April 20, 2013
It’s well worth reading this story about Thomas Herndon, a graduate student who as part of his training set out to replicate a well-known study in his field.
The work he chose, Growth in a Time of Debt by Reinhart and Rogoff, claims to show that “median growth rates for countries with public debt over roughly 90 percent of GDP are about one percent lower than otherwise; average (mean) growth rates are several percent lower.” It has been influential in guiding the economic policy of several countries, reaffirming an austerity-based approach.
So here is Lesson zero, for policy makers: correllation is not causation.
To skip ahead to the punchline, it turned out that Reinhart and Rogoff made a trivial but important mechanical mistake in their working: they meant to average values from 19 rows of their spreadsheet, but got the formula wrong and missed out the last five. Those five included three countries which had experienced high growth while deep in debt, and which if included would have undermined the conclusions.
Therefore, Lesson one, for researchers: check your calculations. (Note to myself and Matt: when we revise the recently submitted Taylor and Wedel paper, we should be careful to check the SUM() and AVG() ranges in our own spreadsheet!)
Herndon was able to discover this mistake only because he repeatedly hassled the authors of the original study for the underlying data. He was ignored several times, but eventually one of the authors did send the spreadsheet. Which is just as well. But of course he should never have had to go chasing the authors for the spreadsheet because it should have been published alongside the paper.
Lesson two, for researchers: submit your data alongside the paper that uses it. (Note to myself and Matt: when we submit the revisions of that paper, submit the spreadsheets as supplementary files.)
Meanwhile, governments around the world were allowing policy to be influenced by the original paper without checking it — policies that affect the disposition of billions of pounds. Yet the paper only got its post-publication review because of an post-grad student’s exercise. That’s insane. It should be standard practice to have someone spend a day or two analysing a paper in detail before letting it have such a profound effect.
And so Lesson three, for policy makers: replicate studies before trusting them.
Ironically, this may be a case where the peer-review system inadvertently did actual harm. It seems that policy makers may have shared the widespread superstition that peer-reviewed publications are “authoritative”, or “quality stamped”, or “trustworthy”. That would certainly explain their allowing it to affect multi-billion-pound policies without further validation. [UPDATE: the paper wasn't peer-reviewed after all! See the comment below.]
Of course, anyone who’s actually been through peer-review a few times knows how hit-and-miss the process is. Only someone who’s never experienced it directly could retain blind faith in it. (In this respect, it’s a lot like cladistics.)
If a paper has successfully made it through peer-review, we should afford it a bit more respect than one that hasn’t. But that should never translate to blind trust.
In fact, let’s promote that to Lesson four: don’t blindly trust studies just because they’re peer-reviewed.
June 23, 2012
Here’s a cool skeleton of the South American pleurodire Podocnemis in the Yale Peabody Museum.
What’s that you’re hiding in your neck, Podocnemis?
Laminae! Here’s a closeup:
The laminae run from the transverse processes to the prezygapophyses and the centrum, which I reckon makes them analogues of the PRDLs and ACDLs of sauropods.
As long as I’m posting on Peabody turtles, here’s Archelon. It’s not bad, if you’re into that sort of thing. Which Mike clearly ain’t, but for a good reason, which will be revealed soon.
In the recent post on serial variation in sauropod cervicals, I wrote:
Even in ‘adult’ sauropods like the big mounted Apatosaurus and Diplodocus skeletons, the anterior cervicals are less complex than the posterior ones. Compared to posterior cervicals, anterior cervicals tend to have simpler pneumatic fossae and foramina, fewer laminae, and unsplit rather than bifid spines. In all of these things the anterior cervicals are similar to those of juveniles of the same taxa, and to those of adults of more basal taxa. This is also true in prosauropods–in Plateosaurus, the full complement of vertebral laminae is not present until about halfway down the neck.
I was working from memory there and actually understated things a bit. Plateosaurus presacral vertebrae don’t have well-developed spinal laminae, but they do eventually get the four major diapophyseal laminae–the anterior centrodiapophyseal lamina (ACDL), posterior centrodiapophyseal lamina (PCDL), prezygodiapophyseal lamina (PRDL), and postzygodiapophyseal lamina (PODL–please see the lamina tutorial if you need a refresher on these and the other 15 commonly identified laminae). But they aren’t all present halfway down the neck–the ACDL doesn’t really show up until the cervicodorsal transition. The other three kick in sequentially down the neck, as shown in the above image. I think that’s pretty cool, that you get different character states expressed at different points along the neck, in one individual organism, at one time. And possibly also at different times–in sauropods, the anterior cervicals tend to look more ‘juvenile’ or ‘primitive’, even in adult animals, so all of the cervicals go through a juvenile stage, but not all of them grow out of it. I don’t know if there’s a word for that–some kind of serial heterochronotopomorphy or the like–but hopefully someone will enlighten me.
I took the original photo in the collections at the Staatliches Museum für Naturkunde Stuttgart in the spring of 2004. Markus Moser and Rainer Schoch were wonderful hosts during my visit. Mike did all the work of turning the raw photo into a figure, so thanks to him for getting this off my hard drive and out into the world.
March 19, 2012
When my youngest brother was about eight years old, he quipped, “French fries: they may be high in fat, they may be high in cholesterol, but doggone it, they’re salty.”
I often think about that in reference to barrier-based academic publishing. It doesn’t serve authors, it doesn’t serve readers, it doesn’t serve academic libraries, but doggone it, at least it costs vastly more than it should.
So why do scientists, who (1) are at least reasonably intelligent (by and large–insert quip about your least favorite scientist here), (2) have careers that depend on being read as widely as possible, and (3) never have enough money to do all the work they need, keep publishing in this almost comically flawed* system?
Mike takes a stab at an explanation in a new article in The Scientist: Academic publishing is broken. Don’t be fooled by the “tell us something we don’t know” title (which, remember, has to reach people who don’t know about the OA wars); the article contains some new facts and analysis and, in my opinion, precisely nails the problem. Go check it out.
Image borrowed from here (with instructions!).
* It would be comical, if it wasn’t actually contributing to human misery.
Update (7th April 2012)
The Scientist article now exists in a Spanish translation, kindly contributed by Gustavo Rodriguez.
March 2, 2012
Today was one of the most interesting days of my life.
Vanessa and I needed ostrich parts for dissection, so I had gotten in touch with Doug Osborne of OK Corral Ostrich Farms in Oro Grande. That was on the recommendation of Andy Farke, who got a bag of ostrich heads from Doug a couple of years ago (those heads are in the other Dr. Wedel’s research freezer, waiting for an ostrich head boiling party). I made plans with Doug to meet him at the farm at 9:00 this morning (Thursday). He warned me that it would have to be a quick visit because he was having a big load of hay delivered at 9:30 and he’d have to go supervise the unloading.
Oro Grande is 60 miles from Claremont and Pomona, in the high desert on the north side of the San Gabriels. I left here at 8:00 and rolled up to the marked parking area right at 9:00.
And immediately I could tell that things had not gone as planned. There were two hay trucks in the big ostrich paddock (post-Jurassic Park, any large outdoor enclosure for theropods must be referred to as a paddock), so the hay had clearly come early.
More worryingly, the gate at the corner of the paddock was open and the ostriches were starting to get out.
I should stop here and mention a couple things. First, when I heard about OK Corral Ostrich Farms I assumed it was like almost every other ostrich farm in the United States: a side-business on a small farm involving a few dozen birds at most. It is emphatically not. Doug has 2500 ostriches, 2000 at Oro Grande and another 500 at a ranch in Elsinore; his operation is the largest ostrich ranch outside of Africa. The ostriches at Oro Grande are not all in the main paddock, but several hundred of them are, and these were starting to trickle out of the open gate when I rolled up.
Second, the open gate wasn’t the fault of the guys in the hay trucks. Doug later determined that the padlock had clicked but failed to engage when one of the ranch hands shut the gate behind the trucks. Stuff happens. He told me it was his first break-out in seven years.
Anyway, when I hopped out of the car there was one ostrich out, but more were moving that way. Fortunately Doug and I had been corresponding by phone so I had his number in my cell. I called him and told him what was up, and he told me to get back in my car (for reasons that will become apparent later on). A few minutes later he rolled up in his pickup, and by that time about a dozen birds were out, including a couple of males.
I jumped out to say hi. I hadn’t been real wild about waiting in the car in the first place. It was clear that getting the ostriches back in the paddock was going to be at least a two-person job, because one person would have to keep each batch of returning birds from running off while the other opened and shut the gate. I told Doug that I had grown up in the country and had to herd cattle before so he’d know I wasn’t as useless as I probably looked. (I hadn’t checked the weather, the temperature was in the 40s F, with a west wind gusting around 40 mph, and I was wearing my ODP t-shirt and no jacket.) He sized me up for about two seconds and said, “Okay, I’m going to start giving you orders.”
And for the next 30 or 40 minutes, that’s what he did. Singly and in groups of two and three, we got all the stray ostriches rounded up and back in the paddock. I’m sure for Doug it was a pain in the arse, having a dozen large, fast, expensive birds on the wrong side of the fence.
For me, it was 100% awesome. I love ostriches. I’ve dissected them, CTed them, measured their bones and sawed them open, looked at their intervertebral joints, eaten their meat, and watched them for ages in zoos, but this was my first experience on the ground with no fence between me and them.
Ostriches are freakin’ huge. I had only dissected babies, or adults piecemeal. It’s one thing to read about how big they are or watch one in a zoo, and quite another to have an 8-foot-tall, 350-lb male ostrich standing 4 feet away, clearly thinking about how freedom is on the other side of this slow, puny, annoying mammal. Doug coached me through flapping my arms and shouting “Ho! Ho! Ho!” and sometimes just getting up in their space and slapping them on the ass. He was keeping a weather eye on them for any aggressive behavior, and I was vacillating between bio-geek squee and healthy fear.
After the ostriches were all back in the paddock, the hay trucks were safely out, and the ranch hands had gotten a stern word about double- and triple-checking the padlock, Doug invited me in for a cup of coffee and we had a nice long chat.
Doug’s an interesting guy. He used to be a Wall Street millionaire, in the executive stratosphere of Merrill Lynch. One year he bought his mother four ostriches as a present. Those ostriches started breeding, his mom started selling them, and Doug realized that there was a living to be made farming ostriches and decided that was more appealing than working on Wall Street. He’s been doing this for 20 years.
As a farmer he has a refreshingly unromantic view of his birds. He loves ostriches, obviously, otherwise he wouldn’t have made a career out of them, but his love for them is grounded in practical matters like cutting the strings off the hay bales so the birds can’t accidentally strangle themselves. To him the birds are interesting but not exotic, and for me it was fascinating to talk with someone who raises them from the egg and works with them every day.
Speaking of eggs, after coffee it was time to go gather them from the paddock. It’s still too early in the season for the females to be laying many, but there were a few. By this time Doug was treating me like one of the team. He gave me an OK Corral trucker hat as a thank-you for my help with the ostrich-wrangling, and I got to ride along on the egg-collecting expedition. There was one small and probably communal nest of half a dozen eggs, and as we drove around the paddock we spotted a couple of isolated “rogue” eggs. The ranch hands gathered most of the eggs, but after they’d gone off to secure the hay I got to get out and pick up the last rogue egg. It was surprisingly heavy, like a shot put, and Doug gave me the same directions I give to students carrying human skulls: “Hold it securely in two hands, all the way to the box.”
I got to see some interesting behavior. The big males would come right up to the pickup, make dominance displays, and snap at us. The truck was dented from having been kicked by ostriches who didn’t want to share their considerable space (the paddock is probably between an eighth and a quarter of a mile on its long axis). Last year Doug was moving birds around and a big male kicked him hard enough to puncture his abdomen and lacerate his liver; he spent two weeks in the hospital. That’s why he wanted me to stay in the car when I first rolled up, and why he didn’t ask for help herding birds until he knew that I had some prior experience moving big animals around.
Oh, way back at OU I had read about ostriches having sizable penises, and I can now attest to that as an eyewitness. One of the males flopped his out in front of the truck and it was about the same dimensions as my arm below the elbow. Elsewhere in the paddock I saw a male and a female working together to make zygotes*.
*That’s biologist-talk for “gettin’ their gangly theropod freak on”.
Back at the ranch house the eggs went into the incubator, Doug went into the walk-in freezer to get the ostrich necks I was there to buy, and I got a few minutes to just wander around and gawk. In addition to the ostriches Doug has about 50 emus in a separate pen, and roaming loose in the big fenced and gated area around the ranch buildings are turkeys, chickens, peacocks, and geese. Three tom turkeys–Los Hermanos Mariachis, Doug calls them–followed me around, puffing up and showing off. I could see some signs of interspecific socialization: the geese hung out with the turkeys by the ranch house, while the peacocks and chickens claimed the area around the little red building where the empty, blown-out eggs are stored. Doug talked about how the “Goose-waffe” would fly down the driveway in formation and use the open truck-shed as a hangar.
My last encounter of the day was also my favorite. Abigail is a tame female ostrich who wanders around the yard with the smaller birds. She broke her ankle when she was a baby, and rather than put her down Doug nursed her back to health (I told you he loves ostriches). She’s quite even-tempered and he said she would tolerate being hugged and petted. So while Doug finished up a last bit of farm business before he could escort me out to the gate, I hugged and petted Abigail. She is my height and my weight, but because her neck and legs are so long and skinny almost all of that weight is concentrated in her torso, which is very bulky and solid. Abigail pecked at my watch a few times and then ignored me; with all the petting and hugging she probably assumed I was an oversized and somewhat slow-witted child. That’s her on the right in this pathetically undersized photo.
I have two regrets from the day. First, the only camera I had along is the crappy one in my POS (positively old school) cell phone, which is why these pictures are few and mostly sucky. More sucky still is that Vanessa missed the ostrich wrangling. She had master’s program responsibilities today and I thought (and Doug thought) this would be a quick stop of just a few minutes to get some necks, not a three-hour ostravaganza. Doug invited us back for a proper tour sometime, and we will definitely go, but unless something goes terribly wrong there won’t be any more ostrich-herding opportunities. I feel like I got in on all the fun.
Previous SV-POW! posts on ratites, from our Things to Make and Do series:
- Part 6: fun with ostrich heads
- Part 6b: Veronica the ostrich head starts to come to pieces
- Part 6c: fragments of ostrich skull
- Part 6d: Veronica the ostrich skull, laid bare
- Part 6e: gloat your eyes, feast your soul, on my ostrich ethmoid ossification
- Part 6f: my dumb observation of the day is that in dorsal view, a partly-assembled ostrich skull looks kind of like a chasmosaurine
- Part 7: fun with rhea necks
- Part 7b: more fun with rhea necks
Elsewhere on the web, Darren has blogged extensively about ratites at Tet Zoo. Dissecting Ozbert the ostrich is a good place to start, and that post has links to several others.
Finally, all of my pre-SV-POW! ratite stuff is linked from the ratite clearing house post on my old blog.
Sweet new paper out today by Bibi et al. in Biology Letters, on some awesome elephant tracks from the United Arab Emirates. I’ve known this was coming for a while, because the second author on the study, Brian Kraatz, has his office about 30 feet down the hall from mine. And I just ran into the lead author, Faysal Bibi, at the Museum fur Naturkunde in Berlin when I was there in December. I knew Faysal when he was an undergrad at Berkeley, and now he’s Dr. Bibi and doing a postdoc in Berlin–how time flies. Congratulations to Faysal, Brian, and the rest of the team on a really cool discovery.
The study is nothing to do with sauropods, but it has a lot of weird connections to SV-POW! Most importantly, the paper is open access, which is both awesome and timely. The life restoration is by the wicked talented Mauricio Antón, who is best known for his paleomammals work but who also restored Brontomerus for National Geographic last year. And some comparative data used in the paper was supplied by SV-POW! favorite and sometime sci-fi author John Hutchinson.
Finally, the elephants that made the tracks were probably Stegotetrabelodon, and although they might not have been full-on Tolkien-by-way-of-Jackson Amphicoelias-sized war-beasts, they were still big four-tusked proboscideans, so I’m calling them oliphaunts. Bibi et al. didn’t find any evidence that the trackmakers were ridden by Haradrim, but they didn’t find any evidence that they weren’t, so that’s how I’m going to imagine them.
For more stuff, including the paper, the full-res version of the image at top, more sweet images, author bios, and so on, see the press page. There are also nice writeups at Not Exactly Rocket Science and Laelaps. Go check it out.
Bibi, F., Kraatz, B., Craig, N., Beech, M., Schuster, M., and Hill, A. 2012. Early evidence for complex social structure in Proboscidea from a late Miocene trackway site in the United Arab Emirates. Biology Letters. doi: 10.1098/rsbl.2011.1185
December 9, 2011
As previously reported, the lot of us are in Bonn for the sauropod biology workshop. Last night we met up at the welcome reception at the Goldfuss Museum. It was the first time for Mike and Darren to meet Vanessa Graff and Paco Gasco in person, and of course we all got to meet people we didn’t know previously who are here for the workshop. There is an outstanding series of talks lined up. Three days with some of the world’s best workers talking about sauropods all the time? Yeah, I reckon we can handle that.
No sauropods in the Goldfuss Museum, so we naturally hung out the biggest saurischian around (even if it is a vulgar, overstudied theropod).
This and any future posts for the next few days will necessarily be brief; gotta go learn about sauropods!