Tutorial 39: how not to conclude a talk or paper
March 19, 2021
“And in conclusion, this new fossil/analysis shows that Lineageomorpha was more [here fill in the blank]:
- diverse
- morphologically varied
- widely distributed geographically
- widely distributed stratigraphically
…than previously appreciated.”
Yes, congratulations, you’ve correctly identified that time moves forward linearly and that information accumulates. New fossils that make a group less diverse, varied, or widely distributed–now that’s a real trick.
Okay, that was snarky to the point of being mean, and here I must clarify that (1) I haven’t been to a conference in more than a year, so hopefully no-one thinks I’m picking on them, which is good, because (2) I myself have ended talks this way, so I’m really sniping at Old Matt.
And, yeah, new fossils are nice. But for new fossils or new analyses to expand what we know is expected. It’s almost the null hypothesis for science communication–if something doesn’t expand what we know, why are we talking about it? So that find X or analysis Y takes our knowledge beyond what was “previously appreciated” is good, but it’s not a particularly interesting thing to say out loud, and it’s a really weak conclusion.
(Some cases where just being new is enough: being surprisingly new, big expansions [like hypothetically finding a tyrannosaur in Argentina], and new world records.)
Don’t be Old Matt. Find at least one thing to say about your topic that is more interesting or consequential than the utterly pedestrian observation that it added information that was not “previously appreciated”. The audience already suspected that before you began, or they wouldn’t be here.
I showed this post to Mike before I published it, and he said, “What first made you want to work on this project? That’s your punchline: the thing that was cool enough that you decided to invest months of effort into it.” Yes! Don’t just tell the audience that new information exists, tell them why it is awesome.
We’ve noted many times over the years how inconsistent pneumatic features are in sauropod vertebra. Fossae and formamina vary between individuals of the same species, and along the spinal column, and even between the sides of individual vertebrae. Here’s an example that we touched on in Wedel and Taylor (2013), but which is seen in all its glory here:
Taylor and Wedel (2021: Figure 5). Giraffatitan brancai tail MB.R.5000, part of the mounted skeleton at the Museum für Naturkunde Berlin. Caudal vertebrae 24–26 in left lateral view. While caudal 26 has no pneumatic features, caudal 25 has two distinct pneumatic fossae, likely excavated around two distinct vascular foramina carrying an artery and a vein. Caudal 24 is more shallowly excavated than 25, but may also exhibit two separate fossae.
But bone is usually the least variable material in the vertebrate body. Muscles vary more, nerves more again, and blood vessels most of all. So why are the vertebrae of sauropods so much more variable than other bones?
Our new paper, published today (Taylor and Wedel 2021) proposes an answer! Please read it for the details, but here’s the summary:
- Early in ontogenly, the blood supply to vertebrae comes from arteries that initially served the spinal cord, penetrating the bone of the neural canal.
- Later in ontegeny, additional arteries penetrate the centra, leaving vascular foramina (small holes carrying blood vessels).
- This hand-off does not always run to completion, due to the variability of blood vessels.
- In extant birds, when pneumatic diverticula enter the bone they do so via vascular foramina, alongside blood vessels.
- The same was probaby true in sauropods.
- So in vertebrae that got all their blood supply from vascular foramina in the neural canal, diverticula were unable to enter the centra from the outside.
- So those centra were never pneumatized from the outside, and no externally visible pneumatic cavities were formed.
Somehow that pretty straightforward argument ended up running to eleven pages. I guess that’s what you get when you reference your thoughts thoroughly, illustrate them in detail, and discuss the implications. But the heart of the paper is that little bullet-list.
Taylor and Wedel (2021: Figure 6). Domestic duck Anas platyrhynchos, dorsal vertebrae 2–7 in left lateral view. Note that the two anteriormost vertebrae (D2 and D3) each have a shallow pneumatic fossa penetrated by numerous small foramina.
(What is the relevance of these duck dorsals? You will need to read the discussion in the paper to find out!)
Our choice of publication venue
The world moves fast. It’s strange to think that only eleven years ago my Brachiosaurus revision (Taylor 2009) was in the Journal of Vertebrate Palaeontology, a journal that now feels very retro. Since then, Matt and I have both published several times in PeerJ, which we love. More recently, we’ve been posting preprints of our papers — and indeed I have three papers stalled in peer-review revisions that are all available as preprints (two Taylor and Wedels and a single sole-authored one). But this time we’re pushing on even further into the Shiny Digital Future.
We’ve published at Qeios. (It’s pronounced “chaos”, but the site doesn’t tell you that; I discovered it on Twitter.) If you’ve not heard of it — I was only very vaguely aware of it myself until this evening — it runs on the same model as the better known F1000 Research, with this very important difference: it’s free. Also, it looks rather slicker.
That model is: publish first, then filter. This is the opposite of the traditional scholarly publishing flow where you filter first — by peer reviewers erecting a series of obstacles to getting your work out — and only after negotiating that course to do get to see your work published. At Qeios, you go right ahead and publish: it’s available right off the bat, but clearly marked as awaiting peer-review:
And then it undergoes review. Who reviews it? Anyone! Ideally, of course, people with some expertise in the relevant fields. We can then post any number of revised versions in response to the reviews — each revision having its own DOI and being fixed and permanent.
How will this work out? We don’t know. It is, in part, an experiment. What will make it work — what will impute credibility to our paper — is good, solid reviews. So if you have any relevant expertise, we do invite you to get over there and write a review.
And finally …
Matt noted that I first sent him the link to the Qeios site at 7:44 pm my time. I think that was the first time he’d heard of it. He and I had plenty of back and forth on where to publish this paper before I pushed on and did it at Qeios. And I tweeted that our paper was available for review at 8:44 — one hour exactly after Matt learned that the venue existed. Now here we are at 12:04 my time, three hours and 20 minutes later, and it’s already been viewed 126 times and downloaded 60 times. I think that’s pretty awesome.
References
- Taylor, Michael P. 2009. A re-evaluation of Brachiosaurus altithorax Riggs 1903 (Dinosauria, Sauropoda) and its generic separation from Giraffatitan brancai (Janensch 1914). Journal of Vertebrate Paleontology 29(3):787-806. [PDF]
- Taylor, Michael P., and Mathew J. Wedel. 2021. Why is vertebral pneumaticity in sauropod dinosaurs so variable? Qeios 1G6J3Q. doi: 10.32388/1G6J3Q [PDF]
- Wedel, Mathew J., and Michael P. Taylor 2013b. Caudal pneumaticity and pneumatic hiatuses in the sauropod dinosaurs Giraffatitan and Apatosaurus. PLOS ONE 8(10):e78213. 14 pages. doi: 10.1371/journal.pone.0078213 [PDF]
Name the journal. Shame the publisher.
September 11, 2020
Here’s an odd thing. Over and over again, when a researcher is mistreated by a journal or publisher, we see them telling their story but redacting the name of the journal or publisher involved. Here are a couple of recent examples.
First, Daniel A. González-Padilla’s experience with a journal engaging in flagrant citation-pumping, but which he declines to name:
Interesting highlight after rejecting a paper I submitted.
Is this even legal/ethical?
EDITOR-IN-CHIEF’S COMMENT REGARDING THE INCLUSION OF REFERENCES TO ARTICLES IN [REDACTED]
Please note that if you wish to submit a manuscript to [REDACTED] in future, we would prefer that you cite at least TWO articles published in our journal WITHIN THE LAST TWO YEARS. This is a polict adopted by several journals in the urology field. Your current article contains only ONE reference to recent articles in [REDACTED].
And here is Waheed Imran’s experience of editorial dereliction:
I submitted my manuscript to a journal back in September 2017, and it is rejected by the journal on September 6, 2020. The reason of rejection is “reviewers declined to review”, they just told me this after 3 years, this is how we live with rejections. @AcademicChatter
@PhDForum
My, my question is, why in such situations do we protect the journals in question? In this case, I wrote to Waheed urging him to name the journal, and he replied saying that he will do so once an investigation is complete. But I find myself wondering why we have this tendency to protect guilty journals in the first place?
Thing is, I’ve done this myself. For example, back in 2012, I wrote about having a paper rejected from “a mid-to-low ranked palaeo journal” for what I considered (and still consider) spurious reasons. Why didn’t I name the journal? I’m not really sure. (It was Palaeontologia Electronica, BTW.)
In cases like my unhelpful peer-review, it’s not really a big deal either way. In cases like those mentioned in the tweets above, it’s a much bigger issue, because those (unlike PE) are journals to avoid. Whichever journal sat on a submission for three years before rejecting it because it couldn’t find reviewers is not one that other researchers should waste their time on in the future — but how can they avoid it if they don’t know what journal it is?
So what’s going on? Why do we have this widespread tendency to protect the guilty?
Update (13 September 2021)
One year later, Waheed confirms that the journal in question not only did not satisfactorily resolve his complaint, it didn’t even respond to his message. At this stage, there really is no point in protecting the journal that has behaved so badly, so Waheed outed it: it’s Scientia Iranica. Avoid.
I think we’ve all had enough of the Impact Factor as a way of measuring the quality of journals. From Ginny Barbour’s forensic account of negotiating PLoS Medicine’s IF back in 2006, via Stephen Curry’s measured rant back in 2012 (“if you use impact factors you are statistically illiterate”) and Björn Brembs’ survey of how very widespread IF negotations are in 2016, to all the recent negotiations with Clarivate about which journals should even have IFs, it’s become increasingly obvious that the Impact Factor is not a metric, it’s a negotiation.
And of course this means that the reason any journal has the particular IF it has is competely opaque.
The world needs a much more transparent metric of journal quality, and I am here to offer it! The Objective Quality Factor (QOF) is assigned in a wholly straightforward way that anyone can understand:
Your journal obtains an OQF of x by paying me x pounds.
That’s it. As soon as I acknowledge your payment, you have the right to display your OQF on the journal home page and in marketing materials.
If another journal in your field obtains a higher OQF than yours, and you need to regain your journal’s position at the top of the totem pole, all you need do is send me more money.
Payments via PayPal to ebay@miketaylor.org.uk please!
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
Matt’s Brachiosaurus in the wild
February 16, 2020
No, not his new Brachiosaurus humerus — his photograph of the Chicago Brachiosaurus mount, which he cut out and cleaned up seven years ago:
This image has been on quite a journey. Since Matt published this cleaned-up photo, and furnished it under the Creative Commons Attribution (CC By) licence, it has been adopted as the lead image of Wikipedia’s Brachiosaurus page [archvied]:
Consequently (I assume) it has now become Google’s top hit for brachiosaurus skeleton:
Last Saturday, Fiona and I went to Birdland, a birds-only zoo in the Cotswolds, about an hour away from where we live. The admission price also includes “Jurassic Journey”, a walking tour of a dozen or so not-very-good dinosaur models. In an interpretive centre in this area, I found this Brachiosaurus skeletal reconstruction stencilled on the wall:
I immediately knew it was the Chicago mount due to the combination of Giraffatitan anterior dorsals and Brachiosaurus posterior dorsals; but I found it more hauntingly familiar than that. A quick hunt turned up Matt’s seven-year-old post, and when I told Matt about my discovery he filled me in on its use in Wikipedia.
So this is 99% of a good story: we’re delighted that this work is out there, and has resulted in a much better Brachiosaurus image at Birdland than the rather sad-looking Stegosaurus next to it. The only slight disappointment is that I couldn’t find any sign of credit, which they really should have included given that Matt put the image out under CC By rather than in the public domain.
But as Matt said: “Even though I didn’t get credited, I’m always chuffed to see my stuff out in the world.” So true.
The keys to success: fear, arrogance, and laziness
January 22, 2020
A student wrote to me to ask where I got the motivation to prep my anatomy lectures. Here’s what I sent back.
I’ll be honest, for me it is partly fear, partly arrogance, and partly laziness:
- Fear of going up in front of 270 smart folks with the internet at their fingertips and not bringing my A game.
- The arrogance to think that I am pretty good at this, and the desire to show off a little by doing it well.
- Laziness because the more I put into the slideshow now, the less work I’ll have to do in the future. I prefer to have the lecture be so self-explanatory that I don’t really need to prep for it (even though I will), I could just go up to the podium and riff off the slides and not worry that I’m going to forget something crucial. Anything crucial goes into the slideshow for me, so even if I draw a blank, the slides will remind me of all the points I want to make.
Related: it’s faster to take 5 minutes right after a lecture and fix the problems with it, than it is to come back in 10 months and spend an hour trying to figure out what I wanted to fix and probably still forgetting half of it. If it’s a choice between doing a little work now and a lot later, I usually go for the first option.
What works for you?
Tutorial 19g: Open Access definitions and clarifications, part 7: why your open-access journal should use the CC By licence
October 15, 2019
Matt and I are about to submit a paper. One of the journals we considered — and would have really liked in many respects — turned out to use the CC By-NC-SA license. This is a a very well-intentioned licence that allows free use except for commercial purposes, and which imposes the same licence on all derivative works. While that sounds good, there are solid reasons to prefer the simpler CC By licence. I wrote to the journal in question advocating a switch to CC By, and then I thought the reasoning might be of broader interest. So here’s what I wrote, lightly edited.
First, CC By neatly expresses the one requirement all academics have of their work: that they get credit for it. When we publish papers, we are happy for them to be freely distributed, but also want people to build on them, re-using parts in whatever way helps, provided we’re credited — and that is exactly what CC By enables.
Second, because of this, many funders that require the work their grantees do to be published open access specifically require the CC By licence, in the expectation that it will provide the greatest societal benefit in exchange for their investment. Most famously, this is the case for the Gates Foundation (the largest private foundation in the world), but for a partial list of the many other funders with this policy, see https://www.springernature.com/gp/open-research/funding/funders-requiring-cc-by-for-articles — funders whose grantees, as things stand, are not allowed to publish their work in your journal.
Third, CC By is almost universal among well established and respected open-access journals, including all the PLOS journals, PeerJ, the BioMed Central journals, the Hindawi journals, eLIFE, Nature’s Scientific Reports, and palaeo journals such as Acta Palaeontologica Polonica and Palarch’s Journal of Vertebrate Paleontology. This is important because CC By-licenced journals can’t freely use material published under more restrictive licences such as your journal’s CC By-NC-SA. Instead, authors of such articles must labouriously seek exemptions from the copyright holders of the material they wish to reuse or adapt.
Fourth and last, other online resources also use CC By (or optionally CC By-SA in the case of Wikipedia), which means that, while material from PLOS ONE, Scientific Reports et al. can be freely used in Wikipedia articles, text and illustrations from articles in your journal cannot, limiting its use in outreach. Similarly, even on our own palaeontology blog, we would have concerns about using By-NC-SA materials as we use Patreon to solicit donations and our blog is arguably therefore commercial. (Part of the problem with the NC clause is that there is no rigorous definition of “commercial”.)
For all these reasons, we believe that your journal would better serve its authors, its readers, the academic community and broader society if its articles were published under the CC By licence. We hope that, if you agree, you are able to some point to help the journal make this transition. And if there’s anything Matt or I can do to assist that process, we’ll be happy to.
Pro tip: turn your talks into photo books
August 21, 2019
First, a short personal backstory. Vicki’s and my extended families both live mostly in Oklahoma and Kansas, so they only get to see our son, London, at the holidays or at infrequent mid-year visits. Starting when London was five, every year I’ve made a photo book of his adventures through the year to give as Christmas presents to all of our relatives. These have also become cherished mementos for the three of us here in Cali. The service I use is Shutterfly, and they have yet to mis-print a book or screw up an order over the space of a decade. So I feel confident recommending them.
About 3-4 times a year I get an offer from Shutterfly for a free 8×8 hardcover photo book, usually like 20 to 26 pages unless I want to pay a little extra. Sometimes if I’ve just taken a vacation or have some other batch of good photos, I’ll burn the free photo book capturing that, but most of time I use the freebies to memorialize my talks. Here are two I had to hand in my office when I got the idea for this post. On the left is my 2014 SVPCA talk on supramedullary airways in birds and dinos, and on the right is Jessie Atterholt’s talk from last year’s SVPCA on the same topic (with loads more data).
The 2014 talk was the first one I turned into a book, and I put it together right after the conference when the logic and cadence of the talk was still in my mind. My talks tend to be very text-light, and the slides basically act as memory triggers for me to riff on at the podium. So for that book I deliberately tried to capture the essence of what I said about each slide, hoping that it would make it easier to write the paper when the time came (and the time is, er, now, since Jessie has written the first draft already).
I also tend to use a lot of slides compared to most other folks, so I doubled up the slides on each page to fit the talk into the confines of a free book. For the recent Haplocanthosaurus presentation at the 1st Palaeontological Virtual Congress (available here), I put a lot of text on the slides to make them self-explanatory, and used fewer slides. So when I made that talk into a book, I just made each slide a full page, with no captions.
You know who appreciates these things? Anyone who wants to hear about your work, but doesn’t want to sit through a 15-minute slide presentation. It’s so much more natural and inviting to hand someone a book and say, “Here’s my talk, feel free to look through it or borrow it for a few days”. It’s like taking some 8×11 printouts of your poster to a conference: making born-digital presentations into physical artifacts may feel old-fashioned, but those artifacts are amazingly useful when you’re talking with other primates in meatspace.
You know who else appreciates these things? Coauthors who couldn’t be at the conference. So occasionally if I have a free book to burn, I’ll make an extra copy of one I already have incarnate, and send it to a coauthor as a gift.
So I recommend doing this. I don’t know how much stuff you have to order from Shutterfly to get free book offers now and then (maybe not very much since they do make some back on shipping), but I know how much your first book will cost if you’re not a Shutterfly user: nothing. The first five new users who use the link below will get a free 8×8 photo book. I’ll get one, too, for bringing people on board, but it’s not a cult, you can leave anytime. I wouldn’t, though, this stuff is too useful.
Here’s that link: https://invite-shutterfly.com/x/DvuNbO
Sauropod Vertebra Picture of the Week 
