January 26, 2017
It’s now been widely discussed that Jeffrey Beall’s list of predatory and questionable open-access publishers — Beall’s List for short — has suddenly and abruptly gone away. No-one really knows why, but there are rumblings that he has been hit with a legal threat that he doesn’t want to defend.
To get this out of the way: it’s always a bad thing when legal threats make information quietly disappear; to that extent, at least, Beall has my sympathy.
That said — over all, I think making Beall’s List was probably not a good thing to do in the first place, being an essentially negative approach, as opposed to DOAJ’s more constructive whitelisting approach. But under Beall’s sole stewardship it was a disaster, due to his well-known ideological opposition to all open access. So I think it’s a net win that the list is gone.
But, more than that, I would prefer that it not be replaced.
Researchers need to learn the very very basic research skills required to tell a real journal from a fake one. Giving them a blacklist or a whitelist only conceals the real issue, which is that you need those skills if you’re going to be a researcher.
Finally, and I’m sorry if this is harsh, I have very little sympathy with anyone who is caught by a predatory journal. Why would you be so stupid? How can you expect to have a future as a researcher if your critical thinking skills are that lame? Think Check Submit is all the guidance that anyone needs; and frankly much more than people really need.
Here is the only thing you need to know, in order to avoid predatory journals, whether open-access or subscription-based: if you are not already familiar with a journal — because it’s published research you respect, or colleagues who you respect have published in it or are on the editorial board — then do not submit your work to that journal.
It really is that simple.
So what should we do now Beall’s List has gone? Nothing. Don’t replace it. Just teach researchers how to do research. (And supervisors who are not doing that already are not doing their jobs.)
October 27, 2016
Quick heads up: Mark Hallett and I are both at the Society of Vertebrate Paleontology meeting in Salt Lake City. Tomorrow afternoon (Friday, October 28) at 4:15 PM we’ll be signing copies of our book, The Sauropod Dinosaurs: Life in the Age of Giants. If you’d like to get a copy of the book, or to have your already-purchased copy signed, please come to the Johns Hopkins University Press booth in the exhibitor/poster area tomorrow afternoon. We’re both generally happy to sign books whenever and wherever, but if you’d like to catch us both at the same time, this is a good opportunity. We’re hoping to do another joint book signing in Los Angeles before long – more info on that when we get it arranged.
In the meantime, or if you’re not at SVP, or if you just like cool things, check out this rad claymation video of fighting apatosaurs, by YouTube user Fred the Dinosaurman. I love this. My favorite thing is that if you’re familiar with the previously-produced, static visual images of neck-fighting apatosaurs (links collected here), you’ll see a lot of those specific poses and moments recreated as transient poses in the video. This was published back in June, but I’d missed it – many thanks to Brian Engh for the heads up.
April 30, 2016
I love Utah. I love how much of the state is given over to exposed Mesozoic rocks. I love driving through Utah, which has a strong baseline of beautiful scenery that is frequently punctuated by the absolutely mind-blowing (Arches, Bryce Canyon, Zion, Monument Valley…). I love doing fieldwork there, and I love the museums, of which there are many. It is not going too far to say that much of what I learned firsthand about sauropod morphology, I learned in Utah (the Carnegie Museum runs a close second on the dragging-Matt-out-of-ignorance scale).
There is no easy way to say this so I’m just going to get it over with: Mike has never been to Utah.
I know, right?
But we’re going to fix that. Mike’s flying into Salt Lake City this Wednesday, May 4, and I’m driving up from SoCal to meet him. After that we’re going to spend the next 10 days driving around Utah and western Colorado hitting museums and dinosaur sites. We’re calling it the Sauropocalypse.
Why am I telling you this, other than to inspire crippling jealousy?
First, Mike and I are giving a pair of public talks next Friday evening, May 6, at the USU-Eastern Prehistoric Museum in Price. The talks start at 7:00 and will probably run until 8:00 or shortly after, and there will be a reception with snacks afterward. Mike’s talk will be, “Why giraffes have such short necks”, and my own will be, “Why elephants are so small”.
Second, occasionally people leave comments to the effect of, “Hey, if you’re ever passing through X, give me a shout.” I haven’t kept track of all of those, so this is me doing the same thing in reverse. Here’s our itinerary as of right now:
May 4, Weds: MPT flies in. MJW drives up from Cali. Stay in SLC/Provo area.
May 5, Thurs: recon BYU collections in Provo. Stay in SLC/Provo area.
May 6, Fri: drive to Price, visit USU-Eastern Prehistoric Museum, give evening talks. Stay in Price.
May 7, Sat: drive to Vernal, visit DNM. Stay in Vernal.
May 8, Sun: visit Utah Field House, revisit DNM if needed, drive to Fruita.
May 9, Mon: visit Rabbit Valley camarasaur in AM, visit Dinosaur Journey museum in PM. Go on to Moab.
May 10, Tues: drive back to Provo, visit BYU collections.
May 11, Weds: BYU collections.
May 12, Thurs: drive to SLC to visit UMNH collections, stay for Utah Friends of Paleontology meeting that evening.
May 13, Fri: BYU collections.
May 14, Sat: visit North American Museum of Ancient Life. MPT flies home. MJW starts drive home.
We’re planning lots of time at BYU because we’ll need it, the quantity and quality of sauropod material they have there is ridiculous. As for the rest, some of those details may change on the fly but that’s the basic plan. Maybe we’ll see you out there.
March 14, 2016
February 29, 2016
Functional Anatomy of the Vertebrates: An Evolutionary Perspective, by Liem et al. (2001), is by some distance my favorite comparative vertebrate anatomy text. When I was a n00b at Berkeley, Marvalee Wake assigned it to me as preparatory reading for my qualifying exams.
The best textbooks, like Knut Schmidt-Nielsen’s Animal Physiology (which deserves a post or even series of its own sometime), have a clarity of writing and illustration that makes the fundamentals of life seem not only comprehensible, but almost inevitable – without losing sight of the fact that nature is complex and we don’t know everything yet. FAotV has both qualities, in spades.
I’m writing about this now because Willy Bemis, second author on FAotV, has just made ALL of the book’s illustrations available for free on his website, in a series of 22 PowerPoint files that correspond to the 22 chapters of the book. All told they add up to about 155 Mb, which is trivial – even the $5 jump drives in the checkout lanes at department stores have five to ten times as much space.
Of course, to get the full benefit you should also pick up a copy of the book. I see used copies going for under $40 in a lot of places online. Mine will have pride of place on my bookshelf until I enter the taphonomic lottery. And I’ll be raiding these PPTs for images from now until then, too.
So do the right thing, and go download this stuff, and use it. Be sure to credit Liem et al. (2001) for the images, and thank Willy Bemis for making them all available. It’s a huge gift to the field. Here’s that link again.
But wait – that’s not all! Starting on June 28, Dr. Bemis will be one of six faculty members from Cornell and the University of Queensland teaching a 4-week massively open online course (MOOC) on sharks. Freakin’ sharks, man!
“What did you do this summer? Hang out and play Nintendo?”
“Yep. Oh, and I also took a course on freakin’ sharks from some awesome shark experts. You?”
As the “massively open” part implies, the course is free, although you have the option of spending $49 to get a certificate of completion (assuming you finish satisfactorily). Go here to register or get more info.
- Liem, K.F., Bemis, W.E., Walker, W.F., and Grande, L. 2001. Functional Anatomy of the Vertebrates. (3rd ed.). Thomson/Brooks Cole, Belmont, CA.
January 28, 2016
Stand by . . . grumpy old man routine compiling . . .
So, someone at Sony decided that an Angry Birds movie would be a good idea, about three years after the Angry Birds “having a moment” moment was over. There’s a trailer for it now, and at the end of the trailer, a bird pees for like 17 seconds (which is about 1/7 of my personal record, but whatever).
And now I see these Poindexters all over the internet pushing their glasses up their noses and typing, “But everyone knows that birds don’t pee! They make uric acid instead! That’s the white stuff in ‘bird poop’. Dur-hur-hur-hurrr!” I am reasonably sure these are the same people who harped on the “inaccuracy” of the peeing Postosuchus in Walking With Dinosaurs two decades ago. (Honestly, how I didn’t get this written and posted in our first year of blogging is quite beyond my capacity.)
Congratulations, IFLScientists, on knowing One Fact about nature. Tragically for you, nature knows countless facts, and among them are that birds and crocodilians can pee. And since extant dinosaurs can and do pee, extinct ones probably could as well.
Now, it is true that crocs (mostly) and birds (always?) release more of their nitrogenous waste as uric acid than as urea. But their bodies produce both compounds. So does yours. We mammals are just shifted waaaay more heavily toward urea than uric acid, and extant archosaurs – and many (but not all) other reptiles to boot – are shifted waaaay more heavily toward uric acid than urea. Alligators also make a crapload of ammonia, but that’s a story for another time.
BUT, crucially, birds and crocs almost always release some clear, watery, urea-containing fluid when they dump the whitish uric acid, as shown in this helpful diagram that I stole from International Cockatiel Resource:
If you’ve never seen this, you’re just not getting to the bird poop fast enough – the urine is drying up before you notice it. Pick up the pace!
Sometimes birds and crocs save up a large quantity of fluid, and then flush everything out of their cloacas and lower intestines in one shot, as shown in the photos dribbled through this post. Which has led to some erroneous reports that ostriches have urinary bladders. They don’t, they just back up lots of urine into their colons. Many birds recapture some water and minerals that way, and thereby concentrate their wastes and save water – basically using the colon as a sort of second-stage kidney (Skadhauge 1976).
[UPDATE the next day: To be perfectly clear, all that’s going on here is that the birds and crocs keep their cloacal sphincters closed. The kidneys keep on producing urine and uric acid, and with no way out (closed sphincter) and nowhere else to go (no bladder – although urinary bladders have evolved repeatedly in lizards), the pee backs up into the colon. So if you’re wondering if extinct dinosaurs needed some kind of special adaptation to be able to pee, the answer is no. Peeing is an inherent possibility, and in fact the default setting, for any reptile that can keep its cloaca shut.]
Aaaanyway, all those white urate solids tend to make bird pee more whitish than yellow, as shown in the photos. I have seen a photo of an ostrich making a good solid stream from cloaca to ground that was yellow, but that was years ago and frustratingly I haven’t been able to relocate it. Crocodilians seem to have no problem making a clear, yellowish pee-stream, as you can see in many hilarious YouTube videos of gators peeing on herpetologists and reporters, which I am putting at the bottom of this post so as not to break up the flow of the rant.
You can explore this “secret history” of archosaur pee by entering the appropriate search terms into Google Scholar, where you’ll find papers with titles like:
- “Technique for the collection of clear urine from the Nile crocodile (Crocodylus niloticus)” (Myburgh et al. 2012)
- “Movement of urine in the lower colon and cloaca of ostriches” (Duke et al. 1995)
- “Plasma homeostasis and cloacal urine composition in Crocodylus porosus caught along a salinity gradient” (Grigg 1981)
- “Cloacal absorption of urine in birds” (Skadhauge 1976)
- “The cloacal storage of urine in the rooster” (Skadhauge 1968)
I’ve helpfully highlighted the operative term, to reinforce the main point of the post. Many of these papers are freely available – get the links from the References section below. A few are paywalled – really, Elsevier? $31.50 for a half-century-old paper on chicken pee? – but I’m saving them up, and I’ll be happy to lend a hand to other scholars who want to follow this stream of inquiry. If you’re really into the physiology of birds pooling pee in their poopers, the work of Erik Skadhauge will be a gold mine.
Now, to be fair, I seriously doubt that any bird has ever peed for 17 seconds. But the misinformation abroad on the net seems to be more about whether birds and other archosaurs can pee at all, rather than whether a normal amount of bird pee was exaggerated for comedic effect in the Angry Birds trailer.
In conclusion, birds and crocs can pee. Go tell the world.
And now, those gator peeing videos I promised:
Jan. 30, 2016: I just became aware that I had missed one of the best previous discussions of this topic, with one of the best videos, and the most relevant citations! The post is this one, by Brian Switek, which went up almost two years ago, the video is this excellent shot of an ostrich urinating and then defecating immediately after:
…and the citations are McCarville and Bishop (2002) – an SVP poster about a possible sauropod pee-scour, which is knew about but didn’t mention yet because I was saving it for a post of its own – and Fernandes et al. (2004) on some very convincing trace fossils of dinosaurs peeing on sand, from the Lower Cretaceous of Brazil. In addition to being cogent and well-illustrated, the Fernandes et al. paper has the lovely attribute of being freely available, here.
So, sorry, Brian, that I’d missed your post!
And for everyone else, stand by for another dinosaur pee post soon. And here’s one more video of an ostrich urinating (not pooping as the video title implies). The main event starts about 45 seconds in.
- Duke, G.E., Degen, A.A. and Reynhout, J.K., 1995. Movement of urine in the lower colon and cloaca of ostriches. Condor, 97, pp.165-173.
- Fernandes, M., Fernandes, L., Souto, P. 2004. Occurrence of urolites related to dinosaurs in the Lower Cretaceous of the Botucatu Formation, Paraná basin, São Paulo State, Brazil. Revista Brasileira de Paleontologia. 7(2), pp.263-268.
- Grigg, G.C., 1981. Plasma homeostasis and cloacal urine composition in Crocodylus porosus caught along a salinity gradient. Journal of Comparative Physiology, 144(2), pp.261-270.
- McCarville, K., Bishop, G. 2002. To pee or not to pee: evidence for liquid urination in sauropod dinosaurs. In: 62nd Annual Meeting of the Society of Vertebrate Paleontology, Abstract Book. Journal of Vertebrate Paleontology 22(3, Supplement), p. 85A.
- Myburgh, J.G., Huchzermeyer, F.W., Soley, J.T., Booyse, D.G., Groenewald, H.B., Bekker, C., Iguchi, T. and Guillette, L.J., 2012. Technique for the collection of clear urine from the Nile crocodile (Crocodylus niloticus). Journal of the South African Veterinary Association, 83(1), pp.1-7.
- Skadhauge, E., 1968. The cloacal storage of urine in the rooster. Comparative Biochemistry and Physiology, 24(1), pp.7-18.
- Skadhauge, E., 1976. Cloacal absorption of urine in birds. Comparative Biochemistry and Physiology Part A: Physiology, 55(2), pp.93-98.
January 12, 2016
I was a bit disappointed to hear David Attenborough on BBC Radio 4 this morning, while trailing a forthcoming documentary, telling the interviewing that you can determine the mass of an extinct animal by measuring the circumference of its femur.
We all know what he was alluding to, of course: the idea first published by Anderson et al. (1985) that if you measure the life masses of lots of animals, then measuring their long-bone circumferences when they’ve died, you can plot the two measurements against each other, find a best-fit line, and extrapolate it to estimate the masses of dinosaurs based on their limb-bone measurements.
This approach has been extensively refined since 1985, most recently by Benson et al. (2014). but the principle is the same.
But the thing is, as Anderson et al. and other authors have made clear, the error-bars on this method are substantial. It’s not super-clear in the image above (Fig 1. from the Anderson et al. paper) because log-10 scales are used, but the 95% confidence interval is about 42 pixels tall, compared with 220 pixels for an order of magnitude (i.e. an increment of 1.0 on the log-10 scale). That means the interval is 42/220 = 0.2 of an order of magnitude. That’s a factor 10 ^ 0.2 = 1.58. In other words you could have two animals with equally robust femora, one of them nearly 60% heavier than the other, and they would both fall within the 95% confidence interval.
I’m surprised that someone as experienced and knowledgeable as Attenborough would perpetuate the idea that you can measure mass with any precision in this way (even more so when using only a femur, rather than the femur+humerus combo of Anderson et al.)
More: when the presenter told him that not all scientists buy the idea that the new titanosaur is the biggest known, he said that came as a surprise. Again, it’s disappointing that the documentary researchers didn’t make Attenborough aware of, for example, Paul Barrett’s cautionary comments or Matt Wedel’s carefully argued dissent. Ten minutes of simple research would have found this post — for example, it’s Google’s fourth hit for “how big is the new argentinian titanosaur”. I can only hope that the actual documentary, which screens on Sunday 24 January, doesn’t present the new titanosaur’s mass as a known and agreed number.
(To be clear, I am not blaming Attenborough for any of this. He is a presenter, not a palaeontologist, and should have been properly prepped by the researchers for the programme he’s fronting. He is also what can only be described as 89, so should be forgiven if he’s not quite as quick on his feel when confronted with an interviewer as he used to be.)
Update 1 (the next day)
Thanks to Victoria Arbour for pointing out an important reference that I missed: it was Campione and Evans (2012) who expanding Anderson et al.’s dataset and came up with the revised equation which Benson et al. used.
Update 2 (same day as #1)
It seems most commenters are inclined to go with Attenborough on this. That’s a surprise to me — I wonder whether he’s getting a free pass because of who he is. All I can say is that as I listened to the segment it struck me as really misleading. You can listen to it for yourself here if you’re in the UK; otherwise you’ll have to make do with this transcript:
“It’s surprising how much information you can get from just one bone. I mean for example that thigh bone, eight feet or so long, if you measure the circumference of that, you will be able to say how much weight that could have carried, because you know what the strength of bone is. So the estimate of weight is really pretty accurate and the thought is that this is something around over seventy tonnes in weight.”
(Note also that the Anderson et al./Campione and Evans method has absolutely nothing to do with the strength of bone.)
Also if interest was this segment that followed immediately:
How long it was depends on whether you think it held its neck out horizontaly or vertically. If it held it out horizontally, well then it would be about half as big again as the Diplodocus, which is the dinosaur that’s in the hall of the Natural History Museum. It would be absolutely huge.
Interviewer: And how tall, if we do all the dimensions?
Ah well that is again the question of how it holds its neck, and it could have certainly reached up about to the size of a four or five storey building.
Needless to say, the matter of neck posture is very relevant to our interests. I don’t want to read too much into a couple of throwaway comments, but the implication does seem to be that this is an issue that the documentary might spend some time on. We’ll see what happens.
- Anderson, J. F., A. Hall-Martin and D. A. Russell. 1985. Long-bone circumference and weight in mammals, birds and dinosaurs. Journal of Zoology 207:53-61.
- Benson, Roger B. J., Nicolás E. Campione, Matthew T. Carrano, Philip D. Mannion, Corwin Sullivan, Paul Upchurch, and David C. Evans. 2014. Rates of dinosaur body mass evolution indicate 170 million years of sustained ecological innovation on the avian stem lineage. PLOS Biology 12(5):e1001853. doi:10.1371/journal.pbio.1001853
- Campione, Nicolás E., and David C. Evans. 2012. A universal scaling relationship between body mass and proximal limb bone dimensions in quadrupedal terrestrial tetrapods. BMC Biology 10:60 (22 pages). doi:10.1186/1741-7007-10-60