Scientific Reports is an objectively bad journal
April 25, 2020
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 than 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
- Taylor, Michael P. 2018. Xenoposeidon is the earliest known rebbachisaurid sauropod dinosaur. PeerJ 6:e5212. doi: 10.7717/peerj.5212
- Vidal, Daniel, P Mocho, A. Aberasturi, J. L. Sanz and F. Ortega. 2020. High browsing skeletal adaptations in Spinophorosaurus reveal an evolutionary innovation in sauropod dinosaurs. Scientific Reports 10(6638). Indispensible supplementary information at https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-020-63439-0/MediaObjects/41598_2020_63439_MOESM1_ESM.pdf
doi:10.1038/s41598-020-63439-0
Sauropod Vertebra Picture of the Week 
April 25, 2020 at 9:32 pm
One additional issue you did not mention is their unenforced data availability policy. You’re lucky if the data are actually in the supplementary materials. I’m tired of seeing papers in Scientific Reports where the authors did not upload their sequence data to any public repository. Sometimes I get a quick response to an email enquiry asking the authors for data; more often, it seems, I get silence, both from the authors and from the journal editors. In 2020 (and long before!), including accession numbers for sequence data should be a minimum standard for publications relying on such data, not something extra.
April 25, 2020 at 9:37 pm
[…] the last post, I catalogued some of the reasons why Scientific Reports, in its cargo-cult attempts to ape print […]
April 25, 2020 at 9:44 pm
Excellent point, Ian. One of my gripes with the Spinophorosaurus paper is that I’ve not been able to find the digital models that they used.
April 25, 2020 at 10:10 pm
Amen!
April 25, 2020 at 10:22 pm
Another problem is that Scientific Reports has not ensured that the nomenclatural acts published in it are registered in Zoobank like other online-only journals have. Now we have a ton of dinosaur names published in SR that are technically unavailable thanks to this oversight.
April 26, 2020 at 3:12 am
Was just going to mention what Tyler said. A (?)complete list of Mesozoic dinosaur taxa published by Scientific Reports, but which are invalid due to not following ICZN Article 8.5.3. (names published electronically must “be registered in the Official Register of Zoological Nomenclature (ZooBank) (see Article 78.2.4) and contain evidence in the work itself that such registration has occurred”) is- “Lingyuanosaurus”, “Fukuivenator”, “Savannasaurus”, “Tongtianlong”, “Corythoraptor”, Daspletosaurus “horneri”, “Isaberrysaura”, “Mierasaurus”, “Xingxiulong”, “Anomalipes”, “Jinyunpelta”, “Yizhousaurus”, “Bajadasaurus”, “Xingtianosaurus”, “Huanansaurus”, “Mosaiceratops”, “Pulanesaura”, “Zhenyuanlong”, “Yunyangosaurus”, “Asfaltovenator”, “Chongmingia” and “Tingmiatornis.”
I checked all the dinosaur taxa from the other potential journal to have this issue, Nature Communications, but they are very consistent and always have a Nomenclatural Acts section.
And yes, abbreviated journal names are a pet peeve of mine as well.
April 26, 2020 at 6:24 am
Yes, Scientific Reports is a bad journal.
In November 2019, they published a very bad paper on Halszkaraptor and paravian phylogeny: see my rebuttal of that paper published in February 2020 in PeerJ for a detailed explanation of why that paper was that bad: https://peerj.com/articles/8672/
April 26, 2020 at 6:54 am
To explain my above comment, my concern is about the terribly bad peer review that should have allowed that Scientific Reports paper to be accepted and published.
April 26, 2020 at 9:24 am
(I assume Andrea is referring to the Halszkaraptor paper, not the Spinophorosaurus one!)
April 26, 2020 at 2:48 pm
Yes, I referred to the Halszkaraptor paper.
April 26, 2020 at 6:13 pm
The comments above about missing data and unregistered names are interesting. I suspect a key reason for the author stampede away from PloS ONE starting in 2014 was the introduction of strict data sharing requirements in that year. This risk was noted at the time by David Crotty:
https://scholarlykitchen.sspnet.org/2014/03/04/plos-bold-data-policy/
Staying loose may have paid off for Scientific Reports in the short term, but I suspect they will come to regret it. A set of papers without supporting data will inevitably contain more fraud than a similar set with data. Look at the recent set of 400+ fakes from the same paper mill: Taylor & Francis, Wiley, Karger and Elsevier published dozens each; Springer-Nature, 17; PLoS, zero.
https://forbetterscience.com/2020/01/24/the-full-service-paper-mill-and-its-chinese-customers/
April 26, 2020 at 9:55 pm
You make an excellent point, Thomas. I rather hope you’re right that cowardly scientists’ fear of revealing their data is behind the drop-off in PLOS submissions — because that would mean that more authors will return as funder requirements about open data become more stringent.
April 27, 2020 at 8:47 am
Oh, I totally agree about the very misleading figure 2: I was browsing the paper when I stopped for a few seconds when I saw it… What came to my mind was someting like “Wut ?”
Now, I can only validate your annoyance regarding the abuse of Supplementary information. Nomenclatural acts MUST be in the core of the paper. Contrary to what many of my colleagues think, biological nomenclature is at the very basis of taxonomy, which is among the pillars of biology.
How can you study some specimen if you do not ascribe it to a taxon ? If you have no taxonomy at all ? How could you even do that without a solid (but certainly improvable) set of rules indicating what name you should use and how ?
What is true of biological nomenclature is obviously true of any other method used in a study. Methods should not be relegated elsewhere, most of the time left to the good will of the authors (the number of times I wasn’t able to the find the data matrices… :-| ). The adequate description of the methods used by the authors is one of the main criterion allowing readers to judge the quality of a study. One of the first things I do when reading a paper describing a new taxon is going directly to the appropriate section… when there is one. New taxa shouldn’t be named in footnotes, neither in supplementary informations, just like clade shouldn’t be named and defined in the text. The procedure and selection of types / specifiers can of course be discussed in the text, but the naming must be in a clear, dedicated section.
By the way, ALL JOURNALS PUBLISHING NEW TAXA / CLADE SHOULD HAVE A COMPETENT EDITOR ON BIOLOGICAL NOMENCLATURE.
The CORRECT USE of biological nomenclature is NOT AN OPTION. It is as ESSENTIAL as using correct equations, correct chemical formulas, correct coordinates.
All of us cannot be as versed as some in the ICZN, sometimes obscure, rules, true enough. But rigourous science can only be made with rigourous methods.
I can’t believe the number of flagrant errors I see published, even in supposed international journals, like these :
> Selecting five associated skeletons of Microvaranops parentis Spindler et al., 2018 as a holotype !
>> Spindler et al. (2018), in Paläontologische Zeitschrift. :-|
> Describing the historical holotype of Steneosaurus rostromajor Geoffroy Saint-Hilaire, 1825, a chimaera of metriorhynchoid and teleosauroid thalattosuchian bones… as an HYBRID, even citing the appropriate section of the ICZN ! Not only a chimaera, but an HYBRID, you read well, of a metryorhynchoid and a teleosauroid !!! You wanted to be scared ? Now you are !! :-[
>> Johson et al. (2020), in Zoological Journal of Linnean Society.
…
It’s okay, I feel better, now. :-D
I’m just angry because I don’t have the time – and neither do my colleagues who are more familiar with the ICZN – to correct these. And few journals would accept a corrigendum about such “trivial” matters, anyway.
Next rants : people not indicating the orientation of the bones they figure ; people not indicating which of the left or right appendicular bone they figure ; people not indicating features they desribe on their figure.
PS : Now, I feel like writing a scenario for The Asylum… weird ! ><
April 27, 2020 at 9:16 am
dimetroblog, your complaints about sloppy biological nomenclature are certainly justified; I just want to clarify that none of those criticisms apply to the Vidal et al. paper that we started with — which is not concerned at all with nomenclature and contains no nomenclatural acts. (Although the relegation of all its terminology to the supplementary information is similarly deplorable.)
April 27, 2020 at 9:43 am
Thanks for this Mike. Worth noting that Nat Sci Rep took a plunge in output in 2018 (below that of Plos One). But it seems to have recovered slightly. Still not back up to its 2017 peak, but Plos One has continued to fall.
April 27, 2020 at 10:13 am
Interesting, Stuart: do you have a comparative source this? (It would be good to see graphs.)
Of course I really ought to take a close look at how RSOS performs on all these counts!
April 27, 2020 at 11:06 am
If I could figure out how to attach a graph as a comment, I would.
Yes, do please look at RSOS – we are always looking to make improvements!
April 27, 2020 at 11:34 am
You can leave a link to a graph in a comment!
April 27, 2020 at 11:48 am
Here you go.
https://drive.google.com/open?id=1ZPBR1KVCpEfwo2bQU66P-w6D3EeT6U8P
April 27, 2020 at 1:18 pm
You are going to laugh.
Supplementary information is nowhere mentioned in the Code.
The Code is not aware that supp. inf. is a thing that exists.
Consequently, nobody knows if the supp. inf. to a validly published paper counts as part of the paper or not. The Commission has simply never said a word about it.
And so, nobody knows if Lisowicia is an available name, to pick one example that comes to mind. There are others.
(“Available”: properly published.
“Potentially valid”: available, and not a junior homonym.
“Valid”: potentially valid, and not a junior synonym.
Names that are unavailable are treated as not existing. They don’t compete for synonymy or homonymy.)
The Code is also remarkably vague on whether a type is a specimen, an individual, or the intersection of both. I found one spot where it implies that it is an individual (except for hapantotypes which don’t concern us in vertebrate paleo- or neontology), but most articles that mention types simply don’t make it clear at all. The Commission doesn’t seem to have given the facts much thought that a specimen can contain several individuals and that parts of an individual can have different specimen numbers.
April 27, 2020 at 3:12 pm
Of course, Mike, I didn’t mean to criticize Vidal et al. regarding nomenclature. The fact that some crucial methodological elements were elsewhere because the publication must short / sexy / etc is abnormal. Or, rather, it should be in a world where scientists and their supervisors are both reasonable and honest (which it is not the case, mind you).
Sorry for the long rant – I think it had been a long time since I was able to unload my nomenclatural frustration. ^^
Now, I think the real question here is : why is there no thagomizer on the reconstruction ? I liked to think that, if Miragaia was a stegosaur that disguise as a sauropod, Spinophorosaurus was a sauropod that disguise as a stegosaur.
A kind of Rupaul’s Dino Race [no offense intended of any kind, LGBTQ friends, for the comparison].
Regarding the ICZN, David, I didn’t know that. But if you like jokes about the ICZN (not like most of our friends, I suspect), it is even worser than you think (ugh !), because nowhere is a specimen defined in the whole Code. Another of these so well-known and used words that no one even bothered in providing a clear definition. Individuals used to define different species are frequent, for instance. When the whole individual has been used, these species are clearly objective synonyms. But when different parts were used, wether because they were collected or sold separately, for instance, are they really objectively synonyms (sensu the Code)?
April 27, 2020 at 3:19 pm
I think Daniel Vidal and co concluded a few years ago that the “tail spikes” were not tail spikes. But I can’t locate the publication where they showed this (if indeed there is one), and sadly the matter is not mentioned at all in either the new paper nor the supplementary information.
April 27, 2020 at 3:28 pm
Too bad… :-(
Here is the abstract I found after your comment :
Daniel Vidal, Francisco Ortega, Ainara Aberasturi & José Luis Sanz 2015. The specialized tail of Spinophorosaurus nigerensis (Sauropoda. Middle Jurassic) and the osteological limits on its range of motion. SVPCA 2015.
April 27, 2020 at 10:10 pm
Actually, it was Emmanuel Tschopp and Octavio Mateus who identified the “tail spikes” of Spinophorosaurus as clavicles, and the reported clavicle of 2009 as the interclavicle, on their must-read 2012 paper at journal of anatomy: https://onlinelibrary.wiley.com/doi/full/10.1111/joa.12012
Our interpretation in 2015 only agreed with theirs.
The size of the clavicles and the fact they are ossified are crucial to the position and orientation of the scapulae in Spinophoro. Sternal ribs (which were not preserved or were not ossified in Spinophoro) and dorsal ribs also had a crucial role in placing the pectoral girdle.
April 28, 2020 at 2:27 pm
Oh yes. Half the Code is like Linnaeus, who assumed everything was obvious anyway and needed no explanation – funnily enough that is why the Code became necessary.
:-o I completely missed that!
Since I’m already talking about terminology: if clavicles are present at all, they are ossified, because they’re dermal bones. Sternal ribs, on the other hand, can be unossified but present, because they start out as cartilage which is, sometimes, replaced by endochondral bone.
April 29, 2020 at 3:41 pm
That is apparently up to the authors: all first names are spelled out in this paper.
April 29, 2020 at 4:36 pm
Ha! Well spotted. How strange (on the authors’ part).
April 29, 2020 at 5:09 pm
Or maybe they got a new editor who lets full names through. Here’s another.
April 29, 2020 at 6:00 pm
That paper is also noteworthy for having the Materials & Methods before the Results.
I’ve just been told many papers that end up in Sci Rep were rejected by Nature and not reformatted.
April 29, 2020 at 6:04 pm
That is certainly easy to believe. Where did you hear it?
April 29, 2020 at 10:40 pm
Pers. comm. from a colleague who further suggested that a particular paper had probably been submitted to Nature Ecology & Evolution first.
Anyway, here’s a Sci. Rep. paper from 2016 that spells all 12 first names out and has the Methods before the Results.
May 1, 2020 at 7:27 pm
[…] was really speaking in support of this modified version. I make no secret of the fact that I think some journals are objectively better than others; but that those with higher impact factors are often worse, not […]