Ten years ago today — on 15 September 2005 — my first palaeo paper was published: Taylor and Naish (2005) on the phylogenetic nomenclature of diplodocoids. It’s strange to think how fast the time has gone, but I hope you’ll forgive me if I get a bit self-indulgent and nostalgic.

TaylorNaish2005-diplodocoid-taxonomy-ABSTRACT

I’d applied to join Portsmouth University on a Masters course back in April 2004 — not because I had any great desire to earn a Masters but because back in the bad old days, being affiliated to a university was about the only way to get hold of copies of academic papers. My research proposal, hilariously, was all about the ways the DinoMorph results are misleading — something that I am still working on eleven years later.

In May of that year, I started a Dinosaur Mailing List thread on the names and definitions of the various diplodocoid clades. As that discussion progressed, it became clear that there was a lot of ambiguity, and for my own reference I started to make notes. I got into an off-list email discussion about this with Darren Naish (who was then finishing up his Ph.D at Portsmouth). By June we thought it might be worth making this into a little paper, so that others wouldn’t need to do the same literature trawl we’d done.

In September of 2004, I committed to the Portsmouth course, sending my tuition fees in a letter that ended:

tuition-fees-letter

On the way to SVPCA that year, in Leicester, I met Darren on the train, and together we worked through a printed copy of the in-progress manuscript that I’d brought with me. He was pretty happy with it, which meant a lot to me. It was the first time I’d had a legitimate palaeontologist critique my work.

At one of the evening events of that SVPCA, I fell into conversation with micro-vertebrate screening wizard Steve Sweetman, then on the Portsmouth Ph.D course, and he persuaded me to switch to the Ph.D. (It was my second SVPCA, and the first one where I gave a talk.) Hilariously, the heart of the Ph.D project was to be a description of the Archbishop, something that I have still not got done a decade later, but definitely will this year. Definitely.

On 7th October 2004, we submitted the manuscript to the Journal of Paleontology, and got an acknowledge of receipt<sarcasm>after just 18 short days</sarcasm>. But three months later (21st January 2005) it was rejected on the advice of two reviewers. As I summarised the verdict to Darren at the time:

It’s a rejection. Both reviewers (an anonymous one and [redacted]) say that the science is pretty much fine, but that there just isn’t that much to say to make the paper worthwhile. [The handling editor] concurs in quite a nice covering letter […] Although I think the bit about “I respect both of you a great deal” is another case of Wrong Mike Taylor Syndrome :-)

This was my first encounter with “not significant enough for our journal” — a game that I no longer play. It was to be very far from my last experience of Wrong Mike Taylor Syndrome.

At this point, Darren and I spent a while discussing what to do: revise and resubmit (though one of the reviewers said not to)? Try to subsume the paper into another more substantial one (as one reviewer suggested)? Invite the reviewers to collaborate with us on an improved version (as the editor suggested)? Or just revise according to the reviewers’ more helpful recommendations and send it elsewhere? I discussed this with Matt as well. The upshot was that on 20th February Darren and I decided to send the revised version to PaleoBios, the journal of the University of California Museum of Paleontology (UCMP) — partly because Matt had had good experiences there with two of his earlier papers.

[Side-note: I am delighted to see that, since I last checked, PaleoBios has now made the leap to open access, though as of yet it says nothing about the licence it uses.]

Anyway, we submitted the revised manuscript on 26th May; and we got back an Accept With Minor Revisions six weeks later, having received genuinely useful reviews from Jerry Harris and Matt. (This of course was long before I’d co-authored anything with Matt. No handling editor would assign him to review one of my papers now.) It took us two days to turn the manuscript around with the necessary minor changes made, and another nine days of back and forth with the editor before we reached acceptance. A week later I got the proof PDF to check.

Back in 2005, publication was a very different process, because it involved paper. I remember the thrill of several distinct phases in the publication process — particularly sharp the first time:

  • Seeing the page proof — evidence that I really had written a legitimate scholarly paper. It looked real.
  • The moment of being told that the paper was published: “The issue just went to the printer, so I will send the new reprints […] when I get them, probably sometime next week.”
  • Getting my copy of the final PDF.
  • The day that the physical reprints arrived — funny to think that they used to be a thing. (They’re so Ten Years Ago now that even the SVPCA auction didn’t have many available for bid.)
  • The tedious but somehow exhilarating process of sending out physical reprints to 30 or 40 people.
  • Getting a physical copy of the relevant issue of the journal — in this case, PaleoBios 25(2).

I suppose it’s one of the sadder side-effect of ubiquitous open access that many of these stages don’t happen any more. Now you get your proof, then the paper appears online, and that’s it. Bam, done.

I’m kind of glad to have lived through the tail end of the old days, even though the new days are better.

To finish, there’s a nice little happy ending for this paper. Despite being in a relatively unregarded journal, it’s turned out to be among my most cited works. According to Google Scholar, this humble little taxonomic note has racked up 28 citations: only two fewer than the Xenoposeidon description. It’s handily outperforming other papers that I’d have considered much more substantial, and which appeared in more recognised journals. It just goes to show, you can never tell what papers will do well in the citation game, and which will sink without trace.

References

We’ve noted that the Taylor et al. SVPCA abstract and talk slides are up now up as part of the SVPCA 2015 PeerJ Collection, so anyone who’s interested has probably taken a look already to see what it was about. (As an aside, I am delighted to see that two more abstracts have been added to the collection since I wrote about it.)

It was my privilege to present a talk on our hypothesis that the distinctive and bizarre toblerone-shaped necks of apatosaurs were an adaptation for intraspecific combat. This talk was based on an in-progress manuscript that Matt is lead-authoring. Also on board is the third SV-POW!sketeer, the silent partner, Darren Naish; and artist/ethologist Brian Engh.

Here is our case, briefly summarised from five key slides. First, let’s take a look at what is distinctive in the morphology of apatosaur cervicals:

Screen Shot 2015-09-12 at 11.22.26

Here I’m using Brontosaurus, which is among the more extreme apatosaurs, but the same features are seen developed to nearly the same extent in Apatosaurus louisae, the best-known apatosaur, and to some extent in all apatosaurs.

Now we’ll look at the four key features separately.

Screen Shot 2015-09-12 at 11.22.57

First, the cervicals ribs of sauropods (and other saurischians, including birds) anchored the longus colli ventralis and flexor colli lateralis muscles — ventral muscles whose job is to pull the neck downwards. By shifting the attachments points of these muscles downwards, apatosaurs enabled them to work with improved mechanical advantage — that is, to bring more force to bear.

Screen Shot 2015-09-12 at 11.23.06

Second, by redirecting the diapophyses and parapophyses ventrally, and making them much more robust than in other sauropods, apatosaurs structured their neck skeletons to better resist ventral impacts.

Screen Shot 2015-09-12 at 11.23.15

Third, because the low-hanging cervical ribs created an inverted “V” shape below the centrum, they formed a protective cradle for the vulnerable soft-tissue that is otherwise exposed on the ventral aspect of the neck: trachea, oesophagus, major blood vessels. In apatosaurus, all of these would have been safely wrapped in layers of connective tissue and bubble-wrap-like pneumatic diverticula. The presence of diverticula ventral to the vertebral centrum is not speculative – most neosauropods have fossae on the ventral surfaces of their cervical centra, and apatosaurines tend to have foramina that connect to internal chambers as well (see Lovelace et al. 2007: fig. 4, which is reproduced in this post).

Screen Shot 2015-09-12 at 11.23.22

Fourth, most if not all apatosaurs have distinctive ventrally directed club-like processes on the front of their cervical ribs. (It’s hard to tell with Apatosaurus ajax, because the best cervical vertebra of that species is so very reconstructed.) How did these appear in life? It’s difficult to be sure. They might have appeared as a low boss; or, as with rhinoceros horns, they might even have carried keratinous spikes.

Putting it all together, we have an animal whose neck can be brought downwards with great force; whose neck was mechanically capable of resisting impacts on its ventral aspect; whose vulnerable ventral-side soft-tissue was well protected; and which probably had prominent clubs or spikes all along the ventral aspect of the neck. And all of this was accomplished at the cost of making the neck a lot heavier than it would have been otherwise. Off the cuff, it seems likely that the cervical series alone would have massed twice as much in apatosaurines as in diplodocines of the same neck length.

Doubling the mass of the neck is a very peculiar thing for a sauropod lineage to do – by the Late Jurassic, sauropods were the leading edge of an evolutionary trend to lengthen and lighten the neck that had been running for almost 100 million years, through basal ornithodirans, basal dinosauromorphs, basal saurischians, basal sauropodomorphs, and basal sauropods. Whatever the selective pressures that led apatosaurines to evolve such robust and heavy necks, they must have been compelling.

The possibility that apatosaurs were pushing or crashing their necks ventrally in some form of combat accounts for all of the weird morphology documented above, and we know that sexual selection is powerful force that underlies a lot of bizarre structures in extant animals, and probably in extinct ornithodirans as well (see Hone et al. 2012, Hone and Naish 2013).

What form of combat, exactly? There are various possibilities, which we’ll discuss another time. But I’ll leave you with Brian Engh’s beautiful illustration of one possible form of combat: a powerful impact of one neck brought down onto the dorsal aspect of another.

ApatoNeckSmashRoughWeb

We’re aware that this proposal is necessarily somewhat speculative. But we’re just not able to see any other explanation for the distinctive apatosaur neck. Even if we’re wrong about the ventrolateral processes on the cervical ribs supporting bosses or spikes, the first three points remain true, and given how they fly in the face of sauropods’ long history of making their necks lighter, they fairly cry out for explanation. If anyone has other proposals, we’ll be happy to hear them.

References

  • Hone, D. W., Naish, D., & Cuthill, I. C. (2012). Does mutual sexual selection explain the evolution of head crests in pterosaurs and dinosaurs?. Lethaia 45(2):139-156.
  • Hone, D. W. E., & Naish, D. (2013). The ‘species recognition hypothesis’ does not explain the presence and evolution of exaggerated structures in non‐avialan dinosaurs. Journal of Zoology 290(3):172-180.
  • Lovelace, D. M., Hartman, S. A., & Wahl, W. R. (2007). Morphology of a specimen of Supersaurus (Dinosauria, Sauropoda) from the Morrison Formation of Wyoming, and a re-evaluation of diplodocid phylogeny. Arquivos do Museu Nacional, Rio de Janeiro 65(4):527-544.

Just under a year ago, the children across the road, who know I’m interested in comparative anatomy, told me that they’d found a dead cat by the side of the road, and asked whether I wanted it. Silly question, of course I did!

I’ve learned from bitter experience that prepping the whole skeleton out of an animal is a very time-consuming process — so time-consuming that I usually just don’t get around to it. This time, I thought I’d just do the skull. So I removed the head (not a pleasant process) and discarded the body.

I did the usual sequence of simmerings with the head, peeling off the skin and fur, then removing muscle, till I was down to just bone, gristle, and the hard-to-remove bits of soft tissue that always adhere in one place or another. At that point, I left the bones in a plastic tub in the woodshed, with a couple of holes in the lid so that invertebrates could get in and deal with the remaining gloop.

Yesterday I had a look (and a smell), and it seems all the soft-tissue is gone, thanks to the hard work of the tiny collaborators who never make it into the acknowledgements. So I soaked the skull pieces in soapy water for a day. Then today, I rinsed them off and left them to soak in pure water for a few hours. Finally, I changed the water, and added some H2O2 to degrease the bones. They are now foaming away merrily. Tomorrow I’ll take them out, rinse them off one more time, dry them, and see what state they’re in.

Here’s how they look today, after rinsing:

IMG_1977

And here is a closeup of a mandible (slightly foreshortened):

IMG_1977-closeup

“But Mike”, you ask, “Why is it in so many pieces?”

I actually don’t know. As I was taking the head apart, it seemed to be whole, but as it got down to the raw bone, it was apparent that the skull was very badly damaged. In the picture above, the main part of the cranium is upside down, half way down the left hand side. Below it is the rest of the cranium, the left side of the upper jaw. Above that is the back of the cranium, most of the braincase. The whole thing just came apart into three pieces — and not along sutures. This is breakage.

I’m not sure how it happened. At first, I thought it must be how the cat died — maybe struck a glancing blow by a car. But I increasingly wonder whether I stupidly did this myself in the process of removing the head from the torso. (I did not use a scalpel.)

Anyway, we’ll see how well the pieces can be reassembled once they have dried out. I’m optimistic that I can still wind up with a pretty good cat skull.

Wouldn’t it be great if, after a meeting like the 2015 SVPCA, there was a published set of proceedings? A special issue of a journal, perhaps, that collected papers that emerge from the work presented there.

Of course the problem with special issues, and edited volumes in general, is that they take forever to come out. After the Dinosaurs: A Historical Perspective conference on 6 May 2008, I got my talk on the history of sauropod research written up and submitted on 7 August, just over three months later. It took another five and a half months to make it through peer-review to acceptance. And then … nothing. It sat in limbo for a year and nine months before it was finally published, because of course the book couldn’t be finalised until the slowest of the 50 or so authors, editors and reviewers had done their jobs.

Taylor (2010: fig. 4). Marsh's reconstructions of Brontosaurus. Top: first reconstruction, modified from Marsh (1883, plate I). Bottom: second reconstruction, modified from Marsh (1891, plate XVI).

Taylor (2010: fig. 4). Marsh’s reconstructions of Brontosaurus. Top: first reconstruction, modified from Marsh (1883, plate I). Bottom: second reconstruction, modified from Marsh (1891, plate XVI).

There has to be a better way, doesn’t there?

Rhetorical question, there. There is a better way, and unsurprisingly to regular readers, it’s PeerJ that has pioneered it. In PeerJ Collections, papers can be added at any time, and each one is published as it’s ready. Better still, the whole lifecycle of the paper can (if the authors wish) be visible from the collection. You can start by posting the talk abstract, then replace it with a preprint of the complete manuscript when it’s ready, and finally replace that with the published version of the paper once it’s been through peer-review.

Take a look, for example, at the collection for the 3rd International Whale Shark Conference (which by the way was held at the Georgia Aquarium, Atlanta, which has awesome whale sharks on view.)

pb-120306-whaleshark-843p.photoblog900

As you can see from the collection (at the time of writing), only one of the constituent papers — Laser photogrammetry improves size and demographic estimates for whale sharks — has actually been published so far. But a dozen other papers exist in preprint form. That means that the people who attended the conference, saw the talks and want to refer to them in their work have something to cite.

The hot news is that Mark Young and the other SVPCA 2015 organisers have arranged for PeerJ to set up an SPPC/SVPCA 2015 Collection. I think this is just marvellous — the best possible way to make a permanent record of an important event.

The collection is very new: at the time of writing, it hosts only five abstracts (one of them ours). We’re looking forward to seeing others added. Some of the abstracts (including ours) have the slides of the talk attached as supplementary information.

talk-title-page

Although I’m lead author on the talk (because I prepared the slides and delivered the presentation), this project is really Matt’s baby. There is a Wedel et al. manuscript in prep already, so we hope that within a month or two we’ll be able to replace the abstract with a complete manuscript. Then of course we’ll put it through peer-review.

I hope plenty of other SVPCA 2015 speakers will do the same. Even those who, for whatever reason, don’t want to publish their work in PeerJ, can use the collection as a home for their abstracts and preprints, then go off and submit the final manuscript elsewhere.

As we’ve previously noted more than once here at SV-POW!, apatosaurine cervicals really are the craziest things. For one thing, they are the only dinosaur bones to have inspired the design of a Star Wars spaceship.

One result of this very distinctive cervical shape, with the ribs hanging down far below the centra, was that the necks of apatosaurines would have been triangular in cross-section, rather than tubular as often depicted. (The Apatosaurus maquette that Matt reviewed gets this right.)

Here’s how I conveyed this in two slides of my SVPCA talk:

Screen Shot 2015-09-07 at 23.38.07

Screen Shot 2015-09-07 at 23.38.12

Although apatosaurs take this to the extreme, the same was essentially true of all sauropod necks. The ventrolateral position of the cervical ribs would have lent the necks a rounded triangular shape, or diamond-shaped in the case of less extreme sauropods whose neck soft-tissue hung below the cervical ribs.

(Previously: Sauropods were tacos, not corn dogs; and Sauropods were corn-on-the-cob, not shish kebabs.)

My last post (Unhappy thoughts on student projects at SVPCA 2015) was stupid and ill-judged. As a result of very helpful conversations with a senior palaeontologist (who was much more courteous about it that he or she needed to be), I have decided to retract that article rather than editing it further to clarify. I deeply wish I’d never posted it, and I offer my apologies to everyone I insulted.

First, and most importantly, to people presenting projects under the influence of nerves, which I misinterpreted as a lack of interest in their own projects. Nervousness particularly affects people giving their first talks — an effect I should have allowed for. It’s awful to think that what I wrote may have been discouraging to people taking first steps into palaeo.

Second, to supervisors who felt that the “roll four dice” section in the middle of the post was aimed at them. All I can say is that it wasn’t. I had no-one in mind when I wrote that: I was just so seduced by the comical imagery of generating a project by rolling dice that I wrote it down without thinking through how it would be interpreted.

Did I have good intentions? I honestly did. Did I have legitimate concerns about the ubiquitous application of techniques that are not always appropriate, and whose results are not always interpreted with a suitable degree of scepticism? I think so. But clearly I should have discussed those concerns privately with more involved people, rather than spilling my brains all over the blog. I welcome the increasing availability of techniques that allow us to bring numerical rigour to our palaeobiological speculations. (I could discuss in more detail when and how I think those techniques should be used, but that’s for another day. My purpose here is to apologise, not to justify myself.)

In short, I had a very bad day at the office on Friday, and I hate the idea that in my carelessness I could have hurt anyone other than myself. To those in that category, I can only ask your forgiveness; and promise to think more before blogging in future.

THIS POST IS RETRACTED. The reasons are explained in the next post. I wish I had never posted this, but you can’t undo what is done, especially on the Internet, so I am not deleting it but marking it as retracted. I suggest you don’t bother reading on, but it’s here if you want to.

 


 

There were some surprises in the the contents of the SVPCA programme this year. Sauropods were woefully under-represented with only two talks (mine on apatosaur neck combat and Daniel Vidal’s on the range of movement of the tail of Spinophorosaurus). In fact non-avian dinosaurs as a whole got short shrift, with two theropod talks, three ornithischian talks and one on dinosaur diversity. This is partly, of course, because so many dinosaur workers among the SVPCA mainstays were absent for one reason or another: Matt Wedel, Paul Upchurch, Paul Barrett, Richard Butler, Roger Benson, Steve Brusatte, David Norman, the list goes on.

But that’s OK. I’ve often found, to my surprise, that the dinosaur talks aren’t always my favourites anyway. (Oddly enough, fish talks can quite often catch my imagination; and pterosaurs are always good for a laugh.)

A more surprising development was the complete absence of any finite element analysis this year — a technique that was crazy trendy a couple of years ago, but seems to have come to the end of its fashion cycle.

Instead, I felt that the talks were strongly dominated by one technique: principal component analysis (PCA). As a technique, I have mixed feelings about it: I don’t go as far as John Conway, who as far as I can tell thinks it’s almost literally meaningless. But I have strong reservations about the plug-and-play way it seems to get used for pretty much everything at the moment, and how very tenuous some of the inferences are that people derive from their morphospace plots. It’s difficult to be specific without criticising individuals, which I’d like to avoid doing. But I do think think that when we draw sweeping and heterodox conclusions about an animal’s lifestyle from a PCA of a single facet of a single bone, the validity of that conclusion is, to put it politely, open to question.

In fact an awful lot of the projects presented in this year’s talks seemed to follow the same template. In an idle (and, yes, unnecessarily snide) moment, I sketched an Automatic Masters Project Generator for lazy supervisors. You just throw four dice, then pick your technique name, body-part, period and taxon from these tables:

Table 1: roll 1d6 for a technique

  1. 2d landmark analysis
  2. principal component analysis
  3. geometric morphometrics
  4. morphospace analysis
  5. finite element analysis
  6. ecomorphological diversity analysis

Table 2: roll 1d6 for a body part

  1. quadrate
  2. mandible
  3. sacrum
  4. pelvis
  5. ulna
  6. astragalus

Table 3: roll 1d6 for a period

  1. Permian
  2. Mesozoic
  3. Jurassic
  4. Late Cretaceous
  5. Eocene
  6. Miocene

Table 4: roll 1d6 for a taxon

  1. lamnid sharks
  2. sauropterygians
  3. ornithopods
  4. corvids
  5. mustelids
  6. golden moles

Try it yourself! Morphospace analysis of the ulna in Miocene mustelids! Ready, steady, go! Your Masters degree will be ready as soon as you can talk reasonably coherently about this combination for fifteen minutes and leap to an obvious but weakly supported conclusion based on vague shapes drawn on a PC1-vs.-PC2 plot that captures only 32.6% of the variation!

(To be clear: I am not saying that PCA is intrinsically worthless. As I found myself repeatedly arguing in pubs with John and others, it’s evidently a very powerful tool for discovering correlations. For me, it goes wrong when very weak results pop out, but are given a veneer of respectability and objectivity because a computer was involved in the process.)

As the week went on, I found myself worrying increasingly about these projects. It’s not just that they are (with a few creditable exceptions) samey to listen to and uninteresting in their results. I worry more that these projects kill the interest of the people who take them on. I may be reading my own biases back into my observations here, but it seemed to me that I detected a distinct lack of enthusiasm in several of the speakers, and my hunch is that for a lot of them this will be their first and last SVPCA. They presumably went into palaeo because they loved some specific extinct taxon; instead, they found themselves spending a year staring at a hundred almost identical photographs of moodily lit tubes of toothpaste. And really, if anything is going to kill the passion of a pterosaur lover stone dead, it’s taking measurements of the distal articular facets of the ulnae of a 154 Miocene mustelids.

So I found myself longing for more talks about taxa, and about ideas, rather than techniques. Most obviously, there was very little pure descriptive palaeontology to be seen this year. But also, our own talk aside, very little of what I would think of as exploratory work — thinking about structures, chewing through their implications, considering alternatives. In short: the fun stuff. I would hate palaeontology to be reduced to a process of harvesting data from specimens (looking only at the aspects needed to fill in the matrix), pouring that data into a sausage machine, and turning the handle until something statistically significant comes out.

We have to be able to offer grad-students more than that. We are, and I say this with all due objectivity, in the most exciting science in the world. People go into palaeo because they love it. I wouldn’t like to think they go straight back out of it, as soon as they have their higher degree, hating it. We need to get students looking at and thinking about and discussing actual specimens — proposing ideas, arguing about them, running into reasons why they might be wrong, figuring out why they might be right after all, putting together an argument. Not sitting in front of computers full time running T-tests.

Of course there is a role, and an important one, for numerical methods. But they have to be the means, not the end. We have to have a more interesting goal than finding a statistically significant correlation. Otherwise we’re going to lose people.

Here I am at SVPCA in 2015. I am haunted by the fact that ten years ago at SVPCA 2005, I gave a talk about the NHM’s Tendaguru brachiosaurid, NHMUK R5937. And the description is still not done and submitted a full decade later. Even though it’s objectively one of the most beautiful specimens in the world:

dorsals-ab-composite

So here is my pledge to the world:

By this time next year (i.e. the start of SVPCA 2016 in Liverpool), I will have written and submitted this description. If I fail, I give you all permission — no, I beg you — to mock me mercilessly. Leave mocking comments on this blog, yes; but more than that, those of you at SVPCA are invited to spend the week pointing contemptuously at me and saying “Ha!”

Let’s hope it doesn’t come to that.

Update (6 September): see also.