As we all know, University libraries have to pay expensive subscription fees to scholarly publishers such as Elsevier, Springer, Wiley and Informa, so that their researchers can read articles written by their colleagues and donated to those publishers. Controversially (and maybe illegally), when negotiating contracts with libraries, publishers often insist on confidentiality clauses — so that librarians are not allowed to disclose how much they are paying. The result is an opaque market with no downward pressure on prices, hence the current outrageously high prices, which are rising much more quickly than inflation even as publishers’ costs shrink due to the transition to electronic publishing.
On Thursday 11 April 2013, Oxford University hosted a conference called Rigour and Openness in 21st Century Science. The evening event was a debate on the subject Evolution or Revolution In Science Communication. During this debate, Stephen Curry of Imperial College noted that his librarian isn’t allowed to tell him how much they pay for Elsevier journals. This is the response of David Tempest, Elsevier’s Deputy Director of Universal Sustainable Research Access.
Heres’ a transcript
Curry [in reference to the previous answer]: I’m glad David Tempest is so interested in librarians being able to make costs transparent to their users, because at my university, Imperial College, my chief librarian can not tell me how much she pays for Elsevier journals because she’s bound by a confidentiality clause. Would you like to address that?
[Loud applause for the question]
Tempest: Well, indeed there are confidentiality clauses inherent in the system, in our Freedom Collections. The Freedom Collections do give a lot of choice and there is a lot of discount in there to the librarians. And the use, and the cost per use has been dropping dramatically, year on year. And so we have to ensure that, in order to have fair competition between different countries, that we have this level of confidentiality to make that work. Otherwise everybody would drive down, drive down, drive drive drive, and that would mean that …
[The last part is drowned in the laughter of the audience.]
So there you have it: confidentiality clauses exist because otherwise everybody would drive down prices. And we can’t have that, can we?
(Is this extracted segment of video unfairly misrepresenting Tempest? No. To see that for yourself, I highly recommend that you watch the video of the whole debate. It’s long — nearly two hours — but well worth the time. The section I used here starts at 1:09:50.)
In his post on Vicki’s new book Broken Bones, Matt told us his twelve-step process for producing stippled illustrations like this one of a crushed skull, which became the cover image of the book:
As soon as I saw that, I found myself thinking that it would look nice with some shading of the bone. Of course the existing stippling is a perfect guide to how dense the shading should be at each point, so I figured there had to be an easy way to do this automatically. There is, and this is what I whipped up in five minutes:
Here’s how I did it.
- I loaded Matt’s image into the GIMP, my image editor of choice.
- For some reason the crucial next step doesn’t work with greyscale images, so I converted it to RGB (Image → Mode → RGB)
- I removed the white background, leaving it transparent (Colours → Colour to Alpha… and click OK on the default colour, white)
- I added a new all-white background layer.
- I duplicated the skull layer, and named it “shading”
- I blurred the shading layer by 50 pixels (Filters → Blur → Gaussian Blur…, set the blur radius to 50 pixels and hit OK.) That gives you the shading you want, but it smudges out past the outline of the skull, hence the last two steps:
- I went back to the skull layer, and using the Fuzzy Select Tool (magic wand) selected the contiguous transparent area outside the skull parts.
- I went back to the shading layer and cut the selected area, leaving only that shading that’s inside the boundary of the skull.
As always with Gimp tutorials, it takes about ten times as long to explain as to actually do.
When I showed this to Matt, I rather immodestly said I was “super-happy with it”. Matt said he was “super-happy with the idea, but only regular happy with this specific execution”. He felt that the blurring was too strong, and that it should be backed off by 30-40%. So I made a new shading layer in the same way as above, but this time blurring by only 30 pixels. Here’s the resulting image:
It’s quite a subtle difference, but clear if you flip back and forth between the images (which you can most easily do by putting them in adjacent tabs of your browser). Personally, I think I prefer the 50-pixel version, since I think the shading clings rather too closely to the lines in this one, but YMMV.
Since I had both blur layers right there in the image, I thought it might be interesting to see how they look together. Here’s the result:
I’m actually rather fond of this version, but it’s a long way from the crisp, clinical feel of the original.
You can thicken up the shading by duplicating one or both of the shading layers as many times as you wish (or or course thin it out by sliding down the opacity level). Its also easy to make the shading coloured: just use Colours → Levels, select the individual colour channels, and bring up their bottom levels to taste.
Putting all that together, here’s one I made with very dense, yellowish (bone-coloured) shading. I did it starting with the 50-pixel shading layer, upping the red output level to 200 and the green to 150, then duplicating that layer, and reducing the 30-pixel shading layer to 50% opacity.
You can play for hours with all these sliders, tweaking as you wish, thanks to the magic of layers. It’s well worth investing a bit of time to learn some of the capabilities of a program like GIMP. Matt and I are very far from wizards, but we have at least got a bit past just using it to cut out backgrounds, and it opens up possibilities.
Vicki’s book, Broken Bones, is out!
December 18, 2013
When we last left my better half, Dr. Vicki Wedel, she was helping to identify a Jane Doe who had been dead for 37 years by counting growth rings in the woman’s teeth. That case nicely illustrated Vicki’s overriding interest: to advance forensic anthropology by developing new methods and refining existing ones. To that end, for the past few years she has been working with her PhD advisor, Dr. Alison Galloway at UC Santa Cruz, to revise and update Alison’s 1999 book, Broken Bones: Anthropological Analysis of Blunt Force Trauma. The revised and much expanded (504 pages vs 371) second edition, co-edited by Vicki and Alison, came out Monday (Amazon, Amazon.co.uk).
You can read the whole table of contents on Amazon (click to look INSIDE!), but the short short version is that the book has three major sections. The first covers the science and practice of trauma analysis (pp. 5-130), and the second classifies hundreds of common fractures throughout the skeleton, with illustrations (pp. 133-313). The chapters in these sections were all written by Vicki, Alison, and another of Alison’s former students, Dr. Lauren Zephro, solo and in varying combinations. Lauren, whom I always think of as “the Amazon cop”, is a 6-foot blackbelt forensic anthropologist for the Santa Cruz County Sheriff’s Office. If push came to shove I have no doubt that she could beat me to death with her bare hands and then produce a technical analysis of my corpse.
The final section (pp. 314-410) consists of nine case studies contributed by forensic anthropologists, pathologists, medical examiners, forensic and medical artists, and a DoD casualty analyst, based across the Anglophone world from Hawaii to Scotland. There’s some grim stuff in there: trauma to the homeless and elderly, from intimate partner violence, and from child abuse. It’s gut-churningly awful that the defenseless suffer from bone-breaking violence; it’s always been amazing to me that people like Vicki, Alison, Lauren, and the other contributors have both the courage to face these horrors and the technical chops to make the unspeakable solvable.
Beyond that unavoidable darkness, if you’re interested in the many, varied, and often just plain weird ways in which people die, the book is a treasure trove. There’s an elderly woman lying on her deathbed for six years, slowly turning into a natural mummy… (wait for it) …while her daughter went on living in the same house. There’s a classification of plane crashes with a description of what human remains will be found and over what area. There are people hit by trains; the funniest line in this very serious book is the deadpan and unsurprising, “The typical pedestrian hit by a train is male and often highly intoxicated.”
That’s from the top of page 122. At the bottom of the same page is my one contribution to the book, which also appears as the cover art (yeah, nepotism, whatcha gonna do). There’s a story behind this. This guy–yes, male, dunno if he was intoxicated–was hit by a train and his head was sheared in half, with the somewhat fractured but mostly intact facial skeleton separated by a lot of missing bone from the occipital region. With no way to obtain the deceased guy’s permission to use his mortal remains in the book, Alison and Vicki didn’t feel comfortable including their photos, so I spent a weekend bashing out a technical drawing for them to use instead. That reawakened my interest in pen-and-ink work and led to the dödö pöst.
I should say two things right here: first, that yes, I am hijacking the rest of the post to talk about myself. (Is anyone really surprised? I thought not.) Second, that I have had no training and possibly my stippling violates Art Rules or best practice guidelines of which I am ignorant. But I hope it also illustrates what can be achieved in a couple of days, with about $15 worth of supplies, by a guy whose only rule is “möre döts”.
So anyway, if you’re curious, here’s the method I use for my pen-and-ink illustrations:
- Get a decent-sized photo of the object to be drawn. I usually roll with $2 8x10s from MalWart, in this case one for each half of the skull.
- Tape the photo down to your work surface. I have a large, incredibly hard, perfectly smooth cutting board that I use for this, but in a pinch you could use just about anything, including just a larger piece of paper. Cardboard off the backs of desk calendars is nice.
- Over the photo, tape down a piece of tracing paper.
- Lightly trace the outline of the photo and all the major details in pencil.
- Once you’ve gone as far as you can with that, peel up one side of the tracing paper, unstick the photo from the work surface, and remove it. Stick the tracing paper back down the work surface.
- Using the uncovered photo as a reference, pencil in any other salient details by eye. Also contour lines for shadows. All of the pencil lines are going to be erased later, so don’t be shy.
- Whenever you decide you’re done with the pencil, get a good pen and start tracing, directly over the pencil lines. I tend not to be too persnicketty about my tools but decent pens are a real help here. For these recent works, I picked up a three-pack of beige-tubed Micron pens for $7 (this set).
- In all of the following pen-related steps, be careful to keep your big stupid hand and arm off the wet ink you just laid down–one careless smear can ruin a few hours’ work. Having a work surface that you can rotate is nice, so your pen hand can approach the drawing from any angle. Anytime I have to lay my hand on the drawing, I put down a piece of clean scrap paper first. Even if the underlying ink is dry, it just feels like a smart precaution.
- Once the lines are on, add döts to taste. With a little experimentation, you can get patterns of dots to not only indicate light and dark but also suggest textures. Different pen tips and amounts of pressure will yield dots of different sizes, which can also be useful. Dense, overlapping dots can produce an effect similar to scratchboard. BTW, sometimes I do “gear down” and place each dot with thought and care, but in the dense sections I just rat-a-tat-tat like a Lilliputian jackhammer. Try different speeds and see what you can tolerate.
- When you’re done dötting, at least to a first approximation, and you’re dead certain the ink is all dry, get a decent eraser and erase all of the pencil lines. I used one of those clicky mechanical erasers because it was cheap and soft enough to not tear up the paper.
- Re-ink any lines lightened by the erasing. I find that the döts are usually unaffected, but lines are often knocked down a bit by the eraser work. I suppose it would be cleaner to just draw natively in pen, with no prior pencilling and therefore no erasing, but the few times I’ve tried it, it hasn’t gone well. YMMV. If you’re drawing a 3D solid, this is a good time to employ an old illustrator’s trick, which is to make the bottom outline heavier and darker than the rest, to subtly convey a sense of weight.
- Scan, touch up as needed in GIMP, post to blog, bask in self-admiration.
In this case I had a few more steps, which consisted of making variants of the drawing and test-driving them by Vicki and Alison so they could pick their favorites.
This is just embarrassing: after scanning the two drawings and doing a little touch-up, I just scooted them together until they looked like a skull. The problem is that the occiput is nowhere near anatomical position. See that flange of bone above the ear-hole, pointed down and right at a 45-degree angle? That’s the back end of the zygomatic arch, and it should be aimed at the forward stump of the arch, which is just down and back from the eye socket.
Here’s the B version, where I was working entirely off of the zygomatic arch ends, and trying to get the skull into anatomical position. Scientifically this is probably the best variant I produced (I’m not claiming it’s the best possible), but aesthetically it’s a little crowded.
I’ll spare you versions C-E, all of which just scooted the back end of the skull around in an attempt to find a balance between scientific and aesthetic concerns. Here’s the winning F version, which got used for the figure, and became the seed variant for the cover.
For the cover, we tried a lot of things, including the white skull on a black background, and one that was simply inverted from the figure. By this point the publisher had sent Vicki some test versions of the cover, and I thought it would be cool if the drawing was in the same color as the cover text, so I sampled that color from the publisher’s sample cover image and applied it to all of the drawn bits. They knocked it down a few tones for the printed version, so happily it’s not this garish.
Incidentally, I had never tried to replace a bunch of discontinuous areas of the same color with another color in GIMP, so I had to look it up. The two key steps are Select > By color, with the threshold set to zero (or not, if you want to grab a bunch of related colors at once), and “Fill whole selection” in the Bucket tool. Hat tip to this dude and his commenters.
One last step: I thought the bare, unfilled yellow version looked too flat, so I tried different levels of fill to make the skull pop out from the background. I didn’t use bucket fill here–too fiddly with so many dots and edges. Instead I created a new layer of solid yellow and dropped the opacity to 17%. Then went to the drawing layer and used the magic wand tool to select the whole non-skull background. Then popped back to the yellow layer and cleared that selection, leaving yellow fill only in the boundaries of the skull outline. I also tried 10% and 25% opacity for the fill layer, but 10% was too subtle and 25% was starting to swamp some of the detail in the drawing. Between goofing around with colors and opacity levels we went through 10 versions at this stage, of which the one above is the ultimate champion.
So, that’s how the cover art came to be. Back to the book. There’s a bibliography with 1237 references (Vicki knows), and an index. The book is hardbound, with a printed cover and no dustjacket, and IMHO reasonably priced at $65, currently a few bucks less on Amazon. You probably already know whether you want a copy. If so, do the right thing–it’s not too late to get it by Christmas.
References
Elsevier steps up its War On Access
December 17, 2013
I thought Elsevier was already doing all it could to alienate the authors who freely donate their work to shore up the corporation’s obscene profits. The thousands of takedown notices sent to Academia.edu represent at best a grotesque PR mis-step, an idiot manoeuvre that I thought Elsevier would immediately regret and certainly avoid repeating.
Which just goes to show that I dramatically underestimated just how much Elsevier hate it when people read the research they publish, and the lengths they’re prepared to go to when it comes to ensuring the work stays unread.
Now, they’re targeting individual universities.
The University of Calgary has just sent this notice to all staff:
The University of Calgary has been contacted by a company representing the publisher, Elsevier Reed, regarding certain Elsevier journal articles posted on our publicly accessible university web pages. We have been provided with examples of these articles and reviewed the situation. Elsevier has put the University of Calgary on notice that these publicly posted Elsevier journal articles are an infringement of Elsevier Reed’s copyright and must be taken down.
That’s it, folks. Elsevier have taken the gloves off. I’ve tried repeatedly to think the best of them, to interpret their actions in the most charitable light. I even wrote a four-part series on how they can regain the trust of researchers and librarians (part 0, part 1, part 2, part 3), under the evidently mistaken impression that that was what they wanted.
But now it’s apparent that I was far too optimistic. They have no interest in working with authors, universities, businesses or anyone else. They just want to screw every possible cent out of all parties in the short term.
Because this is, obviously, a very short-term move. Whatever feeble facade Elsevier have till now maintained of being partners in the ongoing process of research is gone forever. They’ve just tossed it away, instead desperately trying to cling onto short-term profit. In going after the University of Calgary (and I imagine other universities as well, unless this is a pilot harassment), Elsevier have declared their position as unrepentant enemies of science.
In essence, this move is an admission of defeat. It’s a classic last-throw-of-the-dice manoeuvre. It signals a recognition from Elsevier that they simply aren’t going to be able to compete with actual publishers in the 21st century. They’re burning the house down on their way out. They’re asset-stripping academia.
Elsevier are finished as a credible publisher. I can’t believe any researcher who knows what they’re doing is going to sign away their rights to Elsevier journals after this. I hope to see the editorial boards of Elsevier-encumbered journals breaking away from the dead-weight of the publisher, and finding deals that actually promote the work of those journals rather than actively hindering it.
And a reminder, folks: for those of you who want to publicly declare that you’re done with Elsevier, you can sign the Cost Of Knowledge declaration. That’s often been described as a petition, but it’s not. A petition exists to persuade someone to do something, but we’re not asking Elsevier to change. It’s evidently far, far too late for that. As a publisher, Elsevier is dead. The Cost of Knowledge is just a declaration that we’re walking away from the corpse before the stench becomes unbearable.
Bare bear bone: beautiful
December 17, 2013
Yes, it’s bear skulls on the brain lately. I have nothing scientific to say here, I was just going through old files and found myself struck by the beautiful form and texture of the bones. The photos are all close-ups of this skull of an American black bear, Ursus americanus.
Part of the forehead, where the nasal bones (bottom center) and maxillae (either side) meet the frontals (top).
The left temporal bone in posterodorsal view; anterior is to the left. The open web of bone in the middle of the photo is one of the pneumatic sinuses inside the temporal bone. The round hole just above the web enclosed a blood vessel in life. The half-tube on the right is the bottom half of external auditory meatus, or bony ear-hole (where you stick the Q-tip when you clean your ears, if you’re a reckless, safety-warning-diregarding outlaw). All of this got exposed when a bullet or shotgun slug took the back quarter of this bear’s head off, as described here.
Personally I’d be happier if the skull was still in the bear and the bear was still doing its bearish business, but as long as it’s dead anyway, we might as well learn what we can from the remains (my universal policy on dead animals). And also just stop now and then to appreciate their natural intricacy and beauty.
Correlation of impact factor and citations: a personal case-study
December 13, 2013
It’s now widely understood among researchers that the impact factor (IF) is a statistically illiterate measure of the quality of a paper. Unfortunately, it’s not yet universally understood among administrators, who in many places continue to judge authors on the impact factors of the journals they publish in. They presumably do this on the assumption that impact factor is a proxy for, or predictor of, citation count, which is turn is assumed to correlate with influence.
As shown by Lozano et al. (2012), the correlation between IF and citations is in fact very weak — r2 is about 0.2 — and has been progressively weakening since the dawn of the Internet era and the consequent decoupling of papers from the physical journal that they appear in. This is a counter-intuitive finding: given that the impact factor is calculated from citation counts you’d expect it to correlate much more strongly. But the enormous skew of citation rates towards a few big winners renders the average used by the IF meaningless.
To bring this home, I plotted my own personal impact-factor/citation-count graph. I used Google Scholar’s citation counts of my articles, which recognises 17 of my papers; then I looked up the impact factors of the venues they appeared in, plotted citation count against impact factor, and calculated a best-fit line through my data-points. Here’s the result (taken from a slide in my Berlin 11 satellite conference talk):
I was delighted to see that the regression slope is actually negative: in my case at least, the higher the impact factor of the venue I publish in, the fewer citations I get.
There are a few things worth unpacking on that graph.
First, note the proud cluster on the left margin: publications in venues with impact factor zero (i.e. no impact factor at all). These include papers in new journals like PeerJ, in perfectly respectable established journals like PaleoBios, edited-volume chapters, papers in conference proceedings, and an arXiv preprint.
My most-cited paper, by some distance, is Head and neck posture in sauropod dinosaurs inferred from extant animals (Taylor et al. 2009, a collaboration between all three SV-POW!sketeers). That appeared in Acta Palaeontologia Polonica, a very well-respected journal in the palaeontology community but which has a modest impact factor of 1.58.
My next most-cited paper, the Brachiosaurus revision (Taylor 2009), is in the Journal of Vertebrate Palaeontology — unquestionably the flagship journal of our discipline, despite its also unspectacular impact factor of 2.21. (For what it’s worth, I seem to recall it was about half that when my paper came out.)
In fact, none of my publications have appeared in venues with an impact factor greater than 2.21, with one trifling exception. That is what Andy Farke, Matt and I ironically refer to as our Nature monograph (Farke et al. 2009). It’s a 250-word letter to the editor on the subject of the Open Dinosaur Project. (It’ a subject that we now find profoundly embarrassing given how dreadfully slowly the project has progressed.)
Google Scholar says that our Nature note has been cited just once. But the truth is even better: that one citation is in fact from an in-prep manuscript that Google has dug up prematurely — one that we ourselves put on Google Docs, as part of the slooow progress of the Open Dinosaur Project. Remove that, and our Nature note has been cited exactly zero times. I am very proud of that record, and will try to preserve it by persuading Andy and Matt to remove the citation from the in-prep paper before we submit. (And please, folks: don’t spoil my record by citing it in your own work!)
What does all this mean? Admittedly, not much. It’s anecdote rather than data, and I’m posting it more because it amuses me than because it’s particularly persuasive. In fact if you remove the anomalous data point that is our Nature monograph, the slope becomes positive — although it’s basically meaningless, given that all my publications cluster in the 0–2.21 range. But then that’s the point: pretty much any data based on impact factors is meaningless.
References
- Farke, Andrew A., Michael P. Taylor and Mathew J. Wedel. 2009. Sharing: public databases combat mistrust and secrecy. Nature 461:1053.
- Lozano, George A., Vincent Larivière and Yves Gingras. 2012. The weakening relationship between the impact factor and papers’ citations in the digital age. Journal of the American Society for Information Science and Technology 63(11):2140-2145. doi:10.1002/asi.22731 [arXiv preprint]
- Taylor, Michael P. 2009. A re-evaluation of Brachiosaurus altithorax Riggs 1903 (Dinosauria, Sauropoda) and its generic separation from Giraffatitan brancai (Janensch 1914). Journal of Vertebrae Paleontology 29(3):787-806.
- Taylor, Michael P., Mathew J. Wedel and Darren Naish. 2009. Head and neck posture in sauropod dinosaurs inferred from extant animals. Acta Palaeontologica Polonica 54(2):213-230.
Image courtesy of Emma Schachner.
Gotta say, I did not see that coming.
Today sees the publication of a new paper by Emma Schachner and colleagues in Nature, documenting for the first time that unidirectional, flow-through breathing–previously only known in birds and crocodilians–happens in freakin’ monitor lizards. The image above, which is most of Figure 1, pretty much tells the tale.
Some quick background: until the early 1970s, no-one was quite sure how birds breathed. Everyone knew that birds breathe, and that the air sacs had something to do with it, and that the bird lungs are set up as a series of tubes instead of a big array of little sacs, like ours, but the airflow patterns had not been worked out. Then in a series of nifty experiments, Knut Schmidt-Nielsen and his students and colleagues showed that birds have unidirectional airflow through their lungs on both inspiration and expiration. Amazingly, there are no anatomical valves in the lungs or air sacs, and the complex flow patterns are all generated by aerodynamic valving. For loads more information on this, including some cool animations, please see this page (the diagram below is modified from versions on that page). For a short, eminently readable summary of how undirectional airflow in birds was first discovered (among many other fascinating things), I recommend Schmidt-Nielsen’s wonderful little book, How Animals Work.
After 1972, biologists had almost four decades to get used to the idea that birds had this amazing miraculous lung thingy that was unique in the animal kingdom. Then in 2010, Colleen Farmer and Kent Sanders of the University of Utah blew our collective minds by demonstrating that alligators have unidirectional flow-through lungs, too. That means that far from being a birds-only thing, unidirectional flow-through lung ventilation was probably primitive for Archosauria, and was therefore the default state for non-avian dinosaurs, pterosaurs, the other ornithodirans and the hordes of croc-line archosaurs.
Diagrammatic and highly simplified representation of airflow through the dorsobronchi and ventrobronchi during inspiration (A) and expiration (B) in the crocodilian lung, and inspiration (A) and expiration (D) in the avian lung. The avian model is a modification of the Hazelhoff loop (Hazelhoff, 1951). Arrows denote direction of airflow, white arrows show air flowing through the parabronchi, blue arrows show air entering the trachea, the red circled “X” demonstrates the location of the aerodynamic inspiratory valve (i.e., air does not flow through this location during inspiration). Colors represent hypothesized homologous regions of the lung in both groups. Abbreviations: d, dorsobronchi; P, parabronchi; Pb, primary bronchus; v, ventrobronchi. [Figure 10 and caption from Schachner et al. 2013a.]
Now…well, you read the headline. Monitor lizards have unidirectional airflow through their lungs, too. This falls at about the halfway point between “whatisthisIdonteven”–I mean, dude, unidirectional airflow in friggin’ lizards!–and “yeah, that makes a weird sort of sense”. Because to sum up a lot of science unscientifically, monitors just kick a little more ass than other squamates. They have crazy high aerobic capacities for animals that aren’t birds or mammals, they’re ecologically versatile and geographically widespread, they get waaay bigger than any other extant lizards (Komodo dragons) and until recently got even bigger than that (Megalania). Is it going too far to link the success of varanids with their totally pimpin’ flow-through lungs? Maybe, maybe not. But it seems like fertile ground for further study.
Phylogeny for Diapsida showing lungs of representative taxa.
Greyscale images are modified from Milani and transected. The coloured
three-dimensional images are the bronchial tree (right lateral view). Images are
not to scale. a, Diapsida. b, Sphenodon punctatus. c, Crocodile sp. (left) and
Alligator mississippiensis (right). d, Squamata. e, Iguana iguana (left) and
Polychrus marmoratus (right). f, Gekko gecko. g, Lacerta viridis. h, Python sp.
in dorsal view . i, Varanus bengalensis (left) and V. exanthematicus (right).
The blue regions of the phylogeny reflect the hypothesis that unidirectional
airflow evolved convergently; the green arrow shows the alternative hypothesis
of an ancestral origin. [Figure 3 and caption from Schachner et al. (2013b).]
On the gripping hand, uniflow would seem to have been lost in all those other lepidosauromorphs, but maybe it wasn’t. Maybe some of them are in the same state varanids were in until this year: they’ve had uniflow lungs forever and we don’t know because no-one has looked yet. And this is one of the concluding points in the new paper: we need to go look more at how living animals actually work.
A small sample of monitor lung diversity, from Becker et al. (1989).
In fact, we don’t just need to look at more critters in general, we specifically need to look at more monitors. I have been casually throwing around the terms “monitors” and “varanids” as if the findings of Schachner et al. (2013b) apply to all of them. They may not–the new paper is only about airflow in the savannah monitor, Varanus exanthematicus (same species as Mike’s “sauropod” Charlie), and monitor lungs are sufficiently diverse in form to have been used as taxonomic characters (Becker et al. 1989). So monitors may actually provide multiple windows into the evolution of unidirectional, flow-through lung ventilation. This is especially tantalizing because extant monitors cover a much wider range of body sizes and ecologies than extant crocs, so–just maybe–we can find out if and how diversity in lung structure and ventilation is related to body size and mode of life. Somebody get on that, stat.
Figure 6 from Perry (1992).
My favorite part of all this? Something virtually identical to how monitor lungs work was proposed just over two decades ago by Steve Perry, as a hypothetical stage between saccular lungs and bird-like lungs. See the “Euparkerian grade” lung in the above figure, with perforations between adjacent chambers? Compare that to the diagram of the monitor lung in the image at the top of the post–they’re pretty darned similar. Now, two caveats. First, Steve was suggesting this as a plausible ancestral state for archosaurs, not monitors, and as mentioned above, monitors do things a little differently than archosaurs. Second, there are some things in this figure that are now known to be incorrect, primarily the lack of unidirectional airflow in the crocodilian lung. In fact, on the page opposite this figure, Steve explicitly discounted the possibility of unidirectional airflow in croc lungs. Still, he recognized that croc lungs and bird lungs share profound structural similarities, that they are really points on a spectrum of plausible intermediate conditions, and that crocs had the potential to shuttle air around their lungs because of the complex connections between chambers. So if Steve was not completely right, neither was he completely wrong; it might be most accurate to say that he was less wrong than anyone else at the time, and for about 20 more years after. Which is pretty darned good; I’ve had to rebut myself within the space of five years (Wedel 2007: prosauropod pneumaticity is equivocal. Yates et al. 2012: oh no it’s not!).
Here are the thoughts that have been tumbling through my head since I first learned about this. Obviously structures can be simplified or lost through evolution. Birds and turtles lost their teeth, numerous tetrapods have lost one or both pairs of limbs, and, heck, the platypus lost its stomach. But I rarely see hypotheses of derived simplification entertained for organs like hearts and lungs. There seems to be an unstated but widespread assumption that complex = better when it comes to core physiological processes like breathing.
Figure 2 from Perry (1992)
But it ain’t necessarily so. Following Steve Perry’s diapsid-lung-continuum diagrams, I have often wondered if croc lungs are derived from bird lungs instead of the reverse; maybe the ancestral archosaur had a fully bird-like lung/air-sac system and the non-diverticular, not-super-aerobic lungs of crocs represent a simplification of that system to suit their more sedate lifestyle as semiaquatic ambush predators. That’s pretty much what Seymour et al. (2004) suggested for crocodilian hearts, and it seems plausible given that so many early crocodylomorphs were long-legged, terrestrial, and possibly cursorial (e.g., sphenosuchians). In other words, maybe extant crocs are secondarily ectothermic, with secondarily and possibly paedomorphically reduced air sac systems.
Heck, maybe even bird lungs are simplified compared to their ancestral condition. Most birds have nine air sacs: paired cervical, anterior thoracic, posterior thoracic, and abdominal sacs, and an unpaired clavicular air sac. Some have reduced the number further through loss or fusion of adjacent air sacs. But they all start out with 12 embryonic air sacs (the extras fuse together, IIRC almost all of them becoming part of the clavicular sac), which suggests that the ancestors of birds might have had more than the standard nine.
If we assume that there was some diversity in respiratory anatomy in Mesozoic dinosaurs–which is not much of a stretch, given the diversity we see within (let alone among) monitors, crocs, and birds–it would be an awfully big coincidence if the only dinosaur clade to survive the end Cretaceous extinction just happened to have the fanciest lungs. As far as I know, no-one has proposed that birds survived because they out-breathed everyone else. If anything, the decent-to-high survival rates of mammals, crocs, and turtles across the K-Pg boundary, and the complete extinction of air-sac-equipped pterosaurs and non-avian saurischians, suggests that lung ventilation had nothing to do with survivorship. So what are the chances that crown birds have the most complex lungs among ornithodirans? (Don’t say “flight” because enantiornithines and pterosaurs had air sacs and died out, and bats don’t have air sacs and fly just fine.)
I’m not saying these “awesomeness came first” hypotheses are currently more parsimonious than the standard view. But they’re plausible, and at least potentially testable, and if nothing else an antidote to the idea that birds sit at the top of some physiological Great Chain of Being.
Back to the homology-vs-convergence question. If flow-through lungs are primitive for diapsids, maybe they’ll turn up in a few more critters. But maybe evolving undirectional airflow just isn’t that hard, and only requires poking some holes through the walls of adjacent lung chambers–as stated above, we need to go check more critters. But either way, the form and function of the lungs in V. exanthematicus are not only fascinating in their own right, they give us a window into what the early evolution of archosaurian–and maybe even early diapsid!–breathing might have been like. And that’s phenomenal.
I have some more thoughts on this, particularly the implications for sauropods and other dinosaurs, but those will have to wait for another post.
Images and figures from Schachner et al. (2013b) appear here courtesy of Emma Schachner (website), who kindly offered to let me look under the hood before the paper came out. She also created a cool video showing the 3D lung anatomy of V. exanthematicus. Thanks, Emma, and congratulations!
References
- Becker, H.O., Böhme, W., and Perry, S.F. 1989. Die Lungenmorphologie der Warane (Reptilia: Varanidae) und ihre systematisch-stammesgeschichtliche Bedeutung. Bonner Zoologische Beiträge 40(1): 27-56.
- Perry, S.F. 1992. Gas exchange strategies in reptiles and the origin of the avian lung; pp. 149-167 in Wood, S.C., Weber, R.E., Hargens, A.R., and Millard, R.W. (eds.), Physiological Adaptations in Vertebrates. CRC Press, Boca Raton, 432 pp.
- Schachner, E.R., Hutchinson, J.R., and Farmer, C.G. 2013a. Pulmonary anatomy in the Nile crocodile and the evolution of unidirectional airflow in Archosauria. PeerJ 1:e60 http://dx.doi.org/10.7717/peerj.60
- Schachner, E.R., Cieri, R.L., Butler, J.P., and Farmer, C.G. 2013b. Unidirectional pulmonary airflow patterns in the savannah monitor lizard. Nature, advance online publication. http://dx.doi.org/10.1038/nature12871 [DOI not yet active as of this posting]
-
Schmidt-Nielsen, K. 1972. How Animals Work. Cambridge University Press, Cambridge, 114 pp.
- Seymour, R.S., Bennett‐Stamper, C.L., Johnston, S.D., Carrier, D.R., and Grigg, G.C. 2004. Evidence for endothermic ancestors of crocodiles at the stem of archosaur evolution. Physiological and Biochemical Zoology 77(6): 1051-1067.
- Wedel, M.J. 2007a. What pneumaticity tells us about ‘prosauropods’, and vice versa. Special Papers in Palaeontology 77:207-222.
- Yates, A.M., Wedel, M.J., and Bonnan, M.F. 2012. The early evolution of postcranial skeletal pneumaticity in sauropodomorph dinosaurs. Acta Palaeontologica Polonica 57(1):85-100. doi: http://dx.doi.org/10.4202/app.2010.0075
Carnivore Skull Challenge: the reveal
December 10, 2013
Many thanks to everyone who played pin-the-skull-on-the-carnivore. The answers are down at the bottom of this post, so if you’ve just arrived here and want to take the challenge, go here before you scroll down.
To fill up some space, let me point out how crazy variable the skulls of black bears, Ursus americanus, are.
Here’s the one I helped dig up, missing the occipital region. Note the double inflection in the dorsal outline that separates the forehead from both the snout and top of the head, and the way the nasal bones stick out at a very different angle from the maxilla.
Here’s the skull of a black bear from the La Brea tar pits, in the Page Museum in L.A. I don’t know if this one was female or juvenile or what, but the dorsal margin of the skull is one mostly-smooth curve from occiput almost to incisors, with the nasals scarcely deviating at all. Lest you think these differences were caused by evolutionary change rather than intraspecific variation, similar “roundhead” bear skulls from modern times are here and here and near the bottom of this page.
It’s this variability that first got me thinking about doing the Carnivore Skull Challenge. I saw a couple of photos of skulls of wolverines, and except for having carnassial cheek teeth instead of flatter premolars and molars, the wolverine skulls look like they could fit right into the span of black bear skull variability (in shape; obviously they’re not nearly as big). Then I saw a hyena skull and thought that it wasn’t that far off from a wolverine either. A little more searching for plausible distractors and I was all set.
Here are the answers, by the way:
It’s kind of ironic, then, that the first two people to venture identifications picked out the black bear right away. In the very first comment, Dean got it almost all right except for swapping the seal and the fossa. Dean was also the first to get all of the skulls correctly identified, albeit on his second pass. Markus Bühler (of Cthulhu-sculpting fame) was the first to get them all the first time. Tom Nutter, our own Darren Naish, and microecos Neil also aced the test, although in light of the Page Museum bear skull shown above, I was amused to see Darren’s “D: Bear. Because forehead.” I guess it’s one of those presence-of-forehead-means-bear, absence-of-forehead-does-not-rule-out-bear things that logicians are always going on about.
I was really happy to see people getting the wolverine and hyena mixed up, because they really do look strikingly similar to me. It’s almost like hyena + bear = wolverine.
Brian Engh asked on Facebook when I was going to do one for sauropods. Patience, good sir! It’s on my to-do list.
Finally, speaking of bear skulls, you can get a sweet tiny bronze one with a hinged jaw as part of this already successful Kickstarter, or from Fireandbone.com once the Kickstarter ends.
Something very different, and very unexpected, tomorrow.
Know your mammal skulls? Take the Carnivore Skull Challenge!
December 9, 2013
In this image I have assembled photos of skulls (or casts of skulls) of six extant carnivores. I exclusively used photos from the Skulls Unlimited website because they had all the taxa I wanted, lit about the same and photographed from similar angles. The omission of scale indicators is deliberate.
Your mission, should you choose to accept it, is to match these skulls with the animals they came from. Here are their currently-understood hierarchical relationships, scientific names, and common names (aside: I know this is ugly, is there a way to make nested tables in WordPress?).
Carnivora
– – Herpestoidea
– – – – Eupleridae
– – – – – – Fossa, Cryptoprocta ferox
– – – – Hyaenidae
– – – – – – Brown hyena, Hyaena brunnea
– – Arctoidea
– – – – Ursoidea
– – – – – – American black bear, Ursus americanus
– – – – Musteloidea
– – – – – – European badger, Meles meles
– – – – – – Wolverine, Gulo gulo
– – – – Pinnipedia
– – – – – – Mediterranean monk seal, Monachus monachus
If you accept the challenge, leave your guesses as comments below, but only if you’ve played fair–no checking websites, references, or your own skull collection! Don’t worry about being wrong, I freely admit that I would have flunked this bigtime if anyone else had inflicted it on me. I decided to set up this challenge after I noticed the striking similarity between two of these critters in particular; I’ll tell you which two when I post the reveal in a day or two.
Elsevier is taking down papers from Academia.edu
December 6, 2013
Lots of researchers post PDFs of their own papers on their own web-sites. It’s always been so, because even though technically it’s in breach of the copyright transfer agreements that we blithely sign, everyone knows it’s right and proper. Preventing people from making their own work available would be insane, and the publisher that did it would be committing a PR gaffe of huge proportions.
Enter Elsevier, stage left. Bioinformatician Guy Leonard is just one of several people to have mentioned on Twitter this morning that Academia.edu took down their papers in response to a notice from Elsevier. Here’s a screengrab of the notification:
And here is the text (largely so search-engines can index it):
Hi Guy
Unfortunately, we had to remove your paper, Resolving the question of trypanosome monophyly: a comparative genomics approach using whole genome data sets with low taxon sampling, due to a take-down notice from Elsevier.
Academia.edu is committed to enabling the transition to a world where there is open access to academic literature. Elsevier takes a different view, and is currently upping the ante in its opposition to academics sharing their own papers online.
Over the last year, more than 13,000 professors have signed a petition voicing displeasure at Elsevier’s business practices at www.thecostofknowledge.com. If you have any comments or thoughts, we would be glad to hear them.
The Academia.edu Team
(Kudos to the Academia.edu team, by the way, for saying it like it is: “upping the ante in its opposition to academics sharing their own papers online”. It would have been easy for them to give no opinion on this. Much better that they’ve nailed their colours to the mast.)
I was going to comment on Elsevier’s exceedingly short-sighted and mean-spirited manoeuvre, but happily the Twittersphere is on it already. Here are a few thoughts:
- David Winter wrote: Added value! Subs fees pay for lawyers to stop you sharing your work with colleagues…
- Rich FitzJohn speculated: I wonder what their long game is here; petty harassment like that makes me way less inclined to publish in an Elsevier journal.
- To which Rafael Maia responded: so silly…is it really worth it? its like they are proudly embracing being the dicks of academic publishing
- But Dr. Wrasse was more forthright.
This doesn’t directly affect me, of course, since I’ve had the good fortune not to have published in an Elsevier journal. But it’s another horrible example of how organisations that call themselves “publishers” do the exact opposite of publishing. The good people I know at Elsevier — people like Tom Reller, Alicia Wise and The Other Mike Taylor — must be completely baffled, and very frustrated, by this kind of thing.
Every time they start to persuade me that maybe — maybe — somewhere in the cold heart of legacy publishers, there lurks some real will to make a transition to actually serving the scholarly community, they do something like this. It’s like a sickness with them.
Do scholarly publishers really need to be reminded that “publish” means “make public”? Yes. Yes, they do. Apparently. Remember how I called legacy publishers “enemies of science” back at the start of 2012? Yup. Still true. And, astonishingly, as Rafael Maia noted, Elsevier seem determined to lead the way.
Have they learned nothing? Will they never?
Sauropod Vertebra Picture of the Week 