April 13, 2016
the whole idea is idiotic.
Plagiarism is “presenting someone else’s work or ideas as your own“. So self-plagiarism is presenting your own work or ideas as your own. Which is nonsense.
Can we please abandon this unhelpful and misleading phrase?
Note added subsequently, in response to Snarky Mᶜ̵Snarkface’s tweet: my real point is that discussion of the practice is actively confused by the use of this misleading term for it.
March 7, 2016
This one is for journalists and other popularizers of science. I see a lot of people writing that “scientists believe” this or that, when talking about hadrons or hadrosaurs or other phenomena grounded in evidence.
Pet peeve: believing is what people do in the absence of evidence, or despite evidence. Scientists often have to infer, estimate, and even speculate, but all of those activities are grounded in evidence and reason, not belief.1
In addition to doing science, scientists may also believe in the proper, spiritual sense, in which case you are free to explain what certain individual scientists believe. But that’s not how the word “believe” is used most of the time when it comes up in science stories.
So stop it. It’s lazy, and it’s damaging, because it gives (some) people the impression that scientists are clueless buffoons who make stuff up out of the whole cloth in a cynical bid to keep their jobs. Given that we have an entire political party pushing that view and trying to defund science and education at every turn, we don’t need that caricature promoted any further.
Even if you don’t accept that argument, it’s still bad writing. Good writing explains why people think as they do. So do that instead. In addition to the aforementioned “infer”, “estimate”, and “speculate”, you can use “surmise”, “reason”, “predict”, or – if you must – “think”. “Scientists have found” would be better still.
Best of all would be if the “scientists X” clause was preceded by, “Based on this evidence” (which you’ve just explained in the previous sentences), so readers can connect cause (evidence) and effect (scientists think) – which is what science is mostly about in the first place.
1. I realize that I am grossly oversimplifying – evidence, reason, and belief can interact in complicated ways in both spiritual and scientific spheres. But my purpose here is fixing poor word choice, not exploring that interaction.
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 25, 2016
Like Stephen Curry, we at SV-POW! are sick of impact factors. That’s not news. Everyone now knows what a total disaster they are: how they are signficantly correlated with retraction rate but not with citation count; how they are higher for journals whose studies are less statistically powerful; how they incentivise bad behaviour including p-hacking and over-hyping. (Anyone who didn’t know all that is invited to read Brembs et al.’s 2013 paper Deep impact: unintended consequences of journal rank, and weep.)
Its 2016. Everyone who’s been paying attention knows that impact factor is a terrible, terrible metric for the quality of a journal, a worse one for the quality of a paper, and not even in the park as a metric for the quality of a researcher.
Unfortunately, “everyone who’s been paying attention” doesn’t seem to include such figures as search committees picking people for jobs, department heads overseeing promotion, tenure committees deciding on researchers’ job security, and I guess granting bodies. In the comments on this blog, we’ve been told time and time and time again — by people who we like and respect — that, however much we wish it weren’t so, scientists do need to publish in high-IF journals for their careers.
What to do?
It’s a complex problem, not well suited to discussion on Twitter. Here’s what I wrote about it recently:
The most striking aspect of the recent series of Royal Society meetings on the Future of Scholarly Scientific Communication was that almost every discussion returned to the same core issue: how researchers are evaluated for the purposes of recruitment, promotion, tenure and grants. Every problem that was discussed – the disproportionate influence of brand-name journals, failure to move to more efficient models of peer-review, sensationalism of reporting, lack of replicability, under-population of data repositories, prevalence of fraud – was traced back to the issue of how we assess works and their authors.
It is no exaggeration to say that improving assessment is literally the most important challenge facing academia.
This is from the introduction to a new paper which came out today: Taylor (2016), Better ways to evaluate research and researchers. In eight short pages — six, really, if you ignore the appendix — I try to get to grips with the historical background that got us to where we are, I discuss some of the many dimensions we should be using to evaluate research and researchers, and I propose a family of what I call Less Wrong Metrics — LWMs — that administrators could use if they really absolutely have to put a single number of things.
(I was solicited to write this by SPARC Europe, I think in large part because of things I have written around this subject here on SV-POW! My thanks to them: this paper becomes part of their Briefing Papers series.)
Next time I’ll talk about the LWM and how to calculate it. Those of you who are impatient might want to read the actual paper first!
November 10, 2015
One thing that always bemuses me is the near-absolute serendipity of the academic job market. To get into research careers takes at least a decade of very deliberate, directed work, and then at the end you basically toss your diploma into a whirlwind and see where it lands. After all of that careful planning, almost all of us end up where we do based on the random (to us) set of jobs available in the narrow window in which we’re searching.
Did you dream of being curator at Museum X, or professor at University Y? Well, tough, those jobs went to Dr. Graduated-Two-Years-Sooner and Lucky Nature Paper, PhD, and they’re not retiring for three or four decades. Or maybe your dream job comes open right after you, your spouse, and your kids get settled in at your new acceptable-but-not-quite-dream job. Uproot or stay the course? Or what would be your dream job finally comes open but they’re looking for new junior faculty and you just got tenure at Tolerable State U.
This drastic mismatch between carefulness of preparation and randomness of outcome was present even pre-2008. The craptastic academic job market since then has only whetted the central irony’s keen edge. Getting grants and getting jobs is now basically a lottery. I’m not saying that good jobs don’t go to good people – they almost always do – but there are a lot of good people in jobs they never imagined having. And, sadly, plenty of good people who are now working outside of the field they prepared for because of the vicissitudes of the job market. A handful of years sooner or later and they might be sitting pretty.
This is on my mind because I recently had lunch with a physician friend from work and he was talking about applying for jobs as a doctor. “The first thing everyone tells you,” he said, “is decide what part of the country you want to live in first, then apply for the jobs that are there.” Doctors can do that because there are more than 800,000 of them active in the US. Paleontologists are mighty rarified by comparison – it’s hard to say how many of us there are, but probably not more than 2000 active in vert paleo. So the usual advice for budding biologists and paleontologists is exactly opposite that for physicians: “Forget about living where you want. Go wherever the job is and make the best of it.”
Oddly enough, I don’t remember this ever coming up in grad school. It’s something Vicki and I figured out at the end, as we started the process of applying for positions. There are alternate universes where we are at Marshall (they offered us both jobs, but not as attractive as UC Merced at the time), or at Northern Arizona (which is bittersweet because we have totally fallen in love with Flagstaff just in the past three years), or other places. If I were choosing a job site based on everything other than the institution, I’d spring for somewhere in Arizona or the intermountain west in a heartbeat.
But with all that said, we are happy here. It’s funny, when we got the job offers down here I thought, “LA? Crap, there goes the outdoor part of my life.” But Claremont has lots of parks, it’s tucked up against the San Gabriels and I can get into the mountains in 30 minutes, or out to the desert in 90. I’m spending more time outdoors than I have since I was a kid growing up in rural Oklahoma.
So I’m not complaining about my personal situation. Vicki and I both landed on our feet – and the fact that we both managed to stick the landing at the same institution is little short of miraculous. But we still had to step into the job market hurricane to get here.
If you’re a grad student and you’re reading this, I didn’t write it to freak you out. Just to let you know that it’s coming, and there are things you can do to improve your chances. Be aggressively curious. Write. Publish. Give good talks (and give lots of talks so you can become good at it). Broaden your skill set – if you’re going into paleo, knowing how to teach human anatomy probably doubles or triples the number of available jobs at any one time, even if many of them are not the jobs you’ve been dreaming of.
Then, at the end, pour yourself one stiff drink and cast your fortune to the winds.
Copyright: promoting the Progress of Science and useful Arts by preventing access to 105-year-old quarry maps
October 11, 2015
In my recent preprint on the incompleteness and distortion of sauropod neck specimens, I discuss three well-known sauropod specimens in detail, and show that they are not as well known as we think they are. One of them is the Giraffatitan brancai lectotype MB.R.2181 (more widely known by its older designation HMN SII), the specimen that provides the bulk of the mighty mounted skeleton in Berlin.
That photo is from this post, which is why it’s disfigured by red arrows pointing at its epipophyses. But the vertebra in question — the eighth cervical of MB.R.2181 — is a very old friend: in fact, it was the subject of the first ever SV-POW! post, back in 2007.
In the reprint, to help make the point that this specimen was found extremely disarticulated, I reproduce Heinrich (1999:figure 16), which is Wolf-Dieter Heinrich’s redrawing of Janensch’s original sketch map of Quarry S, made in 1909 or 1910. Here it is again:
For the preprint, as for this blog-post (and indeed the previous one), I just went right ahead and included it. But the formal version of the paper (assuming it passes peer-review) will by very explicitly under a CC By licence, so the right thing to do is get formal permission to include it under those terms. So I’ve been trying to get that permission.
What a stupid, stupid waste of time.
Heinrich’s paper appeared in the somewhat cumbersomely titled Mitteilungen aus dem Museum fur Naturkunde in Berlin, Geowissenschaftliche Reihe, published as a subscription journal by Wiley. Happily, that journal is now open access, published by Pensoft as The Fossil Record. So I wrote to the Fossil Record editors to request permission. They wrote back, saying:
We are not the right persons for your question. The Wiley Company holds the copyright and should therefore be asked. Unfortunately, I do not know who is the correct person.
Thank you for your enquiry.
We are currently experiencing a large volume of email traffic and will deal with your request within the next 15 working days.
We are pleased to advise that permission for the majority of our journal content, and for an increasing number of book publications, may be cleared more quickly by using the RightsLink service via Wiley’s websites http://onlinelibrary.wiley.com and www.wiley.com.
Within the next fifteen working days? That is, in the next three weeks? How can it possibly take that long? Are they engraving their response on a corundum block?
So, OK, let’s follow the automated suggestion and try RightsLink. I went to the Wiley Online Library, and searched for journals whose names contain “naturkunde”. Only one comes up, and it’s not the right one. So Wiley doesn’t admit the existence of the journal.
Well, there’s lots to enjoy here, isn’t there? First, and most important, it doesn’t actually work: “Permission to reproduce this content cannot be granted via the RightsLink service.” Then there’s that cute little registered-trademark symbol “®” on the name RightsLink, because it’s important to remind me not to accidentally set up my own rights-management service with the same name. In the same vein, there’s the “Copyright © 2015 Copyright Clearance Center, Inc. All Rights Reserved” notice at the bottom — copyright not on the content that I want to reuse, but on the RightsLink popup itself. (Which I guess means I am in violation for including the screenshot above.) Oh, and there’s the misrendering of “Museum für Naturkunde” as “Museum fÃ¼r Naturkunde”.
All of this gets me precisely nowhere. As far as I can tell, my only recourse now is to wait three weeks for Wiley to get in touch with me, and hope that they turn out to be in favour of science.
It’s Sunday afternoon. I could be watching Ireland play France in the Rugby World Cup. I could be out at Staverton, seeing (and hearing) the world’s last flying Avro Vulcan overfly Gloucester Airport for the last time. I could be watching Return of the Jedi with the boys, in preparation for the forthcoming Episode VII. Instead, here I am, wrestling with copyright.
How absolutely pointless. What a terrible waste of my life.
Is this what we want researchers to be spending their time on?
Update (13 October 2015): a happy outcome (this time)
I was delighted, on logging in this morning, to find I had email from RIGHTS-and-LICENCES@wiley-vch.de with the subject “Permission to reproduce Heinrich (1999:fig. 16) under CC By licence” — a full thirteen working days earlier than expected. They were apologetic and helpful. Here is key part of what they said:
We are of course happy to handle your request directly from our office – please find the requested permission here:We hereby grant permission for the requested use expected that due credit is given to the original source.If material appears within our work with credit to another source, authorisation from that source must be obtained.Credit must include the following components:– Journals: Author(s) Name(s): Title of the Article. Name of the Journal. Publication year. Volume. Page(s). Copyright Wiley-VCH Verlag GmbH & Co. KGaA. Reproduced with permission.
So this is excellent. I would of course have included all those elements in the attribution anyway, with the exception that it might not have occurred to me to state who the copyright holder is. But there is no reason to object to that.
So, two cheers for Wiley on this occasion. I had to waste some time, but at least none of it was due to deliberate obstructiveness, and most importantly they are happy for their figure to be reproduced under CC By.
- Heinrich, Wolf-Dieter. 1999. The taphonomy of dinosaurs from the Upper Jurassic of Tendaguru, Tanzania (East Africa), based on field sketches of the German Tendaguru expedition (1909-1913). Mitteilungen aus dem Museum fur Naturkunde in Berlin, Geowissenschaftliche Reihe 2:25-61.
September 4, 2015
THIS POST IS RETRACTED. The reasons are explained in the next post. I wish I had never posted this, but you can’t undo what is done, especially on the Internet, so I am not deleting it but marking it as retracted. I suggest you don’t bother reading on, but it’s here if you want to.
There were some surprises in the the contents of the SVPCA programme this year. Sauropods were woefully under-represented with only two talks (mine on apatosaur neck combat and Daniel Vidal’s on the range of movement of the tail of Spinophorosaurus). In fact non-avian dinosaurs as a whole got short shrift, with two theropod talks, three ornithischian talks and one on dinosaur diversity. This is partly, of course, because so many dinosaur workers among the SVPCA mainstays were absent for one reason or another: Matt Wedel, Paul Upchurch, Paul Barrett, Richard Butler, Roger Benson, Steve Brusatte, David Norman, the list goes on.
But that’s OK. I’ve often found, to my surprise, that the dinosaur talks aren’t always my favourites anyway. (Oddly enough, fish talks can quite often catch my imagination; and pterosaurs are always good for a laugh.)
A more surprising development was the complete absence of any finite element analysis this year — a technique that was crazy trendy a couple of years ago, but seems to have to the end of its fashion cycle.
Instead, I felt that the talks were strongly dominated by one technique: principal component analysis (PCA). As a technique, I have mixed feelings about it: I don’t go as far as John Conway, who as far as I can tell thinks it’s almost literally meaningless. But I have strong reservations about the plug-and-play way it seems to get used for pretty much everything at the moment, and how very tenuous some of the inferences are that people derive from their morphospace plots. It’s difficult to be specific without criticising individuals, which I’d like to avoid doing. But I do think think that when we draw sweeping and heterodox conclusions about an animal’s lifestyle from a PCA of a single facet of a single bone, the validity of that conclusion is, to put it politely, open to question.
In fact an awful lot of the projects presented in this year’s talks seemed to follow the same template. In an idle (and, yes, unnecessarily snide) moment, I sketched an Automatic Masters Project Generator for lazy supervisors. You just throw four dice, then pick your technique name, body-part, period and taxon from these tables:
Table 1: roll 1d6 for a technique
- 2d landmark analysis
- principal component analysis
- geometric morphometrics
- morphospace analysis
- finite element analysis
- ecomorphological diversity analysis
Table 2: roll 1d6 for a body part
Table 3: roll 1d6 for a period
- Late Cretaceous
Table 4: roll 1d6 for a taxon
- lamnid sharks
- golden moles
Try it yourself! Morphospace analysis of the ulna in Miocene mustelids! Ready, steady, go! Your Masters degree will be ready as soon as you can talk reasonably coherently about this combination for fifteen minutes and leap to an obvious but weakly supported conclusion based on vague shapes drawn on a PC1-vs.-PC2 plot that captures only 32.6% of the variation!
(To be clear: I am not saying that PCA is intrinsically worthless. As I found myself repeatedly arguing in pubs with John and others, it’s evidently a very powerful tool for discovering correlations. For me, it goes wrong when very weak results pop out, but are given a veneer of respectability and objectivity because a computer was involved in the process.)
As the week went on, I found myself worrying increasingly about these projects. It’s not just that they are (with a few creditable exceptions) samey to listen to and uninteresting in their results. I worry more that these projects kill the interest of the people who take them on. I may be reading my own biases back into my observations here, but it seemed to me that I detected a distinct lack of enthusiasm in several of the speakers, and my hunch is that for a lot of them this will be their first and last SVPCA. They presumably went into palaeo because they loved some specific extinct taxon; instead, they found themselves spending a year staring at a hundred almost identical photographs of moodily lit tubes of toothpaste. And really, if anything is going to kill the passion of a pterosaur lover stone dead, it’s taking measurements of the distal articular facets of the ulnae of a 154 Miocene mustelids.
So I found myself longing for more talks about taxa, and about ideas, rather than techniques. Most obviously, there was very little pure descriptive palaeontology to be seen this year. But also, our own talk aside, very little of what I would think of as exploratory work — thinking about structures, chewing through their implications, considering alternatives. In short: the fun stuff. I would hate palaeontology to be reduced to a process of harvesting data from specimens (looking only at the aspects needed to fill in the matrix), pouring that data into a sausage machine, and turning the handle until something statistically significant comes out.
We have to be able to offer grad-students more than that. We are, and I say this with all due objectivity, in the most exciting science in the world. People go into palaeo because they love it. I wouldn’t like to think they go straight back out of it, as soon as they have their higher degree, hating it. We need to get students looking at and thinking about and discussing actual specimens — proposing ideas, arguing about them, running into reasons why they might be wrong, figuring out why they might be right after all, putting together an argument. Not sitting in front of computers full time running T-tests.
Of course there is a role, and an important one, for numerical methods. But they have to be the means, not the end. We have to have a more interesting goal than finding a statistically significant correlation. Otherwise we’re going to lose people.