynamite life restoration, whatever attention Aquilops gets will be due in large part to Brian Engh’s detailed and thoughtful work in bringing it to life – Brian has a nice post about that here. I am very happy to report that the three pieces Brian did for us – the fleshed-out head that appears at the top of this post and as Figure 6C in the paper, the Cloverly environment scene with the marauding Gobiconodon, and the sketch of the woman holding an Aquilops – are also available to world under the CC-BY license. So have fun with those, too.

Finally, I need to thank a couple of people. Steve Henriksen, our Vice President for Research here at Western University of Health Sciences, provided funds to commission the art from Brian. And Gary Wisser in our scientific visualization center used his sweet optical scanner to generate the hi-res 3D model of the skull. That model is also freely available online, as supplementary information with the paper. So if you have access to a 3D printer, you can print your own Aquilops – for research, for teaching, or just for fun.

Cloverly environment with Aquilops and Gobiconodon, by Brian Engh (CC-BY).

Cloverly environment with Aquilops and Gobiconodon, by Brian Engh (CC-BY).

Next time: Aquilöps gets röck döts.

Reference

Farke, A.A., Maxwell, W.D., Cifelli, R.L., and Wedel, M.J. 2014. A ceratopsian dinosaur from the Lower Cretaceous of Western North America, and the biogeography of Neoceratopsia. PLoS ONE 9(12): e112055. doi:10.1371/journal.pone.0112055

Despite the flagrant trolling of its title, Nature‘s recent opinion-piece Open access is tiring out peer reviewers is mostly pretty good. But the implication that the rise of open-access journals has increased the aggregate burden of peer-review is flatly wrong, so I felt obliged to leave a comment explaining why. Here is that comment, promoted to a post of its own (with minor edits for clarity):


 

Much of what is said here is correct and important. Although it would be nice if Nature could make a bit more of an effort to avoid the obvious conflict-of-interest issues that lead it to title the piece so misleadingly as an attack on open access. I am glad that so many of the other commenters on this piece saw straight through that rather snide piece of propaganda.

Only one important error of interpretation here, I think. I quote:

The rise of the open-access (OA) movement compounds this effect [i.e. the increasing number of articles needing peer-review.] The business case for online OA journals, to which authors pay submission fees, works best at high volume. And for many of these journals, submitted work is published as long as it is methodologically sound. It does not have to demonstrate, for example, the novelty or societal relevance that some traditional journals demand.

The implication is that journals of this kind (PLOS ONE, PeerJ, the various Frontiers journals) increase the total peer-review burden. In fact, the exact opposite is the case. They greatly reduce the the total amount of peer reviewing.

It’s an open secret that nearly every paper eventually gets published somewhere. Under the old regime, the usual approach is to “work down the ladder”, submitting the same paper repeatedly to progressively less prestigious journals until it reached one that was prepared to publish work of the supplied level of sexiness. As a result, many papers go through four, five or more rounds of peer-review before finally finding a home. Instead, such papers when submitted to a review-for-soundness-only venue such as PLOS ONE require only a single round of review. (Assuming of course that they are indeed methodologically sound!)

The rise of review-for-soundness-only journals (“megajournals”) is an unequivocal improvement in the scientific publishing landscape, and should be welcomed by all parties: authors, who no longer have to submit to the monumental waste of time and effort that is the work-down-the-ladder system; readers, who get access to new research much more quickly; and editors and reviewers who no longer have to burn hours re-reviewing and re-re-reviewing perfectly good papers that have already been repeatedly rejected for a perceived lack of glamour.

A few bits and pieces about the PLOS Collection on sauropod gigantism that launched yesterday.

2013-10-29-SauropodEbook1-thumb

First, there’s a nice write-up of one of our papers (Wedel and Taylor 2013b on pneumaticity in sauropod tails) in the Huffington Post today. It’s the work of PLOS blogger Brad Balukjian, a former student of Matt’s from Berkeley days. The introduction added by the PLOS blogs manager is one of those where you keep wanting to interrupt, “Well, actually it’s not quite like that …” but the post itself, once it kicks in, is good. Go read it.

Brad also has a guest-post on Discover magazine’s Crux blog: How Brachiosaurus (and Brethren) Became So Gigantic. He gives an overview of the sauropod gigantism collection as a whole. Well worth a read to get your bearings on the issue of sauropod gigantism in general, and the new collection in particular.

PLOS’s own community blog EveryONE also has its own brief introduction to the collection.

And PLOS and PeerJ editor Andy Farke, recently in these pages because of his sensational juvenile Parasaurolophus paper, contributes his own overview of the collection, How Big? How Tall? And…How Did It Happen?

Finally, if you’re at SVP, go and pick up your free copy of the collection. Matt was somehow under the impression that the PLOS USB drives with the sauropod gigantism collection would be distributed with the conference packet when people registered. In fact, people have to go by the PLOS table in the exhibitor area (booth 4 in the San Diego ballroom) to pick them up. There are plenty of them, but apparently a lot of people don’t know that they can get them.

References