This is something I did over Thanksgiving break in 2019. I meant to blog about it sooner, but you know, 2020 and all. So here I am finally getting around to it. (Yes, I know the ruler in the above photo is the worst scale bar ever. I was, uh, making a point. Which you got. So go you!)

For reasons unknown to me, the strip of skin between the mid-snout and the ear on the right side of the head was already off when I took possession from the local butcher. But it did show the ear muscles to good advantage, as well as the parotid gland–the knobbly white thing between the eye and ear that looks like grits, or eggs, or white beans. You have a parotid gland in front of each of your ears, too (par-otid = “next to ear”), each with a duct that crosses the cheek to bring saliva into your mouth. If you push your tongue into the upper-lateral “corners” of your cheeks, you can feel the little papilla where the duct opens, and if you push against the papilla with your tongue you may feel a little saliva leak out. You also have paired submandibular and sublingual salivary glands, but those will have to wait for another day.

Here’s the head from the back, after I’d gotten the right ear off. The bluish-white hyaline cartilage over the occipital condyles is clearly visible about 2/3 of the way up from the bottom, with the faintly yellowish stump of the medulla oblongata in between, going up into the braincase. Tons of neck muscles are visible here, and maybe someday I or someone else will get around to labeling them in this photo–but it is not this day.

What was I doing here? Getting off the ears, and as much skin and subcutaneous fat as possible, in preparation for brining and smoking. I like this photo, the little piggy looks positively happy about having its skull prepped.

Right, into the bag with you then. I did the same brining and smoking routine that I did for my first smoked turkey back when–see this post for details.

And here we are about 15 hours later. Note how much the color of the meat has changed from the brining.

Time to extract the brain. I already showed a version of this photo in my post on the $1 brain-extractor (a.k.a. drain rooter, see this post), but it bears repeating: the brain is mostly lipids and if you cook the head with the brain still in it, the brain will turn into liquid fat and seep into the bones and you’ll spend the rest of your days trying to degrease the skull before you die, unloved and weeping, on a pile of rags. So no matter how you’re planning to cook the head, yoink the brain first.

Onto the grill, with a drip pan underneath, foil heat shields in place to keep the heat indirect, and foil-wrapped mesquite smoke bombs visible under the grill, right on top of the coals. This is about all I do with my grill anymore; smoking is really no more work than anything else and the results are pretty much to die for. YMMV.

Same shot an hour later and the smoking is coming along nicely. I ended up smoking this head for three hours, an hour and a half on each side. 

And into the roasting pan for a few minutes’ rest at the end of the cooking. And it was cooking, not just specimen prep–we ate this pig head in lieu of a turkey for Thanksgiving, and it was amazingly delicious. One thing to note in this photo is how the temporalis fascia has pulled away from the skull at the upper left, exposing some bare bone. This would be a problem later on.

Defleshing, both to get the edible meat off, and to get as much of the rest of the soft tissue off in preparation for simmering. In this anterior view, you can see that the right side of the animal’s forehead (viewer’s upper left) got exposed during the smoking process and the bone is stained brown. 

Even with the meat cooked all the way through, disarticulating the jaw took some doing, and then some follow-up meat removal. Check out the very round, almost hemispherical mandibular condyles, which fit up into the sockets of the temporomandibular joints. Birds and other reptiles mostly do it the opposite way, with rounded quadrates on the cranium that fit into articular sockets on the lower jaw.

Ready for simmering. Pro tip: if you need a really big metal pot in which to simmer skulls or other large osteological specimens, but you don’t want to go bankrupt, look for a tamale-steaming pot. They’re comparatively thin-walled and lightweight, but still plenty sturdy for just about any application you are likely to think of. 

Our kitty, Moe, helped with the clean-up of the roasting pan.

The first simmer. At this remove, I don’t remember how many rounds of simmering I did, but it was at least two, maybe three.

Post-simmer, I put the skull into a sink-full of warm, soapy water for a defleshing. Notable bits you can see on the right side of the photo are the ridged surface of the palate (about 7:00 on the plate), the long straight cartilage of the nasal septum (going vertically up the right side of the plate), and the incisors at the extreme upper right, sitting on the edge of the sink. Most of the incisors fell out during the wash, which was fine, because most of them were horribly stained from the smoking process and would require a lot of scrubbing and bleaching to get back to a nice and natural-looking white.

The condition after the first simmer. You can see that the supraorbital foramina, on the forehead between the eyes, still have goop in them. This was true of pretty much all of the nerve and blood vessel passages. It took a lot of time, some ingenuity, bamboo barbeque skewers, and running water this way and that to flush out all of that crud. And the bones are still weird colors at this stage, pre-whitening, especially the groady dark patches on the forehead. It wasn’t the areas of bone that were directly exposed to smoke that were the problem, it was the areas just adjacent where the periosteum cooked against the bone.

Same stage, left lateral view. Note the empty sockets for the incisors, and the infraorbital foramen (above the upper teeth and about a third of the way between eye socket and the nose), which on this side is divided in two by a strut of bone. There’s another gross dark patch on the back of the zygomatic arch. All of those took pretty aggressive scrubbing to remove.

Back into the pot for another simmer. The perforated plate at the bottom sits on a lip of metal about three inches above the bottom of the pot so you can steam tamales with this thing. I used it to keep the bones off the bottom of the pot so they’d have no chance of getting scorched.

Here’s a significant jump forward in time. By this point I’d degreased and whitened the skull by soaking it in dilute hydrogen peroxide (I use the cheap stuff from the dollar store down the street, and it works fine), applied glue to several of the skull sutures that were threatening to come apart, and epoxied the prenasal bone back into position between the nasal bones above and the premaxillary bones below. The prenasal bone is a pretty cool structure, you can see it in other views (including a cross-section!) in this post. I also glued the incisors back in at this stage.

Believe it or not, this was the largest skull I had ever prepped myself–the largest osteological preparation of any kind, in fact–and it was a lot more work than I anticipated. But the effort was worth it, and now I have a really cool pig skull on my bookcase. I’ll show the finished skull in a follow-up post (no, really, I will!). EDIT: And I did! 

For other posts on pig skulls, see:

When last I blogged about James Herrmann’s art, it was about some cool sculptures of dinosaurs that he had done for the Cincinnati Museum Center. I am particularly taken with the sculptures that are skeleton on one side, and fully-fleshed on the other side.

Now he’s doing mammals, specifically Ice Age megafauna. 

And they’re attracting attention–this very cool American Mastodon won the Lanzendorf-National Geographic PaleoArt Prize in the 3D category at SVP this year.

As nice as the mastodon is, I am really taken with this Bison latifrons.

What can I say, I’m a sucker for high-spined vertebrae.

I really dig these, much more than I would either a naked skeleton or a fully-fleshed restoration on both sides. I hope there are more to come in the future, both from James and from other paleoartists.

For more on James’s work, please visit his website: http://www.herrmannstudio.com/.

Altounian et al. (2015: fig 6).

As has been discussed here before, the recurrent laryngeal nerve (RLN) does not only innervate the larynx, but also parts of the esophagus and trachea (see this post, and in particular this comment). You can see that in this cadaver photo, in which the RLN is sending nice big visible branches into both the esophagus and trachea on its way to the larynx. Why is it doing this? Because the embryonic gut tube, which gives rise to both the digestive and respiratory systems, is serially innervated by the nerves of the pharyngeal arches that the gut tube passes through. Parts of the esophagus and trachea pass through the 4th to 6th pharyngeal arches, so they are innervated by the nerve that serves those arches, which is the recurrent laryngeal nerve. As discussed in the post and comment linked above, the recurrent course of the RLN to the esophagus and trachea is just as dumb as its recurrent course to the larynx, and equally strong evidence of a developmental constraint.

Although all tetrapods have an RLN that innervates the larynx, the axons to the esophagus and trachea aren’t always bound up with it. In dogs and many other mammals, those nerve fibers to the esophagus and trachea form a second recurrent nerve, the pararecurrent nerve or recurrent pharyngeal nerve. In this wonderful, complicated figure by Lemere (1932), the recurrent laryngeal nerve is labeled ‘r’, and the pararecurrent nerve is labeled ‘pa’.

Here’s Lemere’s figure with the RLN and pararecurrent nerve highlighted for easier comparison. The pattern of axonal wiring here is the same as in humans–all the axons have the same connections at the brainstem end on one hand, and at the pharynx and larynx end on the other hand–but the bundling of axons into what we recognize as peripheral nerves is different.

Interestingly, Lemere (1932) mentioned that having the recurrent pathways split into two nerves was the most common pattern in dogs, but occasionally he saw a case in which all of the axons had been bundled into a single RLN that served both the larynx and the esophagus and trachea, as in humans.

Modified from Altounian et al. (2015: fig. 4).

That door of variation swings both ways: a few years ago in our lab, we had a cadaver in which the left RLN only went to the larynx, and the vagus fibers to the esophagus and trachea were carried in a second, variant nerve. I didn’t know what that nerve was for a long time, until I stumbled onto the work of Lemere. So it seems that two nerves is the usual pattern for dogs, with one nerve as a rare variant, and the opposite is true in humans. 

Incidentally, I didn’t find the variant nerve in our lab, my students did. We got as far as putting together a manuscript, which we posted as a preprint (here), but we haven’t gotten it formally published yet. One of my goals for this year is to get some of these old, stalled projects dusted off and properly published. Watch this space.

I also discussed the pararecurrent nerve in my “How to make new discoveries in (human) anatomy” talk from SVPCA 2019, which is also a PeerJ preprint (here).

Other posts on the recurrent laryngeal nerve, and on the peripheral nervous system in general:

References

Get your red-cyan glasses — you do have some, right? — and check out this glorious image. Best full-screen it, it’s worth seeing!

And here is the lame 2D version for those of you who have still not spent 99 lousy cents on a pair of 3D glasses:

What are we looking at here?

Well, the smaller skull at bottom left is my new badger, which we saw a couple of days ago. Since then it has dried out, and I was easily able to figure out which teeth belong where, and glue them in with a drop of wood glue. I’ll photograph it in more detail at some point, but for those of you who can’t wait, there’s always the TNF of my first badger skull.

On the right is, if I’m not mistaken, a sheep — specifically a ram, given the horns. I don’t actually remember this one’s origin story, but it’s been sitting on a box next to our oil tank for a couple of years, with the flesh bits slowly decaying off and the bone cleaning itself up the way nature intended. A couple of days ago I cleaned it up a bit with my trusty toothbrush to remove some bits of moss and lichen, then soaked it for a few hours in very dilute bleach. It’s dried out beautifully, and is very robust. It’s big, too.

Everything else you see belongs to a deer — I assume, based on the horn bases. This is another one recovered from the depths of time. Some years ago, I put it a big water-filled pan and left it outside and forgot about it. In that time, not only had all the meat rotted off the bones, but the water had clarified and everything in it had died, so it didn’t even smell particularly. When I took the bones out, they were a nasty brown colour and little soft, and I thought I was going to have to discard them all. But once they had dried out they seemed a little more robust — though still brown. Then I left them overnight in dilute bleach, and when they had dried from that, they were their present much more appealing whitish colour, so I think they’re going to be OK.

Most of the cranium is intact in a single piece, though some of the sutures are wobbly and will need stabilising with wood glue. The mandible is in two parts, but both seem in decent condition. Right at the bottom left of the photo is a shard of bone by the tip of the mandible: this is the left nasal, which flaked off, but should be repairable. Everything else is vertebrae: atlas right behind the skull, axis by the snout, C3 just above it, and damaged C4 just below the atlas.

When it’s been put together a bit more, I will post some better photos, and I’ll see if anyone can identify the species.

Last week, while Fiona and I were out walking, we noticed a decaying roadkill badger a bit over half a mile from our house. Yesterday we were out walking again, and we saw that it had decayed to the point where there was not much to the flesh at all. I prodded it with my foot and found that the skull was about ready to come away.

So when we got home, I popped straight back out in the car with some plastic bags which I used as improvised gloves, found the badger, managed to pull its head away from the remaining connective tissue (not a pleasant process) and bring it home. I simmered it gently for a couple of hours — outdoors on a portable hob, I’m not a barbarian — then cleaned it with a toothbrush left it to cool. Today I soaked it in a soapy water for a couple of hours, then rinsed it off and soaked it in very diluted bleach for a couple more, taking care to harvest all the loose teeth that came out during each stage. Finally I rinsed it off, and here it!

European badger Meles meles, skull in left lateral view, with teeth. Pound coin for scale.

What next? I’ll give it couple of days to dry properly, then figure out which teeth go in which sockets and glue them in place. Then, bam, I have a second badger skull to go with my first, and I’ll be in a position to directly compare two skulls of the same animal.

This is a really nice, quick process compared with most of my preparations. The trick is to find a carcass that has already gone through the nastier stages of decomposition.

Note that the jaw is articulated, by the way. Unlike most animals, the skull of the badger locks the jaw in place with unusual joints in which the mandibular fossa of the cranium wraps around the cylindrical articular condyles of the jaw. I’ll try to include photos next time.

I leave you with a cheap-and-cheerful 3D anaglyph of the skull. Did I ever mention that you should get some cheap 3D glasses? You should get some cheap 3D glasses.

Here’s an odd thing. Over and over again, when a researcher is mistreated by a journal or publisher, we see them telling their story but redacting the name of the journal or publisher involved. Here are a couple of recent examples.

First, Daniel A. González-Padilla’s experience with a journal engaging in flagrant citation-pumping, but which he declines to name:

Interesting highlight after rejecting a paper I submitted.
Is this even legal/ethical?
EDITOR-IN-CHIEF’S COMMENT REGARDING THE INCLUSION OF REFERENCES TO ARTICLES IN [REDACTED]
Please note that if you wish to submit a manuscript to [REDACTED] in future, we would prefer that you cite at least TWO articles published in our journal WITHIN THE LAST TWO YEARS. This is a polict adopted by several journals in the urology field. Your current article contains only ONE reference to recent articles in [REDACTED].

We know from a subsequent tweet that the journal is published by Springer Nature, but we don’t know the name of the journal itself.

And here is Waheed Imran’s experience of editorial dereliction:

I submitted my manuscript to a journal back in September 2017, and it is rejected by the journal on September 6, 2020. The reason of rejection is “reviewers declined to review”, they just told me this after 3 years, this is how we live with rejections. @AcademicChatter
@PhDForum

My, my question is, why in such situations do we protect the journals in question? In this case, I wrote to Waheed urging him to name the journal, and he replied saying that he will do so once an investigation is complete. But I find myself wondering why we have this tendency to protect guilty journals in the first place?

Thing is, I’ve done this myself. For example, back in 2012, I wrote about having a paper rejected from “a mid-to-low ranked palaeo journal” for what I considered (and still consider) spurious reasons. Why didn’t I name the journal? I’m not really sure. (It was Palaeontologia Electronica, BTW.)

In cases like my unhelpful peer-review, it’s not really a big deal either way. In cases like those mentioned in the tweets above, it’s a much bigger issue, because those (unlike PE) are journals to avoid. Whichever journal sat on a submission for three years before rejecting it because it couldn’t find reviewers is not one that other researchers should waste their time on in the future — but how can they avoid it if they don’t know what journal it is?

So what’s going on? Why do we have this widespread tendency to protect the guilty?

Update (13 September 2021)

One year later, Waheed confirms that the journal in question not only did not satisfactorily resolve his complaint, it didn’t even respond to his message. At this stage, there really is no point in protecting the journal that has behaved so badly, so Waheed outed it: it’s Scientia Iranica. Avoid.

You! Shall not! Pass!

August 22, 2020

OK, technically this is MB.R.3822, a dorsal vertebra of Giraffatitan brancai formerly known as HMN Ar1, in posterior view, rendered from a 3D scan provided by Heinrich Mallison.

But you can’t tell me that when you look at that you don’t see Gandalf shouting at a balrog.

For reasons that I will explain in a later post, I am parting with one of my most treasured possessions: the badger skull that I extracted from my roadkill specimen four years ago.

As a farewell, I finally photographed it properly from all the cardinal directions, and prepared this multiview:

Don’t forget to click though for the full resolution version!

Here’s one of my most prized possessions: a cannon bone from a giraffe. I got it last fall from Necromance, a cool natural history store in LA. Originally they had a matched pair on display in the front window. Jessie Atterholt got one of them last summer, and I got the other a few months later.

The cannon bones of hoofed mammals consist of fused metacarpals (in the forelimbs) or metatarsals (in the hindlimbs). In this case, the giraffe cannon bone in the top photo is the one from the right forelimb, consisting of the fused 3rd and 4th metacarpals, which correspond to the bones in the human hand leading to the middle and ring fingers. Only my third metacarpal is traced in the top photo. For maximum homology goodness I should have traced MC4, too, but I’m lazy.

I didn’t know that this was a right forelimb cannon bone when I got it. In fact, I only figured that out this afternoon, thanks to the figures and text descriptions in Rios et al. (2016), which I got free through Palaeontologia Electronica (you can too). The weirdly large and perfectly circular holes at the ends of my cannon bone were clearly drilled out by somone, I guess maybe for mounting purposes? At first I thought it might have been to help the marrow cook out of the shaft of the bone during simmering and degreasing, but none of the drilled holes intersect the main marrow cavity, they’re just in the sponge of trabecular bone at the ends of the element.

This post is a sequel to one from last year, “Brachiosaurus and human metacarpals compared“, which featured metacarpal 3 from BYU 4744, the partial skeleton of Brachiosaurus from Potter Creek, Colorado. I know what everyone’s thinking: can we make these two high-browsing giants throw hands?

Yes, yes we can. The giraffe cannon bone is 75.5cm long, and the brachiosaur metacarpal is 57cm long, or 75.5% the length of the giraffe element. I scaled the two bones correctly in the above image. My hands aren’t the same size because they’re at different distances from the camera, illustrating the age-old dictum that scale bars are not to be trusted.

The Potter Creek brachiosaur is one of the largest in the world–here’s me with a cast of its humerus–but ‘my’ giraffe is not. World-record giraffes are about 19 feet tall (5.8m), and doing some quick-and-dirty cross-scaling using the skeleton photo above suggests that the metacarpal cannon bone in a world-record giraffe should be pushing 90cm. So the giraffe my cannon bone is from was probably between 15.5 and 16 feet tall (4.7-4.9m), which is still nothing to sniff at.

I don’t know how this bone came to be at Necromance. I assume from an estate sale or something. I only visited for the first time last year, and at that time they had three real bones from giraffes out in the showroom: the two cannon bones and a cervical vertebra. They might have put out more stuff since–it’s been about six months since I’ve been there–but all of the giraffe bones they had at that point have been snapped up by WesternU anatomists. Jessie and I got the cannon bones, and Thierra Nalley got the cervical vertebra, which is fair since she works on the evolution of necks (mostly in primates–see her Google Scholar page here). I don’t know if there are any photos of Thierra’s cervical online, but Jessie did an Instagram post on her cannon bone, which is nearly as long as her whole damn leg.

There will be more anatomy coming along soon, and probably some noodling about sauropods. Stay tuned!

Reference

Ríos M, Danowitz M, Solounias N. 2016. First comprehensive morphological analysis on the metapodials of Giraffidae. Palaeontologia Electronica 19(3):1–39.

 

 

As I was figuring out what I thought about the new paper on sauropod posture (Vidal et al. 2020) I found the paper uncommonly difficult to parse. And I quickly came to realise that this was not due to any failure on the authors’ part, but on the journal it was published in: Nature’s Scientific Reports.

A catalogue of pointless whining

A big part of the problem is that the journal inexplicably insists on moving important parts of the manuscript out of the main paper and into supplementary information. So for example, as I read the paper, I didn’t really know what Vidal et al. meant by describing a sacrum as wedged: did it mean non-parallel anterior and posterior articular surfaces, or just that those surfaces are not at right angles to the long axis of the sacrum? It turns out to be the former, but I only found that out by reading the supplementary information:

The term describes marked trapezoidal shape in the
centrum of a platycoelous vertebrae in lateral view or in the rims of a condyle-cotyle (procoelous or opisthocoelous) centrum type.

This crucial information is nowhere in the paper itself: you could read the whole thing and not understand what the core point of the paper is due to not understanding the key piece of terminology.

And the relegation of important material to second-class, unformatted, maybe un-reviewed supplementary information doesn’t end there, by a long way. The SI includes crucial information, and a lot of it:

  • A terminology section of which “wedged vertebrae” is just one of ten sub-sections, including a crucial discussion of different interpretation of what ONP means.
  • All the information about the actual specimens the work is based on.
  • All the meat of the methods, including how the specimens were digitized, retro-deformed and digitally separated.
  • How the missing forelimbs, so important to the posture, were interpreted.
  • How the virtual skeleton was assembled.
  • How the range of motion of the neck was assessed.
  • Comparisons of the sacra of different sauropods.

And lots more. All this stuff is essential to properly understanding the work that was done and the conclusions that were reached.

And there’s more: as well as the supplementary information, which contains six supplementary figures and three supplementary tables, there is an additonal supplementary supplementary table, which could quite reasonably have gone into the supplementary information.

In a similar vein, even within the highly compressed actual paper, the Materials and Methods are hidden away at the back, after the Results, Discussion and Conclusion — as though they are something to be ashamed of; or, at best, an unwelcome necessity that can’t quite be omitted altogether, but need not be on display.

Then we have the disappointingly small illustrations: even the “full size” version of the crucial Figure 1 (which contains both the full skeleton and callout illustrations of key bones) is only 1000×871 pixels. (That’s why the illustration of the sacrum that I pulled out of the paper for the previous post was so inadequate.)

Compare that with, for example, the 3750×3098 Figure 1 of my own recent Xenoposeidon paper in PeerJ (Taylor 2018) — that has more than thirteen times as much visual information. And the thing is, you can bet that Vidal et al. submitted their illustration in much higher resolution than 1000×871. The journal scaled it down to that size. In 2020. That’s just crazy.

And to make things even worse, unrelated images are shoved into multi-part illustrations. Consider the ridiculousness of figure 2:

Vidal et al. (2020: figure 2). The verticalization of sauropod feeding envelopes. (A) Increased neck range of motion in Spinophorosaurus in the dorso-ventral plane, with the first dorsal vertebra as the vertex and 0° marking the ground. Poses shown: (1) maximum dorsiflexion; (2) highest vertical reach of the head (7.16 m from the ground), with the neck 90° deflected; (3) alert pose sensu Taylor Wedel and Naish13; (4) osteological neutral pose sensu Stevens14; (5) lowest vertical reach of the head (0.72 m from the ground at 0°), with the head as close to the ground without flexing the appendicular elements; (6) maximum ventriflexion. Blue indicates the arc described between maximum and minimum head heights. Grey indicates the arc described between maximum dorsiflexion and ventriflexion. (B) Bivariant plot comparing femur/humerus proportion with sacrum angle. The proportion of humerus and femur are compared as a ratio of femur maximum length/humerus maximum length. Sacrum angle measures the angle the presacral vertebral series are deflected from the caudal series by sacrum geometry in osteologically neutral pose. Measurements and taxa on Table 1. Scale = 1000 mm.

It’s perfectly clear that parts A and B of this figure have nothing to do with each other. It would be far more sensible for them to appear as two separate figures — which would allow part B enough space to convey its point much more clearly. (And would save us from a disconcertingly inflated caption).

And there are other, less important irritants. Authors’ given names not divulged, only initials. I happen to know that D. Vidal is Daniel, and that J. L. Sanz is José Luis Sanz; but I have no idea what the P in P. Mocho, the A in A. Aberasturi or the F in F. Ortega stand for. Journal names in the bibliography are abbreviated, in confusing and sometimes ludicrous ways: is there really any point in abbreviating Palaeogeography Palaeoclimatology Palaeoecology to Palaeogeogr. Palaeoclimatol. Palaeoecol?

The common theme

All of these problems — the unnatural shortening that relagates important material into supplementary information, the downplaying of methods, the tiny figures that ram unrelated illustrations into compound images, even the abbreviating of author names and journal titles — have this in common: that they are aping how Science ‘n’ Nature appear in print.

They present a sort of cargo cult: a superstitious belief that extreme space pressures (such as print journals legitimately wrestle with) are somehow an indicator of quality. The assumption that copying the form of prestigious journals will mean that the content is equally revered.

And this is simply idiotic. Scientific Reports is an open-access web-only journal that has no print edition. It has no rational reason to compress space like a print journal does. In omitting the “aniel” from “Daniel Vidal” it is saving nothing. All it’s doing is landing itself with the limitations of print journals in exchange for nothing. Nothing at all.

Why does this matter?

This squeezing of a web-based journal into a print-sized pot matters because it’s apparent that a tremendous amount of brainwork has gone into Vidal et al.’s research; but much of that is obscured by the glam-chasing presentation of Scientific Reports. It reduces a Pinter play to a soap-opera episode. The work deserved better; and so do readers.

References