Accidental anaglyphs
October 16, 2020
Everyone knows that the very first thing you should do to improve your specimen photography is to use a tripod: it eliminates hand-shake and gives you much crisper photos. In most respects, my photographs have got much, much better since I’ve been habitually using a tripod.
But it has meant I’ve not been able to benefit from happy accidents like the one that gave me this 3D anaglyph of the Archbishop‘s Cervical S in dorsal view:
(Do you have red-cyan glasses? Yes? Good! You will be able to appreciate all the delicious morphological information in this photo. No? Go and order some right now — they cost literally a dollar.)
The reason I was able to make this very useful image is because back in the old pre-tripod days I would sometimes accidentally move a little bit between taking two more-or-less identical photographs. Here are the two images that I was able to composite into the anaglyph above:
Each of them is pretty uninformative alone: who can tell one nondescript area of brown bone from another? But when combined, they are extraordinarily more informative. If you don’t have 3D glasses then (A) get some! and (B) you can get some idea of how helpful the 3D information is from the crude wigglegram below, which simply switches back and forth between the two images.
And I can’t overstate how enormously helpful I have found these accidentally sourced anaglyphs as I write the descriptive part of the Archbishop manuscript. Even at this level of crudity, they have shown me several important points of morphology that I would certainly have missed if I’d been working only from my orthogonal-view photos, and saved me from more than one misinterpretation.
The moral is twofold:
- When taking specimen photographs, use a tripod — but deliberately get some pairs of shots where the camera is moved to the side by about 7 cm (the distance between the pupils in an average human).
- If you don’t have any red-cyan glasses, get some!
Hey, Mike! Why haven’t you been blogging much lately?
October 14, 2020
Well, one reason is the utterly rancid “block editor” that WordPress has started imposing with increasing insistence on its poor users. If there is one thing that world really doesn’t need, it’s a completely new way of writing text. Seriously, WordPress, that was a solved problem in 1984. As Henry Spencer very nearly said back in the eighties, “thy creativity is better used in solving problems than in creating beautiful new impediments to productivity“.
But enough pointless whining: instead, check out this bad boy:
Taylor (in prep. for 2020: Figure V). NHMUK PV R5937, “The Archbishop”, cervical vertebra V (most anterior preserved cervical vertebra, probably C6), left side still encased in plaster. A. Reconstruction of right lateral view with neural spine, prezygapophysis, diapophysis, condyle, cotyle and cervical rib restored. The prezygapophysis from the succeeding vertebra that has adhered to this element is shown in red. B. Dorsal view with anterior to the right. C. Posterior view. D. Right lateral view. E. Anterior view. F. Ventral view with anterior to the right. Scale bar 20 cm.
Yes, it’s your friend and mine, The Archbishop! It’s a big titanosauriform sauropod excavated by F. W. H. Migeod for the British Museum (Natural History) back in 1930, from the same Tendaguru Formation that yielded the awesome Giraffatitan specimens in the Museum für Naturkunde Berlin.
Yes, I admit I have been working on the Archbishop for more than sixteen years, and that I gave a talk about it at SVPCA 2005, and that I failed utterly to get it done as part of the Paleo Project Challenge 2010, and that as early as 2011 I was in despair about ever finishing it, and that I promised to do it by SVPCA 2016 but didn’t.
But in 2018 I did something significant, which was to actually start writing the paper in public. Now anyone can follow the progress of the project — and it’s progressing. The manuscript currently runs to about fifty printed pages, although that length is inflated by twenty-odd beautiful illustrations — of which the “Cervical V” image above is just one. (Do click through to see it in all its glory.)
So, yeah. That’s the main reason I am not blogging much. Because I am writing the paper. Finally.
Work on the Archbishop begins!
May 28, 2018
I know, I know — you never believed this day would come. And who could blame you? Nearly thirteen years after my 2005 SVPCA talkSweet Seventy-Five and Never Been Kissed, I am finally kicking the Archbishop descriptive work into gear. And I’m doing it in the open!
In the past, I’ve written my academic works in LibreOffice, submitted them for peer-review, and only allowed the world to see them after they’ve been revised, accepted and published. More recently, I’ve been using preprints to make my submitted drafts public before peer review. But there’s no compelling reason not to go more open than that, so I’ll be writing this paper out in the open, in a public GitHub repository than anyone can access. That also means anyone can file issues if they thing there’s something wrong or missing, and anyone can submit pull-requests if they have a correction to contribute.
I’ll be writing this paper in GitHub Flavoured Markdown so that it displays correctly right in the browser, and so that patches can be supported. That will make tables a bit more cumbersome, but it should be manageable.
Anyway, feel free to follow progress at https://github.com/MikeTaylor/palaeo-archbishop
The very very skeletal manuscript is at https://github.com/MikeTaylor/palaeo-archbishop/blob/master/archbishop-manuscript.md
Just write the Archbishop description already!
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.
Photography and illustration talk, Part 7: Manipulating photographs
February 21, 2014
Can PeerJ really be only a year old?
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?”
Dorsals A and B (probably D8 and D9) of NHM R5937, “The Archbishop”, a still-undescribed brachiosaurid sauropod from the Upper Jurassic Tendaguru Formation of Tanzania, which I will get done this year, and which is destined for PeerJ. Top row: dorsal view with anterior to the right. Bottom row, from left to right: left lateral, posterior, right lateral, anterior.
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.)
Barosaurus lentus holotype YPM 429, Vertebra Q (C?13). Top row: left ventrolateral view. Middle row, from left to right: anterior view, with ventral to the right; ventral view; posterior view, with ventral to the left. Bottom row: right lateral view, inverted. Inset shows diapophyseal facet on right side of vertebra, indicating that the cervical ribs were unfused in this individual despite its great size. Note the broad, flat prezygapophyseal facet visible in anterior view. (Taylor and Wedel 2013b: figure 6)
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.
Photography and illustration talk, Part 2: Taking good photographs
February 8, 2014
Specimen photos with desaturated backgrounds
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?
And a happy Christmas from me, too!
December 23, 2011
Necks, I win; tails, Wedel loses –or– The SV-POW! Palaeo Paper Challenge
December 14, 2011
This year, I missed The Paleo Paper Challenge over on Archosaur Musings — it was one of hundreds of blog posts I missed while I was in Cancun with my day-job and then in Bonn for the 2nd International Workshop on Sauropod Biology and Gigantism. That means I missed out on my annual tradition of promising to get the looong-overdue Archbishop description done by the end of the year.
Brachiosauridae incertae sedis NMH R5937, "The Archbishop", dorsal neural spine C, probably from an anterior dorsal vertebra. Top row: dorsal view, anterior to top; middle row, left to right: anterior, left lateral, posterior, right lateral; bottom row: ventral view, anterior to bottom.
But this year, Matt and I are going to have our own private Palaeo Paper Challenge. And to make sure we heap on maximum pressure to get the work done, we’re announcing it here.
Here’s the deal. We have two manuscripts — one of them Taylor and Wedel, the other Wedel and Taylor — which have been sitting in limbo for a stupidly long time. Both are complete, and have in fact been submitted once and gone through review. We just need to get them sorted out, turned around, and resubmitted.
(The Taylor and Wedel one is on the anatomy of sauropod cervicals and the evolution of their long necks. It’s based on the last remaining unpublished chapter of my dissertation, and turned up in a modified form as my SVPCA 2010 talk, Why Giraffes Have Such Short Necks. The Wedel and Taylor one is on the occurrence and implications of intermittent pneumaticity in the tails of sauropods, and turned up as his SVPCA 2010 talk, Caudal pneumaticity and pneumatic hiatuses in the sauropod dinosaurs Giraffatitan and Apatosaurus.)
We’re going to be realistic: we both have far too much going in (incuding, you know, families) to get these done by the end of 2011. But we have relatively clear Januaries, so our commitment is that we will submit by the end of January 2012. If either of us fails, you all have permission to be ruthlessly derisive of that person.
… and in other news …
Some time while we were all in Bonn, the SV-POW! hit-counter rolled over the One Million mark. Thanks to all of your for reading!
