This tired old argument came up again on Twitter this evening, in light of Elsevier’s me-too announcement of a preprint archive:

Brian Nosek‏: Elsevier enters the biology #preprints space: https://www.elsevier.com/solutions/ssrn/biorn
Me: KILL IT WITH FIRE
Brian Lucey‏: I’ve used SSRN from its inception. Never ever felt it as anything but useful. That’s not changed with Elsevier.

And elsewhere in the same thread:

Me: We want preprints to be supported by community-owned initiatives that will not try to take total control.
William Gunn: Well, you said the same stuff about Mendeley and it wasn’t true then, either, so…

So what’s the problem? Mendeley and SSRN are still around, right

Yes, they are. But they continue to exist only by the grace of Elsevier. At any moment, that could change. And here’s why.

Subway is a chain of fast-food outlets that makes sandwiches. As it happens there is a branch in Cinderford, the nearest town to where I live. Which is nice.

Now everyone knows and understands that Subway is a corporation that exists to enrich its shareholders. That’s fine: no-one resents it, because it’s what it is. If the Cinderford branch makes money for them, they’ll keep it open and everyone will be happy. But if it doesn’t, then they’ll close that branch and no-one will be surprised. Because Subway’s mission is not to bring dining options to rural England, but to make money. No harm, no foul, that is just what they are.

But by the same token, Elsevier is a corporation that exists to enrich its shareholders. That’s not a controversial claim, it’s a simple statement of fact. And it’s not a criticism, it’s just recognising reality. We don’t even need to resent it: we just need to recognise it, and make our choices accordingly.

Now, from Elsevier’s perspective, Mendeley and SSRN, and indeed BioRN, are simply branches of Subway. They exist to make money for their shareholders. That’s their mission. Once more, not a criticism: just a fact.

But what this means is that the moment they are not making money, they will be shut down, just as the Cinderford branch of Subway would be. And, for that matter, just as BioMedNet, ChemWeb and ElsevierEngineering were shut down. Because Elsevier’s mission is not to further scholarship, it’s to make money. Again, not a criticism: just a fact.

What does it mean for Mendeley and SSN to “make money”? It may be that these branches of the Elsevier empire provide very little in the way of direct revenue. But someone will have run the numbers and shown that what they cost to run is less than their value to the corporation in terms of visibility, PR, drawing customers into other Elsevier products, etc. If it weren’t so, then they wouldn’t be running these services — because their responsibility is to shareholders, not scholars.

And you can bet that as soon as they day comes that they conclude Mendeley and SSRN are not paying for themselves, those services will go down in flames.

Now. It’s fine if Subway run their Cinderford branch for eighteen months and then decide it’s not working out. if they close it, I can just go down the road and get a kebab or a Chinese. But it’s not fine if scholarly infrastructure vanishes, or changes its terms, or becomes available only to members, or what have you. We need to be able to rely on scholarly infrastructure. Which is why in the end it needs to be owned and run by the scholarly community.

This is why I am becoming more and more convinced of the importance of the Principles for Open Scholarly Infrastructure, which lay out the conditions for a service to be reliable, sustainable and safe from hijacking. (I expect to write more about the Principles some time soon.)

The bottom line is just this: Elsevier’s mission is money and their duty is to shareholders. But our mission is research and our duty is to the world. We and they are simply not aligned. That doesn’t mean they can’t provide and charge for useful services. But it does mean that they can’t be allowed to own and control infrastructure.

That’s why no-one should submit preprints to BioRN. Let this effort move directly from cradle to grave without passing Go. There are already plenty of good preprint options for bioscientists: PeerJ preprints, BiorXiv, arXiv’s q-bio category, the whole ASAPbio initiative) and even for palaeontologists in particular (PaleorXiv).

Use those. Don’t give Elsevier control over scholarly infrastructure.

Here’s my face.

I went to the dentists’ office recently for a regular checkup and cleaning, and when my dentist learned that I taught human anatomy, he volunteered to send me a high-res copy of my panoramic x-ray. I couldn’t think of any plausible scenario wherein someone could use it for evil, and it has lots of cool stuff in it besides teeth, so decided to post it so I could yakk about it.

First things first: my teeth are in pretty good shape. I had to have my wisdom teeth (3rd molars) pulled back in 2009, and my upper 1st molar on the left has a root canal and a porcelain crown, which stands out bright white on the radiograph. Everyone else is present and looking good. If it’s been a while since you’ve covered this, the full human dentition consists of 2 incisors, 1 canine, 2 premolars, and 3 molars on each side, top and bottom, for a total of 32 teeth. Because I’ve had all four 3rd molars removed, I’m down to 28.

I could go on and on about the cool stuff in this image. Here are 12 things that stand out:

  1. The mandibular condyle, which is the articular end of the mandible that fits into the mandibular fossa, a shallow socket on the inferior surface of the temporal bone, to form the temporomandibular joint (TMJ). There’s an articular disk made of fibrocartilage inside the joint, which separates it into two fluid-filled spaces, one against the condyle and one against the fossa. This allows us to do all kinds of wacky stuff with our lower jaws besides simply opening and closing them, such as slide the jaw fore and aft or side to side. This is a strong contrast to most carnivores, which bite down hard and therefore need a jaw joint that works as a pure hinge. See this post for pictures and discussion of the jaw joint in a bear skull.
  2. The coronoid process of the mandible, which is a muscle attachment site. A few fibers of the masseter and buccinator muscles can encroach onto the coronoid process, but mostly it is buried in the temporalis, one of the primary jaw-closing muscles. Put your fingers on the side of your head a little above and in front of your ear and bite down. That muscle you feel bulging outward is the temporalis. Back in the 1960s, Melvin Moss (1968) discovered that if he removed the temporalis muscles from newborn rats, the coronoid processes would fail to develop. Moss’s ambition was to discover the quanta of anatomy, which in his view were “functional matrices” – finite sets of soft tissues related by development and function, which might contain “skeletal units” that grew because of the morphogenetic demands of the functional matrices. His tagline was, “Functional matrices evolve, skeletal units respond”. Not all of Moss’s ideas have aged well in light of what we now know about the genetic underpinnings of skeletal development, but he wasn’t completely wrong, either, and functional matrix theory is still an interesting and frequently productive way to think about the interrelationships of bones and soft tissues. For more horrifying/enlightening Moss experiments on baby rats, see this post.
  3. The mandibular angle, which is another muscle attachment. The medial pterygoid muscle attaches to the medial surface, and the masseter attaches laterally. You can feel this, too, by putting your fingers over your mandibular angle and biting down – that’s the masseter you feel bulging outward. Note that the angle flares downward and outward on either side of my jaw. This flaring of the angle tends to be more pronounced in males than in females, and it is one of many features that forensic anthropologists (like the one I belong to) take into account when attempting to determine biological sex from human skeletal remains. Like most sexually dimorphic features of the skeleton, this is a tendency along a spectrum of variation rather than a binary yes/no thing. There are women with flared jaw angles (Courtney Thorne-Smith, probably) and men with slender mandibles, so you wouldn’t want to sex a skeleton by that feature alone.
  4. The mandibular canal, a tubular channel through the mandible that houses the inferior alveolar artery, vein, and nerve. This neurovascular bundle provides innervation and blood supply to the tooth-bearing part of the mandible and to the teeth themselves, and emerges through the mental foramen to provide sensory innervation and blood supply to the chin.
  5. The upper surface of the hard palate, formed by the palatine process of the maxilla anteriorly and by the palatine bones posteriorly. The palate is the roof of the mouth and the floor of the nasal airways.
  6. The median septum of the nasal cavity, formed by cartilage anteriorly, the perpendicular plate of the ethmoid bone superiorly, and the vomer posteriorly and inferiorly.
  7. The blue lines are the inferior margins of my maxillary sinuses – air-filled spaces created when pneumatic diverticula of the nasal cavity hollow out the maxillae. You have these, too, as well as air spaces in your frontal, ethmoid, sphenoid, and temporal bones. It looks like many of the roots of my upper molars stick up into my maxillary sinuses. This is not an illusion, as shown below.
  8. When I had the root canal on my left upper 2nd molar, the endodontist filled the pulp cavities of the tooth roots with gutta-percha, a rigid natural latex made from the sap of the tree Palaquium gutta. Gutta-percha is bioinert, so it makes a good filling material (it was also used to insulate transoceanic telegraph cables), and it’s radiopaque, which allows endodontists to confirm that the cavities have been filled completely. The other teeth show the typical structure of a dense enamel crown, less dense dentine forming the bulk of the tooth, and radiolucent pulp cavities containing blood vessels and nerves.
  9. This is the rubber bit I gripped with my incisors to keep my teeth apart and my head motionless while the CT machine rotated around me to make the scan. Not that cool in a science sense, but I figured it deserved a label.
  10. Note that the roots of the canines go farther into the jaws than those of the other teeth. This is true for all four canines, it’s just easiest to see with this one. This is a pretty standard mammalian thing, for taxa that still have canines – they tend to be big and mechanically important, so they have deep roots. Even though our canines are absolutely and proportionally much smaller than those in the other great apes, we can still see traces of their earlier importance, like these deep roots.
  11. In places you can see the trabecular internal structure of my mandible clearly. As someone who geeks out pretty much anytime I get a look inside a bone, this tickled me.
  12. The remains of an alveolus or tooth socket. I had my 3rd molars out almost a decade ago, and by now the sockets will have mostly filled in with new trabecular bone. But you can still see the ghostly outline of at least this one – a sort of morphogenetic trace fossil buried inside my mandible. I assume that in another decade or two this will have disappeared through regular bone remodeling.

Here’s a closeup of my left upper 2nd premolar and first two (and only remaining) molars. The gutta-percha filling the pulp cavities of the three roots of the 1st molar is obvious. The disparity in root length is mostly illusory – this was an oblique shot and the two ‘short’ roots are foreshortened.

Here’s the same image with the roots of the 2nd molar traced in pink, and the inferior margin of the maxillary sinus traced in blue. It’s not that uncommon for upper molar roots to stick up into the maxillary sinuses. That was true of my 3rd molars as well, and when I had them taken out, the endodontist had to put stitches into my gums to close the holes. Otherwise I would have had open connections between my oral cavity and maxillary sinuses, which would have sucked and been dangerous. Nasal mucus in the maxillary sinuses could have drained into my mouth, and food I was chewing could have been forced up into the sinuses, where it would have decomposed and caused a truly vile sinus infection.

In a developmental sense, it’s not that the roots of the teeth grow upward into the sinuses, it’s that the sinuses grow downward, eroding the bone around the roots of the teeth. This happens well after the teeth are done forming – the sinuses continue to expand as long as the skull is growing, and they retain the potential to remodel the surrounding bone for as long as we live. Even in cases like mine where the roots of the molars stick up into the sinuses, the tooth roots are still covered by soft tissue, including branches of the superior alveolar artery, vein, and nerve that enter the pulp cavities of the tooth roots through foramina at their tips.

If you ask your dentist for copies of your own dental x-rays, you’ll probably get them. If you do, have fun exploring the weird territory inside your head.

Reference

  • Moss, M. L. (1968). A theoretical analysis of the functional matrix. Acta Biotheoretica, 18(1), 195-202.

Upcoming book signings

April 19, 2017

Come gawk at this weirdo in public!

I’ll be signing copies of The Sauropod Dinosaurs: Life in the Age of Giants at regional events the next two weekends.

This this coming Saturday, April 22, I’ll be at the Inland Empire Science Festival, which will run from 10 AM to 4 PM at the Western Science Center in Hemet, California. There will be a ton of other special exhibits and activities, too. I don’t know all of them off the top of my head, but I know that Brian Engh will have the table next to mine, so come by and get two doses of awesome paleo art.

The following Friday, April 28, I’ll be at Beer N’ Bones 2017, which runs from 7-11 PM at the Arizona Museum of Natural History in Mesa, Arizona. In addition to signing books, I’ll also be in the “Speed Dating a Scientist” thing, where small groups of people get five minutes each at a table with a researcher, to ask whatever they want. Not just paleontologists, but scientists of all stripes. That said, I know of a couple of other local paleontologists who will also be there as guests – Andy Farke and Thierra Nalley. I was at Beer N’ Bones last year and it was a blast. As you might suspect from the name, it is 21-and-over only.

I’ll have books for sale – at a healthy discount – at both events. Hopefully I’ll see you out there.

I was fortunate to get to visit some pretty cool places last year, and to photograph some awesome critters, many of which I had never seen so well before. Here are the best of the lot.

In March I went out to Black Mesa with my mentor, Rich Cifelli, and a Native Explorers crew led by Kent Smith. Rich and I saw this pronghorn on the way in, and I got the shot by holding my phone up to Rich’s binoculars.

Later that same day, I caught these pronghorns crossing the highway in front of us. You can tell from the glare and splotches that I was shooting through the windshield. It was that or no shot.

A few days later, we got absurdly lucky. Everyone was driving back to base at the end of the day, with Rich’s truck at the end of the train. This herd of bighorn sheep picked that time to jump a fence and run across the road, right in front of Rich’s truck. Everyone else missed it, they were too far ahead. The bighorns crossed the road in front of our caravan again a couple of days later, and Kent Smith and Jeff Hargrave got some good photos of their own.

I like this landing-and-recovery sequence, illustrated by four different individuals.

Check out the two at the edge of the road, running in step.

A final wide shot. Thank goodness for burst mode shooting. These are all cropped iPhone photos, by the way.

Then in June I got to go with my son’s 5th grade field trip group to Santa Cruz Island in Channel Islands National Park, where we camped for three days and two nights. The dwarf island foxes were always around.

I think people have actually been good about not feeding them because they don’t beg. Neither are they afraid of humans. They treated us as non-threatening and inedible chunks of ambulatory matter. This one was startled by something in the bush and decided that running past me was the lesser of two evils. It might have been another fox, we saw and heard several get into tussles.

Another burst mode catch was this raven on the beach.

Here’s a crop. Not bad, sez me. For a shot of a stinkin’ theropod.

And here’s my favorite shot of that trip, and my second-favorite of the entire year. On the boat ride out to the island, a pod of dolphins came and surfed our bow wake. They did this for quite a while, and everyone who wanted to was able to cycle through the front of the boat and get close-up shots. I’d seen dolphins from shore before, when we lived in NorCal, but I’d never gotten to see them up close from the water. This is yet another burst-mode catch, taken just as this dolphin was breaking the water and before most of the bubbles coming out of its blowhole had popped.

I’m going to use my son’s standing as a tetrapod to sneak this in: sunset at Dead Horse Point, near Moab, Utah. That’s the Colorado River down there, 2000 feet below the clifftops. If you’re ever in that neck of the woods, this is the place to come see the sun set. Trust me on this.

Back in 2012, in response to the Cost Of Knowledge declaration, Elsevier made all articles in “primary math journals” free to read, distribute and adapt after a four-year rolling window. Today, as David Roberts points out, it seems they have silently withdrawn some of those rights. In particular, the “free” articles can no longer be redistributed or adapted — which, for example, prevents their use in teaching or in Wikipedia articles.

We don’t know when this changed. It just did, quietly, at some point after the Cost of Knowledge anger had died down, when no-one was watching them carefully. So here, once more, Elsevier prove that they are bad actors who simply cannot be trusted.

There is a broader and more important point here: we simply can’t build a meaningfully open scholarly infrastructure that is dependent on the whims of corporations. It can’t be done.

Whatever corporations like Elsevier give us one day, they can and will take away another day. They can’t help themselves. It’s in their nature. And, really, it’s unreasonable of us to expect anything different from a corporation whose reason for existing is to enrich its shareholders.

So to have a genuinely open scholarly infrastructure, there is no real alternative to building it ourselves, within the scholarly community. It’s worse that useless to sit around waiting for likes of Elsevier to gift us the infrastructure we need. It’s not in their interests.

So once more, folks: there’s no need for us to be hostile to Elsevier et al. Just walk away. Do not deal with them. They are not on your side. They never have been, and they never will be. They will give just enough ground to defuse anger when it threatens their bottom line; that’s all. Then they will take the ground back when it suits them.


Note. This post is based on a series of tweets.

This is very belated, but back in the summer of 2014 I was approached to write a bunch of sections — all of them to do with dinosaurs, naturally — in the book Evolution: The Whole Story. I did seven group overviews (Dinosauria overview, prosauropods, sauropods, stegosaurs, ankylosaurs, marginocephalians, and hadrosaurs), having managed to hand the theropod work over to Darren.

My author copy arrived in February 2016 (which, yes, is over a year ago. Your point?) It’s really nice:

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And at 576 heavy, glossy pages, it’s a hefty tome.

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My contribution was fairly minimal, really: I provided about 35 pages. Darren wrote a lot more of it. Still, I’m pleased to have been involved. It’s nicely produced.

Here a sample spread — the first two of a four-page overview of sauropods, showing some nice illustrations and a typical timeline across the bottom of the page.

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And here’s one of the ten “highlights” sections I did, mostly on individual dinosaurs. This is the best one, of course, based on sheer taxon awesomeness, since it deals with Giraffatitan:

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Unfortunately, not all of the artwork is of this quality. For example, the life restoration that graces my spread on Argentinosaurus makes me want to stab my own eyes out:

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Still, putting it all together, this is an excellent book, providing a really helpful overview of the whole tree of life, each section written by experts. It’s selling for a frankly ludicrous £16.55 in the UK — it’s easily worth two or three times that; and $30.24 in the US is also excellent value.

Highly recommended, if I do say it myself.

The previous post (Every attempt to manage academia makes it worse) has been a surprise hit, and is now by far the most-read post in this blog’s nearly-ten-year history. It evidently struck a chord with a lot of people, and I’ve been surprised — amazed, really — at how nearly unanimously people have agreed with it, both in the comments here and on Twitter.

But I was brought up short by this tweet from Thomas Koenig:

That is the question, isn’t it? Why do we keep doing this?

I don’t know enough about the history of academia to discuss the specific route we took to the place we now find ourselves in. (If others do, I’d be fascinated to hear.) But I think we can fruitfully speculate on the underlying problem.

Let’s start with the famous true story of the Hanoi rat epidemic of 1902. In a town overrun by rats, the authorities tried to reduce the population by offering a bounty on rat tails. Enterprising members of the populace responded by catching live rats, cutting off their tails to collect the bounty, then releasing the rats to breed, so more tails would be available in future. Some people even took to breeding rats for their tails.

Why did this go wrong? For one very simple reason: because the measure optimised for was not the one that mattered. What the authorities wanted to do was reduce the number of rats in Hanoi. For reasons that we will come to shortly, the proxy that they provided an incentive for was the number of rat tails collected. These are not the same thing — optimising for the latter did not help the former.

The badness of the proxy measure applies in two ways.

First, consider those who caught rats, cut their tails off and released them. They stand as counter-examples to the assumption that harvesting a rat-tail is equivalent to killing the rat. The proxy was bad because it assumed a false equivalence. It was possible to satisfy the proxy without advancing the actual goal.

Second, consider those who bred rats for their tails. They stand as counter-examples to the assumption that killing a rat is equivalent to decreasing the total number of live rats. Worse, if the breeders released their de-tailed captive-bred progeny into the city, their harvests of tails not only didn’t represent any decrease in the feral population, they represented an increase. So the proxy was worse than neutral because satisfying it could actively harm the actual goal.

So far, so analogous to the perverse academic incentives we looked at last time. Where this gets really interesting is when we consider why the Hanoi authorities chose such a terribly counter-productive proxy for their real goal. Recall their object was to reduce the feral rat population. There were two problems with that goal.

First, the feral rat population is hard to measure. It’s so much easier to measure the number of tails people hand in. A metric is seductive if it’s easy to measure. In the same way, it’s appealing to look for your dropped car-keys under the street-lamp, where the light is good, rather than over in the darkness where you dropped them. But it’s equally futile.

Second — and this is crucial — it’s hard to properly reward people for reducing the feral rat population because you can’t tell who has done what. If an upstanding citizen leaves poison in the sewers and kills a thousand rats, there’s no way to know what he has achieved, and to reward him for it. The rat-tail proxy is appealing because it’s easy to reward.

The application of all this to academia is pretty obvious.

First the things we really care about are hard to measure. The reason we do science — or, at least, the reason societies fund science — is to achieve breakthroughs that benefit society. That means important new insights, findings that enable new technology, ways of creating new medicines, and so on. But all these things take time to happen. It’s difficult to look at what a lab is doing now and say “Yes, this will yield valuable results in twenty years”. Yet that may be what is required: trying to evaluate it using a proxy of how many papers it gets into high-IF journals this year will most certainly mitigate against its doing careful work with long-term goals.

Second we have no good way to reward the right individuals or labs. What we as a society care about is the advance of science as a whole. We want to reward the people and groups whose work contributes to the global project of science — but those are not necessarily the people who have found ways to shine under the present system of rewards: publishing lots of papers, shooting for the high-IF journals, skimping on sample-sizes to get spectacular results, searching through big data-sets for whatever correlations they can find, and so on.

In fact, when a scientist who is optimising for what gets rewarded slices up a study into multiple small papers, each with a single sensational result, and shops them around Science and Nature, all they are really doing is breeding rats.

If we want people to stop behaving this way, we need to stop rewarding them for it. (Side-effect: when people are rewarded for bad behaviour, people who behave well get penalised, lose heart, and leave the field. They lose out, and so does society.)

Q. “Well, that’s great, Mike. What do you suggest?”

A. Ah, ha ha, I’d been hoping you wouldn’t bring that up.

No-will be surprised to hear that I don’t have a silver bullet. But I think the place to start is by being very aware of the pitfalls of the kinds of metrics that managers (including us, when wearing certain hats) like to use. Managers want metrics that are easy to calculate, easy to understand, and quick to yield a value. That’s why articles are judged by the impact factor of the journal they appear in: the calculation of the article’s worth is easy (copy the journal’s IF out of Wikipedia); it’s easy to understand (or, at least, it’s easy for people to think they understand what an IF is); and best of all, it’s available immediately. No need for any of that tedious waiting around five years to see how often the article is cited, or waiting ten years to see what impact it has on the development of the field.

Wise managers (and again, that means us when wearing certain hats) will face up to the unwelcome fact that metrics with these desirable properties are almost always worse than useless. Coming up with better metrics, if we’re determined to use metrics at all, is real work and will require an enormous educational effort.

One thing we can usefully do, whenever considering a proposed metric, is actively consider how it can and will be hacked. Black-hat it. Invest a day imagining you are a rational, selfish researcher in a regimen that uses the metric, and plan how you’re going to exploit it to give yourself the best possible score. Now consider whether the course of action you mapped out is one that will benefit the field and society. If not, dump the metric and start again.

Q. “Are you saying we should get rid of metrics completely?”

A. Not yet; but I’m open to the possibility.

Given metrics’ terrible track-record of hackability, I think we’re now at the stage where the null hypothesis should be that any metric will make things worse. There may well be exceptions, but the burden of proof should be on those who want to use them: they must show that they will help, not just assume that they will.

And what if we find that every metric makes things worse? Then the only rational thing to do would be not to use any metrics at all. Some managers will hate this, because their jobs depend on putting numbers into boxes and adding them up. But we’re talking about the progress of research to benefit society, here.

We have to go where the evidence leads. Dammit, Jim, we’re scientists.