I’m a bit shocked to find it’s now more than five years since Robert Harington’s Scholarly Kitchen post Open Access: Fundamentals to Fundamentalists. I wrote a response in the comments, meaning to also post it here, but got distracted, and then half a decade passed. Here it is, finally. The indented parts are quotes from Harington.


I must admit to being rather tired of the fundamentalism that pervades discussions around open access policies and business models. On the one hand there are the advocates, and through the laws of conservation of energy, the equal and opposite reaction of anti-open access advocacy. There seems little room for rational debate about open access in the midst of such an antagonistic atmosphere.

It’s always a powerful rhetorical move to call your opponent a fundamentalist. It’s also a lazy one. It absolves you from the tedious responsibility of bothering to understand what the opponent actually wants: just dismiss him has a fundamentalist and call it done. I’d hope we’re better than that. At best, this seems like a fine demonstration of the principle that “there seems little room for rational debate about open access in the midst of such an antagonistic atmosphere”.

You want a rational debate? You want to talk about fundamentals? Fine, let’s do that. Here is the most fundamental question of all: what is research for? Our answer to this will profoundly affect every stance we adopt regarding publishing, OA, researcher evalution and more.

The greatest problem we have in discussing these issues is when person A assumes right off the bat that person B has the same answer to that fundamental question, and is then surprised to find that B disagrees over numerous implementation details. All those details flow from the fundamental mismatch. A and B are literally trying to solve two different problems — no wonder they can’t agree on the solution!

So what is research for? Here are three possible answers.

A. Some people believe (or maybe I should say assume) that research is for the world — for the betterment of the lot of society as a whole, the eradication of illness, the understanding of the environment, and generally the benefit of humanity. As pleasant side-effects, it also feeds publishing businesses and advances researchers’ careers.

B. Some people believe (or assume) that research is primarily for the benefit of the economy: that the principle purpose of the whole process is the financial benefit that accrues to publishers and related professions. As pleasant side-effects, it also advances the world’s knowledge and advances researchers’ careers.

C. Some people believe (or assume, or at least give the impression of assuming) that research is mostly about the careers of researchers — about giving them a way to prove their merit and advance up the career ladder. As pleasant side-effects, it also advances the world’s knowledge and feeds publishing businesses.

All of these fundamental positions exist. (There may be others that I missed.) We could probably all classify various individuals into these groups (but I’ll resist the temptation to throw in examples, as that would surely result in an epic sidetrack).

Notice that one can’t reach one of these three positions by any amount of thought about what happens within the research/publication ecosystem. It’s more fundamental than that. That decision has to come from somewhere outside. For example, my own position is no secret: I am an “A”, and the reason is because I feel it follows from the Golden Rule (“Do to others as you would have them do to you”, Luke 6:31) — probably the most universally agreed ethical principle in any religion (and among those who profess none).

And so when Robert Harrington asks:

The real debate here is to understand more about the motivations and needs of a researcher, who may or may not be funded directly. What is the best business model that will allow a researcher to publish work effectively and allow readers access to that work?

That is really two ——quite separate questions that may have completely different answers: 1, what business model will allow a researcher to publish work effectively?; and 2, what business model will allow readers access to that work? If you are an “A”, you’ll care most about the second question; if you’re a “C” you’ll care about the first question; and if you’re a “B” you might still be thinking about the business model mentioned at the start of the question.

It’s fruitless to expect “A”s, “B”c and “C”s to agree on an answer to a question when each group is hearing a different question.

Here’s another example:

The real story here is that the rights and desires of academics are being represented by organizations that do not reflect their needs, and that perhaps do not even understanding them. There is a form of fundamentalism that dictates to academics that this is what you need; just let us lead the way and we will make things right for you.

This statement suggests a “C” mindset: that the rights and desires of researchers are paramount. But if the organisations in question are “A”s (as for example you’d expect the Alliance for Taxpayer Access or RCUK to be), then this complaint is a non-issue. Of course they don’t reflect researchers’ desires — that’s not what they’re there for. They reflect the needs of broader society (which are often aligned with those of researchers, but by no means always).

That’s not a bug. That’s a feature.

And similarly:

I would suggest that there is nothing fundamentally wrong with a subscription model.

This may be true for “B”s (who might prefer the subscription model because they think it yields the most revenue) and for “C”s (who might want to place their work in a specific paywalled journal that is well regarded in their field). But it’s much less likely for “A”s, who see great public benefit in free access, and conversely great harm in arbitrary barriers.

So there you go. Fundamentals.

 

 

Down in flames

August 25, 2018

I first encountered Larry Niven’s story/essay “Down in Flames” in the collection N-Space in high school. This was after I’d read Ringworld and most of Niven’s Known Space stories, so by the time I got to “Down in Flames” I had the context to get it. (You can read the whole thing for free here.)

Here’s the idea, from near the start:

On January 14, 1968, Norman Spinrad and I were at a party thrown by Tom & Terry Pinckard. We were filling coffee cups when Spinny started this whole thing.

“You ought to drop the known space series,” he said. “You’ll get stale.” (Quotes are not necessarily dead accurate.) I explained that I was writing stories outside the “known space” history, and that I would give up the series as soon as I ran out of things to say within its framework. Which would be soon.

“Then why don’t you write a novel that tears it to shreds? Don’t just abandon known space. Destroy it!”

“But how?” (I never asked why. Norman and I think alike in some ways.)

The rest of the piece is just working out the details.

“Down in Flames” brain-wormed me. Other than Ray Bradbury’s “A Sound of Thunder” I doubt if there is another short story I’ve read as many times. Mike once described the act of building something complex and beautiful and then destroying it as “magnificently profligate”, and that’s the exact quality of “Down in Flames” that appeals to me.

I also think it is a terrific* exercise for everyone who is a scientist, or who aspires to be one.

* In both the modern sense of “wonderful” and the archaic sense of “causing terror”.

Seriously, try it. Grab a piece of paper (or open a new doc, or whatever) and write down the ideas you’ve had that you hold most dear. And then imagine what it would take for all of them to be wrong. (When teams and organizations do this for their own futures, it’s called a pre-mortem, and there’s a whole managerially-oriented literature on it. I’d read “Down in Flames” instead.)

It feels like this! Borrowed from here.

Here are some questions to help you along:

  • Which of your chains of reasoning admit more than one end-point? If none of them might lead other places, then either you are the most amazing genius of all time (even Newton and Einstein made mistakes), or you are way behind the cutting edge, and your apparent flawlessness comes from working on things that are already settled.
  • If there is a line of evidence that could potentially falsify your pet hypothesis, have you checked it? Have you drawn any attention to it? Or have you gracefully elided it from your discussions in hopes that no-one will notice, at least until after you’re dead?
  • If there’s no line of evidence that could falsify your pet hypothesis, are you actually doing science?
  • Which of your own hypotheses do you have an emotional investment in?
  • Are there findings from a rival research team (real or imagined) that you would not be happy to see published, if they were accurate?
  • Which hypotheses do you not agree with, that you would be most dismayed to see proven correct?

[And yes, Karl, I know that according to some pedants hypotheses are never ‘proven’. It’s a theoretical exercise already, so just pretend they can be!]

I’ll close with one of my favorite quotes, originally published in a couple of tweets by Angus Johnson in May of 2017 (also archived here):

If skepticism means anything it means skepticism about the things you WANT to be true. It’s easy to be a skeptic about others’ views. Embracing a set of claims just because it happens to fit your priors doesn’t make you a skeptic. It makes you a rube, a mark, a schnook.

So, don’t be that rube. Burn down your house of ideas – or at least, mentally sift through the rubble and ashes and imagine how it might have burned down. And then be honest about that, minimally with yourself, and ideally with the world.

If you’re a true intellectual badass, blog the results. I will. It’s not fair to give you all homework – painful homework – and not take the medicine myself, so I’m going to do a “Down in Flames” on my whole oeuvre in the next a future post. Stay tuned!

Here’s BYU 12866, a mid-cervical of a neosauropod from Dry Mesa Quarry. It’s cataloged as Brachiosaurus, an identification I’ve never found any compelling reason to doubt. It’s definitely brachiosaurid, and for now Brachiosaurus is the only game in town for the Late Jurassic of North America. I expect that will change when more and better material comes to light, based on the different coracoid shapes of the Brachiosaurus holotype and the “Ultrasauros” scapulocoracoid.

I reckon it’s probably a C5 or so, based on its proportions and comparisons with Giraffatitan (for example).

As you can see, it’s a bit distorted, sheared over with the dorsal side to the right and the ventral side to the left.

I don’t think there’s any major anterior/posterior shearing – the zygs are set forward of their respective centrum ends by about the same amount in this specimen as in Giraffatitan.

Kent Sanders and I CT scanned this vert back in the day and those scans made it into several papers, including Wedel et al. (2000b) on Sauroposeidon and Wedel (2005) on sauropod pneumaticity and mass estimates.

I have the original, uncropped, full-res photos, and I’ll probably get them posted at some point (faster if people bug me to do so, so speak up in the comments if you want them). But for now I’m sticking to getting stuff posted quickly, easily, and regularly, and I found these as-is on my hard drive, so here we are.

References

 

Old drawings (of heads)

June 25, 2017

I was organizing my files in DropBox and I found a folder of old drawings I’d almost forgotten about. I drew this back in the late 90s. It was used on a t-shirt by the OU Zoology Department. I got the general idea of making a head out of animals, and the specific idea of using a butterfly wing for the ear, from Wayne Douglas Barlowe’s cover for the novel Wild Seed by Octavia Butler. The snake I stole from ancient Egypt. I think everything else is in there just because I thought it was cool. Note that inverts, fish, herps, birds, and mammals are all represented, with a good balance of aquatic, terrestrial, and volant forms. It looks awfully hippie-dippie from 20 years out, but heck, what doesn’t?

“Solitude” by Mathew Wedel. CC BY-NC 4.0.

Well, this, I suppose.

I drew this about the same time. I was reading The Gnostic Gospels by Elaine Pagels and lots of stuff about ancient monastic traditions and thinking that if the world is an illusion that must be penetrated, then the evidence of one’s senses can only mislead. Also, Vicki was working for the state medical examiner in Oklahoma City and they used wooden dowels to represent the paths of bullets when reconstructing the skulls of those killed by gunfire. So here’s the skull of a monk, with all of the lethal pathways of distraction and temptation clearly marked as such. At last he can contemplate the eternal mysteries in perfect solitude.

Obviously I didn’t get on board the world-is-an-illusion, sensation-is-bad train – skewed pretty hard in the opposite direction, in fact. Possibly because years earlier the Chessmen of Mars by Edgar Rice Burroughs had shown me that pursuing ‘pure’ intellectual and spiritual inquiry would ultimately lead one to a pathetic existence as a disembodied head living in a cave (high culture, meet low culture). Anyway, whatever interest I might have had in that philosophy I exorcised through this drawing. Stripped of any art-making-a-point baggage, I still think it’s pretty bitchin’. I should make t-shirts.

Actually, I probably will make t-shirts of this one if there’s any interest. Hence the CC BY-NC license I put on it, as opposed to the normal CC BY for almost everything else on this site. Look at me, boldly experimenting with new licenses.

This, obviously, is a lot more recent. I was collating all of my scanned drawings and I realized that I’d gone to the trouble of drawing the cranium and lower jaw of Aquilops separately, but I’d never posted the version from before I composited them back into articulation. It is very unlike me to do work and then hide it, so here it is.

It wasn’t until I the post mostly written that I realized that all three drawings are of heads, none of them are saurischians (although the first includes a saurischian, but not the cool kind), and two are stinkin’ mammals (and not the cool kind). I stand ready for your slings and arrows.

For previous posts on my drawings, see:

Wedel 2005 Morrison sauropod cervicals 1 - Diplodocus

When I was back in Oklahoma in March, I met with Anne Weil to see some of the new Apatosaurus material she’s getting out of her Homestead Quarry. It’s nice material, but that’s a post for another day. Anne said something that really resonated with me, which was, “I love it when you guys post about vertebral morphology, because it helps me learn this stuff.” Okay, Anne, message received. This will begin to make things right.

Wedel 2005 Morrison sauropod cervicals 2 - Barosaurus and centra shapes

I spent a week at BYU back in 2005, collecting data for my dissertation. One of the first things I had to do was teach myself how to identify the vertebrae of different sauropods, because BYU has just about all of the common Morrison taxa. These are the notes I made back then.

Wedel 2005 Morrison sauropod cervicals 3 - Brachiosaurus and Apatosaurus

I always planned to do something with them – clean them up, get them into a more usable form. There are a lot of scribbly asides that are probably hard for others to read, and it would be more useful if I put the easily confused taxa next to each other – Barosaurus next to Brachiosaurus, for example. And I didn’t go into serial changes at all.

Wedel 2005 Morrison sauropod cervicals 4 - Camarasaurus and Haplocanthosaurus

Still, hopefully someone will find these useful. If there are things I missed or got wrong, the comment thread is open. And if you want all four spreads in one convenient package, here’s a PDF: Wedel 2005 notes on Morrison sauropod cervicals

Mike and I leave for the Sauropocalypse tomorrow. I’m hoping to post at least a few pretty pictures from the road, as I did for the Mid-Mesozoic Field Conference two years ago. Stand by…

ostrich peeing

cormorant peeing

alligator peeing

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.

So, you know . . . try to show a little respect.

So, you know . . . try to show a little respect.

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:

International Cockatiel Resource bird pee guide

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).

Rhea peeing by Markus Buhler

Many thanks to Markus Bühler for permission to post his well-timed u-rhea photo.

[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.

ostrich excreting

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.

ostrich excreting 3

In conclusion, birds and crocs can pee. Go tell the world.

And now, those gator peeing videos I promised:

UPDATE

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.

References

tornado debris

Hey, look, there goes my future!

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.

IMG_5787

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.

Good luck.

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