September 3, 2015
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:
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.
April 20, 2011
A few months ago, prosauropod supremo Adam Yates blogged about the Aardonyx cake that the BPI honours class baked in his honour. In the comments, I mentioned that my wife Fiona once made me a BMNH R5937:D9 cake (i.e. a cake in the form of the more posterior of the pair of nicely preserved dorsal vertebrae of The Archbishop, in right lateral view). At the time, I couldn’t find the photo that I knew had been taken, and Adam asked me to post it when it turned up.
And here, once more, is the real thing for comparison:
(Note that the topology of the lateral lamination is spot on, with a single infradiapophyseal lamina which forks into anterior and posterior branches only some way ventral to the diapophysis. That’s what you look for in a cake.)
Update (21 April)
Silly me, of course what I should have shown is the cake and the vertebra side by side. Here they are — together at last!
October 15, 2010
This post is nearly three weeks late — it’s based on a piece of artwork that appeared on 25 September, and which I wanted to write about immediately. But it got washed away in the flood of camel necks (which by the way is not over yet), and then in the festival of articular cartilage, then by the whole “Amphicoelias brontodiplodocus” thing and the subsequent discussion of amateurs in palaeo, and then by what was already an overdue announcement of my sauropod history paper and the attendant copyright nonsense. So it’s been a stupidly busy time here at SV-POW! Towers, but now the air has cleared a little, and it’s time to look at this beauty:
This would be a beautiful piece of art by any standards — the world can always use brachiosaur art! — but what makes this extra special for me is that it is the first ever life restoration of my very own brachiosaur, BHM R5937, the Tendaguru specimen known as The Archbishop. It’s by SV-POW! regular Nima, and I am absolutely delighted to see it. It’s very Greg Paul-like, and I mean that in the most positive sense. (I may not be a fan of Greg’s taxonomic vicissitudes, but his art is just beautiful.)
Over on his blog, Nima has described in detail how he created this piece, and shows four progressively refined versions (of which the one above is the last) — I urge you to check it out if you’re interested in art, brachiosaurs or both.
Nima’s blog-post also includes a brief history of the Archbishop, mostly taken from my 2005 SVPCA talk. It’s a good summary, but I do have a few comments to make. (I typed a lot of this in as a comment to the original post, but Blogger ate my comments as usual.)
- The specimen is not known as M23, and has never been — that is in fact the designation of the Tendaguru quarry from which is was excavated. Paul (1988) mistakenly conflated the quarry name with a specimen number, and referred to this specimen as BMNH M23, and Glut’s (1977) encyclopaedia perpetuated the error, but it’s always been R5937.
- “The giant Brachiosaurus finds of the Germans” are now, of course, Giraffatitan.
- “Controversy lingered” — well, no, not really. The problem was worse than that: no-one paid a blind bit of notice to the specimen before 2004.
- “It turns out the double spine claim was totally bogus and unscientific” — well, we don’t really know that yet. It’s certainly true that none of the prepared vertebrae (five cervicals, two complete dorsals and an additional dorsal spine) have bifid spines; but Migeod reported these from the anterior dorsals, and it’s not clear that we have those. A fair bit of material remains in jackets, and more has probably been lost or destroyed. So it is possible, if unlikely, that one day we’ll open one of those jackets and find good evidence for bifid spines.
- “Close-up of the Archbishop vertebrae (doesn’t look much like the mitre of an archbishop to me, but who knows” — well, the name The Archbishop is not based on any resemblance of the bones to a mitre. (Nor is it based on anything else. It’s completely arbitrary.)
Last 0f all, what about the actual picture? Well, the long, thin, snakelike neck is beautiful art, but I don’t think it’s great science. The height of the cervicals that we have for this animal show that the neck would have had to be quite a bit dorsoventrally taller than shown here. And because there were only 13 cervical vertebrae — 12 if you omit the atlas, which is really a whole nother kettle of badgers, a neck bent into a strongly sigmoid pose like this would exhibit noticable kinks at some of the intervertebral joints — as you can see in giraffes when they twist their necks.
That aside, though, this is great. Again, I am really delighted that it’s out there. Congratulations to Nima!
November 18, 2009
Last week, for the first time ever, I spent the entire working week on palaeo. I took a week away from my job, and spent it staying in London, working on the Archbishop at the Natural History Museum. (For those of you who have not been paying attention, the Archbishop is the informal name of the specimen NHM R5937, a brachiosaurid sauropod from the same Tendaguru area that produced Giraffatitan brancai, and which has been generally assumed to represent that species.)
My main goal was to take final publication-quality photographs that I can use in the description (which I have committed to try really, really hard to get submitted by the end of 2009). There’s quite a bit of material (more than for Xenoposeidon, anyway!) — six cervicals in various states of preservation/preparation, cervical ribs, two complete dorsals, two more dorsal centra and a dorsal spine, some scap scraps, a partial ?pubis, a long-bone fragment and “Lump Z“, whatever that is. What you see above is my best lateral-view photograph of what I’ve designated “Cervical U”. One of these days, I’m going to do a post on how to photograph large fossils — something it’s taken me five years to get the hang of — but for today, I want to tell you about an exciting adventure with Cervical U. [Update: I wrote the How To post a few months later.]
Because my other big goal on this trip was to get it CT-scanned. Thanks to the generosity of John Hutchinson of the Royal Veterinary College, and to the help of the NHM people in arranging a loan, everything was set up for my host Vince Bickers and me to ferry the specimen up to the RVC, scan it and return it.
But first it had to be packed:
Lorna and Sandra spent a long time looking for a crate big enough to pack the bone in, but came up empty — there was one that was long enough but not wide enough, one that was tall enough but not long enough, and so on. In the end we sat the bone, on its very solid plaster base, on a plastic pallet, and wrapped it in pillows, bubble-wrap and that blue stuff whose name I don’t know.
As it happened, the scan had to be delayed for a day due to lack of personnel at RVC, but Vince and I took the vertebra up on the Thursday anyway; he had to return to work on the Friday, but I took public transport to RVC for the big day. Before we went into the scanning room, John showed me his freezer room:
I found it amusing that they have enough Segments Of Awesome that they have to label the various elephant-part freezers differently. And further down the aisle:
Then it was off to the scanning facility, where we found that we had to unpack the vertebra: it was small enough to go through the machine, but there was no way the pallet was going through. Once we’d unpacked it and removed it, it fit pretty nicely:
Because the scanner spits out X-rays in all directions, it’s controlled from a separate room, behind lead-impregnated glass:
We ran three scans before we got the settings right — we needed more voltage to get through the bone and matrix than we’d first realised, and a filter was causing unhelpful moire patterns. The third scan was definitely the best, and the one I expect to be working with.
[Boring technical side-note: I plan to use 3D Slicer for visualisation thanks to Andy Farke’s series of tutorials. But, frustratingly, I wasn’t able to load the DICOM files from the scan into that program: it crashes when trying to load them (segmentation fault) even though it works fine on the ankylosaur skull that Andy walked us through in the tutorials. I fixed this by gluing the 300-odd files together into a single stack file that 3D Slicer was able to read. For the benefit of anyone else who needs to do this, the command (on a Ubuntu Linux box) was: medcon -f *.dcm -c dicom -stack3d -n -qc]
Here is an example slice, showing part of the condyle in posterior view:
The grey blobs at the bottom of the image are the plaster jacket that supports the vertebra; the white is bone, and the light grey inside it is matrix that fills the pneumatic spaces. I’m showing the condyle here because its cavities are clearly visible: further back in the vertebra, they are harder to pick out, perhaps in part because of the iron bars scattering the X-rays. It’s notable that this vertebra is less pneumatic than would be expected for a brachiosaurid — by eye, it looks like like the condyle is only 20-30% air, and this slice is not unrepresentative. Most neosauropods would be at least twice this pneumatic, so we may have an Archbishop autapomorphy here.
I’ve not yet persuaded 3D Slicer to build a 3D model for me, but I’m pleased to say that before I left RVC, John mocked up a quick-and-dirty render of the bone using only density threshholding, and I can at least show you that.
Here we see the bone from the left side, previously obscured by solid plaster. From a single static image, it’s not easy to make out details, but we can at least see that there is a solid ventral floor to the centrum … and that those two crossed iron bars obscure much that we would like to see. You will get more of an idea from the rotating video that this is screencapped from.
Looking at this and comparing it with the right-lateral photo at the top of the post, it’s apparent that the density threshhold was set too high when making this model: all the bone along the lower right margin of the middle part of the centrum is good, but it’s been omitted from the model. In other words, the vertebra is more complete than this proof-of-concept model suggests. Hopefully I will shortly be able to show you a better model.
November 22, 2008
If you’ve been following SV-POW! closely – perhaps a little too closely – you will know of BMNH R5937, a Tendaguru sauropod collected in 1930 on one of the British Museum (Natural History) expeditions, and reported in 1931 by Frederick Migeod (pronounced ‘mee-zhou’). Discovered in the ‘M23’ quarry at Tendaguru, the specimen was assumed by Migeod and all subsequent authors to be another specimen of Brachiosaurus brancai, but what’s notable is that Migeod mentioned several features in the vertebrae of the specimen that really sounded quite un-Brachiosaurus-like. Despite the size and quality of the specimen however, nobody ever got round to studying it properly – until Mike did exactly this. An abstract and talk slides on the specimen can be found here. For whatever reason, the specimen has become known as The Archbishop.
While Migeod wrote about The Archbishop, he never published any illustrations of it (with the exception of a quarry map). I don’t think I’m betraying any secrets by letting on that Mike is working on a full technical desciption of the specimen, wherein it will of course be illustrated properly. Little known however is that The Archbishop has appeared in the literature before, but (unsurprisingly, and in keeping with tradition) has been misidentified as Brachiosaurus. After all, it’s a big sauropod and it comes from Tendaguru, so it must be Brachiosaurus, right? Here’s the proof: it’s p. 94 of David Lambert’s Ultimate Dinosaur Book, published by Dorling Kindersley in 1993. The Archbishop photo is, of course, up there at top right, masquareding as the dorsal vertebrae of Brachiosaurus brancai.
September 15, 2015
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.
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:
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 :-)
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.
February 12, 2014
Today (12th February) is the one-year anniversary of the first PeerJ papers! As Matt put it in an email this morning:
Hard to believe it’s been a year already. On the other hand, it’s also hard to believe that it’s only been a year. PeerJ is just such an established part of my worldview now.
That’s exactly right. PeerJ has so completely rewritten the rule-book (on price, speed and quality of service) that now when I’m thinking about new papers I’m going to write, the question I ask myself is no longer “Where shall I send this?” but “Is there any reason not to send it to PeerJ?”
Yesterday in the comments of a post on The Scholarly Kitchen, Harvey Kane asked me “I am curious as to where you get the notion that publishing OA is less expensive and in some way “better” than the traditional model?” My reply was (in part):
My notion that OA publishing yields better results than traditional is rooted in the online-only nature of articles, which allows them to ignore arbitrary limits on word-count, number of figures, use of colour, etc., and to exploit online-only formats such as video, 3d models, CT-slice stacks, etc. In my own field of vertebrate palaeontology, it’s now routine to see in PLOS ONE descriptive articles that are many times more comprehensive than their equivalents in traditional journals — see for example the recent description of the frog Beelzebufo.
Of course there is nothing specific to open-access about this: there is no technical reason why an online-only subscription journal shouldn’t publish similarly detailed articles. But my experience so far has been that they don’t — perhaps because they are tied to the mindset that pages and illustrations are limited resources.
For Beelzebufo in PLOS ONE, read baby Parasaurolophus in PeerJ, which we described as “the world’s most open-access dinosaur“. This paper is 83 pages of technicolour goodness, plus all the 3d models you can eat. And the crazy thing is, this sort of detail in descriptive papers is not even exceptional any more — see for example the recent description of Canardia in PLOS ONE, or this analysis of croc respiration in PeerJ
Years ago, I said that in the Archbishop descriptions I wanted to raise the bar for quality of illustration. Well, I’ve taken so long over getting the Archbishop done that the bar has been raised, and now I’m scrambling to catch up. Certainly the illustrations even in our 2011 description of Brontomerus are starting to look a bit old-fashioned.
And of course, the truly astonishing thing about PeerJ is that it does this so very cheaply. Because I’m already a member (which cost me $99), the Archbishop description is going to be free to me to publish this year. (This year for sure!) If we also get our Barosaurus neck preprint published properly this year,then I’ll have to find $100 to upgrade my Basic membership to Enhanced. That’s cheap enough that it’s not even worth going through the hassle of trying to get Bristol to pay for me. And if I ever hit a year when I publish three or more papers, I’ll upgrade once more (for another $100) to the Investigator plan and then that’s it: I’m done paying PeerJ forever, however many papers I publish there. (Matt jumped straight to the all-you-can-eat plan, so he wouldn’t even have to think about it ever again.)
PeerJ’s pricing is making PLOS ONE’s $1350 APC look distinctly old-fashioned; and the $3000 charged by the legacy publishers (for a distinctly inferior product) is now frankly embarrassing. You might expect that as such low prices, PeerJ’s quality of service would suffer, but that’s not been our experience: editing, reviewing, typesetting and proofing for our neck-anatomy paper were all up there with the best we’ve received anywhere.
And it’s great to see that it’s not just minor researchers like Matt and me who are persuaded by PeerJ: they’ve now accumulated a frankly stellar list of 20 universities (so far) with institutional plans for researchers to publish there. When I say “stellar” I mean that the list includes Harvard, MIT, Cambridge, Berkeley, Stanford, Johns Hopkins, UCL, Carnegie Mellon, Duke … the list goes on.
We can only hope that the next year, and the next ten and twenty, are as successful for PeerJ as the first has been; and that other New Generation publishers will join it in pushing the field forward.
I leave the last word to Matt:
I’m getting Vicki a lifetime membership for Valentine’s Day. Because I’m a romantic.
She’s a lucky, lucky woman.
January 30, 2014
Following on from Matt’s post about the difficulty of photographing big specimens without distortion, I thought I’d have a play with our best Sauroposeidon C8 photo, which I think is this one:
(That’s been the basis for classic SV-POW! posts such as Your neck is pathetic and Darren’s new indeterminate Wealden maniraptoran is inadequate.)
I was motivated by Andy Farke’s comment:
Another–and perhaps more important–area where surface models excel is when you can remove colors on the original specimen that wash out relevant details…I bet this is probably the case for the example vertebra of Sauroposeidon. How many fossae and foramina just don’t show up well on the photos above?
Andy was talking about completely colourless 3d surface models, in which the 3d shape allows a render to make shadows that bring out the subtle shapes. But it made me wonder whether we could get anywhere just by washing out the most prevalent colour in the photo.
I started by doing a big, fat Gaussian blur on a duplicate layer — 500 pixels in each direction — and sampling the colour in the middle, to get a rough-and-ready average. (There may be a better way — please shout if you know one.) That average colour was#7e6b2f. I used it to run Colour To Alpha on another duplicate of the original layer, so that we’d be left with only residual colours. Here’s the result:
I’m in two minds about this. It may be informative, but it sure is ugly. To compromise, I reinstated the original layer underneath this mostly-transparent one, and turned its opacity down to 75%. Here’s the result — a nice compromise:
Of course, there are endless other approaches you can take — that’s the blessing and the curse of image-editing programs like GIMP. For example, here’s what I got doing a simple Colours → Auto → White Balance:
I’m not sure that isn’t the best of the bunch, in terms of informativeness.
I also tried something else — not amazingly successfully, but I think it’s worth seeing. Since the two photos that Matt showed in the previous post were evidently taken from somewhat different angles, I thought I’d have a go at compositing them into a red-cyan anaglyph. Because the variation in camera position is mostly dorsoventral rather than anteroposterior, the vert has to be pointed upwards for the two eyes to see the two versions from different horizontal points. Here’s the best I could do:
I would say this is of some value; but it’s nowhere near as good as, for example, the anaglyph of Cervical S of the Archbishop. I could sit and look at that one all day. The problems with this one arise for three reasons.
First, I had to reduce both parts of the Sauroposeidon anaglyph to monochrome (since one was already in that form), so all colour information was lost.
Second, I had to scale the high-resolution picture to the same size as the lower-resolution one, throwing away more detail.
Finally, and most important, the two photos were not taken with the intention that they should be used to make an anaglyph. To work well, this has to be done with the images taken under the same lighting conditions, at the same distance from the specimen, from perspectives differing by about the distance between the pupils of the viewer, and with the camera-position difference being perfectly in the plane of the specimen. Needless to say, none of these conditions was met in this case, so it’s actually quite impressive that it works as well as it does.
We have a lot of options for illustrating specimens these days. Postage-stamp-sized greyscale photos really don’t cut it any more.
April 25, 2013
Generally when we present specimen photos in papers, we cut out the backgrounds so that only the bone is visible — as in this photo of dorsal vertebrae A and B of NHM R5937 “The Archbishop”, an as-yet indeterminate Tendaguru brachiosaur, in right lateral view:
But for some bones that can be rather misleading: they may be mounted in such a way that part of the bone is obscured by structure. For example — and this is a very minor case — the ventral margins of the centra in the photo above are probably slightly deeper than they appear, because the centra are slightly sunk within the plinth that holds the vertebrae upright.
So I’ve been toying with a different idea: instead of cutting the background out completely, leaving it in place but toning it down. Then the supporting structure is visible, but clearly distinct from the actual bone. (For a more extreme case, see the “Apatosaurus” minimus sacrum.)
Here’s how the image above looks if I desaturate the background:
I’m not sure what to make of this. It looks a bit strange to me, but that might only be the strangeness of unfamiliarity.
And it might not work so well (or indeed it might work better) for photos taken against a busier background.
What do you think?