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.
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?
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.
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!
August 6, 2011
Matt just wrote this, in an email exchange. It struck a chord in me, and I thought it deserved a wider audience:
I hate to admit it, but those two papers (i.e., Taylor et al. 2009 and 2011) that had particularly protracted gestations and lots of review time are among the ones I am most proud of. There might be a lesson there — but if so, I’d rather not learn it.
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!
June 28, 2010
For reasons that seemed good to me at the time, I took my best shot at photographing the right cervical rib from cervical vertebra 3 of my ostrich, Veronica [see earlier Part A, Part B and Part C for context]. I thought you might like to see the result, so here it is:
For some reason, cervical ribs don’t seem to get a lot of love in the literature: the only paper I know that figures them in half-decent detail is Osborn and Mook’s classic (1921) monograph on Camarasaurus, and even there, the job is done in rather a half-hearted fashion. I’m planning to buck this trend by properly figuring the cervical ribs of the Archbishop when I finally get around to finishing that paper, and I included a sneak preview of the rib that I’ve arbitrarily designated X1 a while back. It’s instructive to compare that illustration with this one. In fact, here it is again:
Update (the next day)
It occurs to me that I should have composed the ostrich-cervical-rib illustration in the same orientation and order as the Archbishop one, for easier comparison. So that’s what I’ve done below. Since the Archbishop rib X1 is from the left side, I’ve also flipped the right-sided ostrich rib to match. Here it is:
January 31, 2010
I hope you have a pair of 3D glasses. If you do, then check this baby out:
(This is of course the same vertebra that we last saw in a multi-view composite figure at the end of the Brachiosaurus coracoid post.)
I’ve started to get into the habit recently of photographing some specimens from two slightly different angles: I couldn’t tell you exactly how much rotation I use, but I would guess it’s something like three to five degrees. That’s because I’ve found that flipping back and forth between the two images can give a useful sense of depth. If you don’t believe me, here are two not-quite-identical photos of the Archbishop’s Cervical S: open each of them in a tab, then flick back and forth between them:
It had occurred to me a while back that, just for fun, it would be interesting to composite them into a red-cyan 3D image. But I was prodded into action by two things. First, the free Lego marketing magazine that my boys get sent every month arrived, and with it a freebie pair of cheap cardboard red-cyan glasses. And second, Matt published a steropair of moon images on his blog. Matt’s friend Jarrod is a professional digital effects artist — in fact he’s won Emmies for stuff like blowing up Los Angeles for 24 — and threw together an anaglyph from the moon pictures. I got instructions from Jarrod on how to do this, and was gratified how easy it was. Here you go:
- Open the two photos as two layers of a single image.
- Using the Colour Levels dialogue, turn the red channel of one of the photos all the way down to zero (so that it appears in shades of cyan)
- Using the same dialogue, turn both the blue and green channels of the other photo down to zero (so that it appears in shades of red)
- Change the Layer Mode of the top layer to Brighten Only
That’s it, you’re done! Save the resulting composite image as a JPEG and upload it to your sauropod-vertebra blog. Jarrod uses PhotoShop; I use the Gimp, which is a free more-or-less equivalent program — the same technique works fine with both.
If I was pleasantly surprised at how simple the technique is, I was astounded at the quality of the result. I’d expected all the colour of the image to be gone, and to see a vague monochrome haze. Instead, I saw rock-solid 3D in full colour — truly informative images that convey the morphology of complex bones far better than any published figure I’ve ever seen. Seriously, go get your red-cyan glasses, you won’t regret it.
Here is another anaglyph of the same vertebra, in posterior view close-up, showing in detail what looks suspiciously like a hyposphene below and between the postzygs. (If this is indeed a hypophene, then I believe it’s unique among sauropods.)
Journals have occasionally published stereopair images of palaeo specimens: small images a couple of inches wide, next to each other, which you can supposedly see as a single 3D image if you cross your eyes in just the right light provided the wind is from the southeast — personally, I have never been able to see these things, thought Matt can. But these big, full-colour 3d images are orders of magnitude more information.
I’ve never seen one in a journal, in part of course because colour printing is such an insanely expensive luxury. But as Matt says, we all live in the future now, and I hope that’s about to change. I will be sending the Archbishop description, when it’s done, to PLoS ONE, which because of its electronic-only format can include any number of full-colour figures at no cost. I plan to send a few anaglyphs among the more conventional figures. Fingers crossed that they make it into the published version — I guess if I get a traditionalist reviewer, he might think these are frivolous and demand that I remove them. But they are not frivolous: they may be the most informative figures I have ever prepared.
Finally, I leave you with our old friend the pig skull, from all the way back in Things To Make And Do part 1 — but this time in glorious 3D!
January 27, 2010
[Hello to any redditors who have followed a link here. Please scroll down to find the more interesting articles; sorry that your introduction to SV-POW! is a backlink article.]
Excuse the self-promotion, but some SV-POW! readers might be interested to know that I have an Ask Me Anything going over at the social news aggregator site reddit com. I posted a long comment on someone else’s submission on whale size, and a lot of people asked me questions, so I started a separate thread, which you can read here.
I seem to be at the top of the IAMA page:
January 25, 2010
In my not-long-quite-so-recent-any-more paper on Brachiosaurus and Giraffatitan, I gave as one of the autapomorphies of Brachiosaurus proper that the glenoid articular surface of its coracoid is laterally deflected. Although we’ve discussed this a little in comments on SV-POW!, it’s not yet made it into one of our actual articles. I hestitated to feature it here since it’s so darned appendicular, but in the end I concluded that it was too interesting and potentially important to overlook.
So here it is!
The deflected surface is most apparent in the posterior view at the right of the fiigure, in which it appears deflected about 55 degrees from the horizontal. That’s misleading, though — partly because the shape is more complex in three dimensions than can be easily visualised from these orthogonal shots, and partly because of course the coracoid was not held perfectly vertical in life. In fact, the orientation of the coracoid in sauropods, and of the entire shoulder girdle, remains rather controversial. It’s not an area I’ve got involved in so far, but this Mystery Coracoid Of Weirdness (hereafter MCOW) might just be my gateway into the wacky world of pectoral girdles.
The ventral view at the bottom of the figure is also informative: as you can see from that angle, the articular surface extends a long way laterally (i.e. towards the top of the figure in this orientation). Once you’ve got your eye in with those images, it’s easy to see the facet in the lateral-view photo, despite the less than ideal saturated lighting: it’s shaped like a raindrop falling towards bottom left. (Well, not really: raindrops are actually vertically flattened spheroids rather then raindrop-shaped, but that’s not the point.)
Observations and interpretations on this oddity will be very welcome.
Finally, here is your regularly scheduled sauropod vertebra: