Two days ago, I wrote about what seemed to be an instance of peer review gone very wrong. I’ve now heard from two of the four authors of the paper and from the reviewer in question — both by email, and in comments on the original post — and it’s apparent that I misinterpreted the situation. When the lead author’s tweet mentioned “pushing it through eight rounds of review”, I took this at face value as meaning eight rounds at the same journal with the same reviewers — whereas in fact the reviewer in question reviewed only four drafts. (That still seems like too many to me, but clearly it’s not as ludicrous as the situation as I misread it.) In this light, my assumption that the reviewer was being obstructive was not warranted.

I have decided to retract that article and I offer my apologies to the reviewer, Dave Grossnickle, who approached me very politely off-list to offer the corrections that you can now read in his comment.

THIS POST IS RETRACTED. The reasons are explained in the next post. I wish I had never posted this, but you can’t undo what is done, especially on the Internet, so I am not deleting it but marking it as retracted. I suggest you don’t bother reading on, but it’s here if you want to.

 


Neil Brocklehurst, Elsa Panciroli, Gemma Louise Benevento and Roger Benson have a new paper out (Brocklehurst et al. 2021, natch), showing that the post-Cretaceous radiation of modern mammals was not primarily due to the removal of dinosaurs, as everyone assumed, but of more primitive mammal-relatives. Interesting stuff, and it’s open access. Congratulations to everyone involved!

Neil Brocklehurt’s “poster” explaining the new paper in broad detail. From the tweet linked below.

Neil summarised the new paper in a thread of twelve tweets, but it was the last one in the thread that caught my eye:

Thanks to all my co-authors for their tireless work on this, pushing it through eight rounds of review (my personal best)

I’m impressed that Neil has maintained his equanimity about this — in public at least — but if he is not going to be furious about it then we, the community, need to be furious on his behalf. Pushed to explain, Neil laid it out in a further tweet:

Was just one reviewer who really didn’t seem to like certain aspects, esp the use of discrete character matrices. Fair enough, can’t please everyone, but the editor just kept sending it back even when two others said our responses to this reviewer should be fine.

Again, somehow this tweet is free of cursing. He is a better man than I would be in that situation. He also doesn’t call out the reviewer by name, nor the spineless handling editor, which again shows great restraint — though I am not at all sure it’s the right way to go.

There is so, so much to hate about this story:

  • The obstructive peer reviewer, who seems to have to got away with his reputation unblemished by these repeated acts of vandalism. (I’m assuming he was one of the two anonymous reviewers, not the one who identified himself.)
  • The handling editor who had half a dozen opportunities to put an end to the round-and-round, and passed on at least five of them. Do your job! Handle the manuscript! Don’t just keep kicking it back to a reviewer who you know by this stage is not acting in good faith.
  • The failure of the rest of the journal’s editorial board to step in and bring some sanity to the situation.
  • The normalization of this kind of thing — arguably not helped by Neil’s level-headed recounting of the story as though it’s basically reasonable — as someting authors should expect, and just have to put up with.
  • The time wasted: the other research not done while the authors were pithering around back and forth with the hostile reviewer.

It’s the last of these that pains me the most. Of all the comforting lies we tell ourselves about conventionl peer review, the worst is that it’s worth all the extra time and effort because it makes the paper better.

It’s not worth it, is it?

Maybe Brocklehurst et al. 2021 is a bit better for having gone through the 3rd, 4th, 5th, 6th, 7th and 8th rounds of peer review. But if it is, then it’s a marginal difference, and my guess is that in fact it’s no better and no worse that what they submitted after the second round. All that time, they could have been looking at specimens, generating hypotheses, writing descriptions, gathering data, plotting graphs, writing blogs, drafting papers — instead they have been frittering away their time in a pointless and destructive conflict with someone whose only goal was to prevent the advancement of science because an aspect of the paper happened to conflict with a bee he had in his bonnet. We have to stop this waste.

This incident has reinforced my growing conviction that venues like Qeios, Peer Community in Paleontology and BiorXiv (now that it’s moving towards support for reviewing) are the way to go. Our own experience at Qeios has been very good — if it works this well the next time we use it, I think think it’s a keeper. Crucially, I don’t believe our paper (Taylor and Wedel 2021) would have been stronger if it had gone through the traditional peer-review gauntlet; instead, I think it’s stronger than it would have been, because it’s received reviews from more pairs of eyes, and each of them with a constructive approach. Quicker publication, less work for everyone involved, more collegial process, better final result — what’s not to like?

References

Anatomical features of the neural canal in birds and other dinosaurs. A. MWC 9698, a mid caudal vertebra of Apatosaurus in posterodorsal view. Arrows highlight probable vascular foramina in the ventral floor of the neural canal. B. LACM 97479, a dorsal vertebra of Rhea americana in left anterolateral view. Arrows highlight pneumatic foramina inside the neural canal. C. A hemisected partial synsacrum of a chicken, Gallus domesticus, obtained from a grocery store. Anterior is to the right. The bracket shows the extent of the dorsal recess for the glycogen body, which only spans four vertebrae. Arrows highlight the transverse grooves in the roof of the neural canal for the lumbosacral organ. D. Sagittal (left) and transverse (right) CT slices through the sacrum of a juvenile ostrich, Struthio camelus. The bracket shows the extent of the lumbosacral expansion of the spinal cord. Indentations in the roof of the neural canal house the lumbosacral organ. In contrast to the chicken, the ostrich has a small glycogen body that does not leave a distinct osteological trace. Yellow arrows show the longitudinal troughs in the ventral floor of the neural canal that house the ventral eminences of the spinal cord. Wedel et al. (2021: fig. 4).

This is the second in a series of posts on our new paper about the expanded neural canals in the tail vertebrae of the Snowmass Haplocanthosaurus. I’m not going to talk much about Haplo in this post, though. Instead, I’m going to talk about chickens, and about how you can see a lot of interesting spinal anatomy in a living dinosaur for about two bucks.

You know by now that Academia Letters publishes peer reviews, which is one of the things that drew me to this fairly new journal. More on that in a later post, but in the meantime, the peer reviews for the Haplo paper are on the right sidebar here. I confess, I had a total forehead-slap moment when I read the opening lines of Niels Bonde’s review: 

This paper is interesting, and should be published and discussed by others with interest in dinosaur-bird relations. However, as these publications are also meant for the general public, I would recommend that 2 – 3 illustrations were added of the features mentioned for birds under nos. 3 – 6, because the general public (and many paleontologists) have no ideas about these structures, and what they look like.

The original submission only had figures 1 and 2. And this request is totally fair! If you are going to discuss six alternative hypotheses for some mysterious anatomical structure, it’s just responsible reporting to illustrate those things. That goes double if, as Niels Bonde noted, the anatomy in question is unfamiliar to a lot of people, even many paleontologists. Huxley’s quote after first reading Darwin’s Origin of Species flashed through my head: “How extremely stupid not to have thought of that.”

Slide 21 of my 2014 SVPCA talk on supramedullary diverticula in birds and other dinosaurs, illustrating pneumatic foramina in the roof, walls, and floor of the neural canal.

At the time I read that review, I already had images illustrating five of the six hypotheses. A juvenile ostrich synsacrum that Jessie Atterholt and I had CT scanned gave us three of them all by itself: the lumbosacral expansion of the spinal cord to run the hindlimbs, as in all limbed tetrapods and in some fish with sensitive fins; the transverse channels in the dorsal wall of the neural canal to accommodate the lumbosacral balance organ; and the paired troughs in the floor of the neural canal that house the ventral eminences of the spinal cord (Figure 4D in the image at the top of this post). I had good photos of pneumatic foramina in the walls and floor of the neural canal in a dorsal vertebra of a rhea from my 2014 SVPCA talk (Figure 4B), and some photos of small foramina, presumably for blood vessels rather than air spaces, in the floor of the neural canal in a caudal vertebra of Apatosaurus (Figure 4A).

What I did not have is a photo illustrating the fairly abrupt, dome-shaped space in the sacral neural canal that houses the glycogen body of birds. I mean, I had published images, but I didn’t want to wrestle with trying to get image reproduction rights, or with redrawing the images. Instead, I went to the grocery store to buy some chicken.

I don’t know how universally true this is, but IME in the US when you buy a quartered chicken, the vertebrae are usually nicely hemisected by the band saw that separated the left and right halves of the animals. So you can see the neural canal in both the dorsal and sacral parts of the vertebral column. Here are the hemisected dorsal vertebrae in the breast quarter from a sectioned rotisserie chicken:

That’s just how it came to lie on my plate, but it’s not in anatomical position. Let’s flip it over to sit upright:

And label it:

I could and probably should do a whole post just unpacking this image, but I have other fish to fry today, so I’ll just note a couple of things in passing. The big interspinous ligament is the same one you can see in transverse section in the ostrich dissection photos in this post and this one. Also, the intervertebral joints heading toward the neck, on the left of the image, have much thicker intervertebral cartilage than the more posterior dorsals. That’s because the posterior ones were destined to fuse into a notarium. You can see a diagram and a photograph of a chicken notarium in figures 4 and 5, respectively, here. And finally, the big takeaway here is that the neural canal is normal, just a cylindrical tube to hold the spinal cord.

The thigh quarter usually has the pelvis and the hemisectioned synsacrum attached. Here’s a lateral view of the left half of the pelvis and synsacrum:

And the same thing labeled:

And now flipped around so we can see it in medial view:

And now that image labeled:

And, hey, there are three of our alternative hypotheses on display: the long (many vertebral segments) lumbosacral expansion of the spinal cord, which is reflected in a gradually expanded neural canal in the synsacrum; the shorter, higher dome-shaped recess for the glycogen body; and finally the transverse spaces for the lumbosacral balance organ.

As a refresher, there’s nothing terribly special about the lumbosacral expansion of the spinal cord — you have one, labeled as the ‘lumbar enlargement’ in the above diagram. Where the spinal cord has adjacent limbs to run, it has more neurons, so it gets fatter, so the neural canal gets fatter to accommodate it. The cord itself doesn’t look very expanded in the chicken photo above, but that chicken has been roasted rotisserie-style, and a lot of lipids probably cooked out of the cord during that process. What’s more important is that the neural canal is subtly but unmistakably expanded, over the span of many vertebrae.

The lumbosacral spinal cord of a 3-week-old chick in dorsal view. The big egg-shaped mass in the middle is the glycogen body. Watterson (1949: plate 1).

That’s in contrast to the recess for the glycogen body, which is colored in blue in the chicken photo. Glycogen bodies, like the egg-shaped one in the young chicken in the image immediately above, tend not to go on for many vertebral segments. Instead they balloon up and subside over the space of just 4 or 5 vertebrae, so they leave a different skeletal trace than other soft tissues.

Finally, there are the transverse spaces for the lumbosacral balance organ, which I discussed in this post. Those are the things that look like caterpillar legs sticking up from the sacral endocasts in the above figure from Necker (2006). In life, the spaces are occupied by loops of meningeal membranes, through which cerebrospinal fluid can slosh around, which in turn puts pressure on mechanoreceptive cells at the edge of the spinal cord and gives birds a balance organ in addition to the ones in their heads. In the photo of the cooked chicken, the delicate meninges have mostly fallen apart, leaving behind the empty spaces that they once occupied.

I really liked that chicken synsacrum, and I wanted to use it as part of Figure 4 of the new paper, but it needed a little cleaning, so I simmered it for a couple of hours on low heat (as one does). And it promptly fell apart. At least in the US, most of the chickens that make it to table are quite young and skeletally immature. That particular bird’s synsacrum wasn’t syn-anything, it was just a train of unfused vertebrae that fell apart at the earliest opportunity. I had anticipated that might be an issue, so I’d gotten a lot of chicken, including a whole rotisserie chicken and four thigh quarters from the deli counter at the local supermarket. Happily this fried chicken thigh quarter had a pretty good neural canal:

And it cleaned up nicely:

And with a little cropping, color-tuning, and labeling, it was ready for prime time:

I didn’t label them in the published version, for want of space and a desire not to muddy the waters any further, but the jet-black blobs I have colored in the lower part of that image are the exit holes that let the spinal nerves out of the neural canal so they could go serve the hindlimbs, pelvic viscera, and tail. We have them, too.

At my local grocery store, a fried chicken thigh costs about $1.65 if you get it standalone, or you can buy in bulk and save. You get to eat the chicken, and everything else I’ve done here required only water, heat, soap, and a little time. The point is that if I can do this, you can do this, and if you do, you’ll get to see some really cool anatomy. I almost added, “which most people haven’t seen”, but given how much chicken we eat as a society these days, probably most people’s eyes have fallen on the medial surface of a cooked chicken thigh quarter at one time or another. Better to say, “which most people haven’t noticed”. But now you can. Go have fun. 

Way back in January of 2019, I finished up “Things to Make and Do, Part 25b” with this line: “I have one more thing for you to look for in your bird vertebrae, and that will be the subject of the next installment in this series. Stay tuned!” Here we are, 2.3 years later, and I’ve finally made good. So if there’s a promised post you’ve been waiting for, stick around, we may get to it yet.

References

A. Recovered skeletal elements of Haplocanthosaurus specimen MWC 8028. B. Caudal vertebra 3 in right lateral view. C. The same vertebra in posterior view. Lines show the location of sections for D and E. D. Midsagittal CT slice. The arrow indicates the ventral expansion of the neural canal into the centrum. E. Horizontal CT slice at the level of the neural arch pedicles, with anterior toward the top. Arrows indicate the lateral expansions of the neural canal into the pedicles. B-E are shown at the same scale. Wedel et al. (2021: fig. 1).

New paper out today:

Wedel, Mathew; Atterholt, Jessie; Dooley, Jr., Alton C.; Farooq, Saad; Macalino, Jeff; Nalley, Thierra K.; Wisser, Gary; and Yasmer, John. 2021. Expanded neural canals in the caudal vertebrae of a specimen of Haplocanthosaurus. Academia Letters, Article 911, 10pp. DOI: 10.20935/AL911 (link)

The paper is new, but the findings aren’t, particularly. They’re essentially identical to what we reported in our 1st Paleo Virtual Conference slide deck and preprint, and in the “Tiny Titan” exhibit at the Western Science Center, just finally out in a peer-reviewed journal, with better figures. The paper is open access and free to the world, and it’s short, about 1600 words, so this recap will be short, too.

A. Photograph of a 3D-printed model of the first three caudal vertebrae of Haplocanthosaurus specimen MWC 8028, including endocasts of the neural canal (yellow) and intervertebral joints (blue), in right lateral view, and with the neural canal horizontal. B. Diagram of the same vertebrae in midsagittal section, emphasizing the volumes of the neural canal (yellow) and intervertebral joint spaces (blue). Anterior is to the right. Wedel et al. (2021: fig. 2).

John Foster and I described Museum of Western Colorado (MWC) specimen 8028, a partial skeleton of Haplocanthosaurus from Snowmass, Colorado, in late 2014. One weird thing about that specimen (although not the only weird thing) is that the neural canals of the tail vertebrae are bizarrely expanded. In most vertebrae of most critters, the neural canal is a cylindrical tunnel, but in these vertebrae the neural canals are more like spherical vacuities.

John and I didn’t know what to make of that back in 2014. But a few years later I started working with Jessie Atterholt on bird anatomy, which led me to do a little project on the whole freaking zoo of weird stuff that birds and other dinosaurs do with their neural canals, which led to the 1PVC presentation, which led to this. 

Caudal vertebra 3 of Haplocanthosaurus specimen MWC 8028 in left posterolateral (A), posterior (B), and right posterolateral (C) views, with close-ups (D and E). In A and B, a paintbrush is inserted into one of the lateral recesses, showing that the neural canal is wider internally than at either end. Wedel et al. (2021: fig. 3).

Of course there will be more posts and more yapping, as signaled by the ‘Part 1’ in the post title. Although I am extremely satisfied with the streamlined, 1600-word missile of information and reasoning that just dropped, there are parts that I want to unpack, that haven’t been unpacked before. But the paper launched at midnight-thirty, Pacific Daylight Time, I’m up way too late finishing this first post, and I reckon the rest will keep for a few hours at least.

Anatomical features of the neural canal in birds and other dinosaurs. A. MWC 9698, a mid caudal vertebra of Apatosaurus in posterodorsal view. Arrows highlight probable vascular foramina in the ventral floor of the neural canal. B. LACM 97479, a dorsal vertebra of Rhea americana in left anterolateral view. Arrows highlight pneumatic foramina inside the neural canal. C. A hemisected partial synsacrum of a chicken, Gallus domesticus, obtained from a grocery store. Anterior is to the right. The bracket shows the extent of the dorsal recess for the glycogen body, which only spans four vertebrae. Arrows highlight the transverse grooves in the roof of the neural canal for the lumbosacral organ. D. Sagittal (left) and transverse (right) CT slices through the sacrum of a juvenile ostrich, Struthio camelus. The bracket shows the extent of the lumbosacral expansion of the spinal cord. Indentations in the roof of the neural canal house the lumbosacral organ. In contrast to the chicken, the ostrich has a small glycogen body that does not leave a distinct osteological trace. Yellow arrows show the longitudinal troughs in the ventral floor of the neural canal that house the ventral eminences of the spinal cord. Wedel et al. (2021: fig. 4).

I have a ton of people to thank. John Foster, obviously, for initiating the line of research that led here. Julia McHugh for access to the MWC collections, and for being an excellent sounding board regarding the Morrison Formation, sauropod dinosaurs, and crafting ambitious but tractable research projects. Anne Weil for helping me be methodical in thinking through the logic of the paper, and Mike Taylor for helping me get it polished. Niels Bonde, Steven Jasinski, and David Martill for constructive reviews, which were published alongside the paper. We couldn’t take all of their suggestions because of space limitations, but figures 3 and 4 were born because they asked for them, and that’s not a small thing. Vicki and London Wedel for putting up with me at various points in this project, especially in the last few days as I’ve been going bonkers correcting page proofs. And finally, because I’m the one writing this blog post, my coauthors: Jessie Atterholt, Alton Dooley, Saad Farooq, Jeff Macalino, Thierra Nalley, Gary Wisser, and John Yasmer, for their contributions and for their patience during the unusually long gestation of this very short paper.

More to say about all that in the future. For now, yay, new paper. Have fun with it. Here’s the link again.

References

I have several small ordered sequences of data, each of about five to ten elements. For each of them, I want to calculate a metric which captures how much they vary along the sequence. I don’t want standard deviation, or anything like it, because that would consider the sequences 1 5 2 7 4 and 1 2 4 5 7 equally variable, whereas for my purposes the first of these is much more variable.

Here is a matric that I think does what I want, and will allow me to compare different sequences for variability-along-the-sequence.

For the n-1 pairs along the sequence of n elements, I take the difference (absolute value, so always positive) between elements i and i+1. Then I average all those differences. Then I divide the result by the average of the values themselves, to normalise for magnitude.

Some example calculations:

  • For the sequence 1 5 2 7 4, the differences are 4 3 5 3, for a total of 15 and an average of 3.75. The average of the values is 1+5+2+7+4 = 19/5 = 3.8, which gives me a metric of 3.75/3.8 = 0.987.
  • For the sequence 1 2 4 5 7, the differences are 1 2 1 2, for a total of 6 and an average of 1.5. The average of the values is again 3.8, which gives me a metric of 1.5/3.8 = 0.395.
  • So the first sequence is 0.987/0.395 = 2.5 times as sequentially variable as the second sequence.
  • And for the sequence 10 20 40 50 70 (which is the same as the previous one, but all values ten times greater), the differences are 10 20 10 20, for a total of 60 and an average of 15. The average of the values is 38, which gives me a metric of 15/38 = 0.395, the same as before — which is as it should be.

And now, my question! Does this metric, or something similar, already exist? If so, what is it called? Or if I should be using something else instead, what is it?

(It happens that my sequences are the aspect ratios of the cotyles of consecutive vertebrae, but that’s not important: whatever metric we land on should work for any sequences.)

Taylor 2015: Figure 8. Cervical vertebrae 4 (left) and 6 (right) of Giraffatitan brancai lectotype MB.R.2180 (previously HMN SI), in posterior view. Note the dramatically different aspect ratios of their cotyles, indicating that extensive and unpredictable crushing has taken place. Photographs by author.

Back in 2017, I showed the world 83.33% of my collection of sauropod-themed mugs. Time passes, and I have lost some of them and gained some more. The tally now stands at eight, and here they are:

My missing Brontomerus mug never did turn up. In the mean time, I have also lost or maybe broken the Sauroposeidon mug, the old black-and-white Archbishop mug, and the single-view Xenoposeidon mug. The dissertation mug still survives, but has faded into total illegibility, so I don’t count it any more.

On the more positive side, the sexual selection mug — second from the right in the old photo, and bottom left in the new one — survives, in fact the only one to have done so. All the others are new acquisitions. Let’s take a look:

Back row, left to right:

  1. The new, improved Archbishop dorsals A and B mug. Unlike the original, this is in glorious colour, and rearranges the elements to show anterior view on the front, and left and right lateral on the sides.
  2. The new, improved Xenoposeidon mug. It’s laid out the same way with the anterior view on the front and left and right lateral views on the sides.
  3. One that Fiona made for my birthday, showing one of the publicity photos from the original Xenoposeidon description: the one of which a newspaper columnist wrote “I wish my husband looked at me the way he looks at this bone”.
  4. A mug made by Mark Witton, which I saw at TetZooCon 2019 and made him an offer for. It shows his own Diplodocus artwork, an update of an earlier piece that he did for Matt, Darren and me to publicise our 2009 paper on sauropod neck posture. (Details here.)

Front row, left to right:

  1. The sole survivor, showing the introductory here’s-what-sauropod-necks-are-like illustration from our 2011 paper on why those necks were not sexually selected.
  2. The sauropod neck gallery used as Figure 3 in my and Matt’s 2013 PeerJ paper “why giraffes have short necks”.
  3. One of the world’s few caudal pneumaticity mugs, using all the illustrations from Matt’s and my 2013 paper, and inspired by the freakily consistent colour palette of those illustrations.
  4. This one needs a bit of explaining. See below.

For reasons that no-one — least of all he — understands, my youngest son bought a pair of Dawn French mugs as a birthday or Christmas present for Fiona. (No-one in our family is particularly a fan, it was one of those random things.) Since then, he has given her five or six more identical mugs.

Because I do not like these, I insist that they hang on one mug tree, and the sauropod mugs on another. It was to break down this mug apartheid that our eldest made for us this final mug, which shows both Dawn French and a reconstruction of the Xenoposeidon vertebra (from my 2018 paper). Where does it live? Usually, it sits on the shelf between the two mug trees.

So this is how things stand. (I drink a lot of tea, so these mugs all see plenty of action.) I really should make myself a new Brontomerus mug, and perhaps a pneumatic variation one.

Here’s Easty dirty, with a dull-looking shell and a pretty serious ‘tub ring’ of hard-water stains around the crown of her carapace. This shot is a few years old, but she looks about the same now when she’s filthy. But here’s how she cleans up:

On Saturday I gave her a good soak in some warm distilled water and scrubbed her shell with a toothbrush. She shined up beautifully. I should have tried shooting a video, because the keratinous scutes on her shell are a bit translucent, and when full sunlight hits them they take on a depth and luster that I had not previously appreciated (heh).

I shot some reference images in the cardinal directions. If you need dorsal, lateral, or ventral views of an adult female Three-toed box turtle, Terrapene carolina triunguis, it’s your lucky day.

The lateral view is interesting, because you can clearly see the joint between the two halves of her plastron, both of which can raise like drawbridges to completely seal her behind an impenetrable wall of bone and keratin. You can also tell that her posterior plastron is gently convex, which is a female trait. As in many other turtles, male box turtles tend to have at least a gently concave posterior plastron, to help them stay on top of the females during mating.

And a ventral view, giving a good look at her plastron. Note her tiny, tiny tail, with the swelling for the vent just visible in the shadow of the plastron, about even with the edge of the carapace — that’s another female trait, whereas males have longer tails and a more distal vent for mating. You can also see yellow lines cutting across some of the scutes of her plastron — those are the outlines of her plastral bones showing through the overlying keratin. As in carapace, the keratinous scutes overlap the edges of the bones to form a sort of biological plywood. A lot of the growth lines have been worn off of her plastron, which is totally normal, but for the most part you can tell where the growth centers were originally located.

I also gave baby turtle a proper bath, with supervision. Baby box turtles can swim just fine, but if the water is inconveniently deep they can sometimes get flipped over on their backs, be unable to right themselves, and drown. She really did not like not having something to haul out on, so I put in the black jar lid you see in the photo. This particular pic is overexposed, which was a happy accident, because now you can see that the apparently dark and featureless areas of her shell and head are in fact very intricately patterned (compare to her dry photo at the top of this post). I’m really looking forward to seeing how her colors come in over the next few years.

And here’s her plastron. Baby turtle is a different subspecies from Easty — she’s a true Eastern box turtle, Terrapene carolina carolina — so she should have stronger patterns on both her carapace and her plastron when she gets bigger. Her head my also be more vibrantly colored, although Easty is no slouch in that department.

I put the two of them next to each other for a very closely-supervised comparison shot. I had been worried that Easty might have a go at baby turtle, but actually the opposite was true. The wee monster frankly terrorized Easty by nipping at her toes –and this was after eating two small slugs from the back yard — so I brought that experiment to a swift end, and got nipped on the finger for my trouble. I happened to be filming when baby turtle nipped Easty’s toe and my finger, and I will try to get those videos cleaned up and posted soon. Watch this space.

Click to embiggen. Trust me on this.

What I think of as our phylogenetically-extended nuclear family grew by one this week: we got a baby box turtle. We got her from a local hobbyist, who hatched her last summer. We haven’t named her yet, so for now she’s just Baby Tiny Turtle. Unlike Easty, who is the three-toed subspecies, Terrapene carolina triunguis, baby turtle is an Eastern box turtle sensu stricto, Terrapene carolina carolina, so she might end up being quite colorful (f’rinstance). She already has pretty complex patterns of lines and spots on the sides and top of her head and on her beak, but she’s so small that you can’t really see them unless you take a photo and zoom in.

(Aside: how do we know she’s a she and not a he? Personally I’d be lost, but the guy who hatched her says that at this age he can sex the babies correctly about 80% of the time, based on the position of the cloaca — it’s farther from the base of the tail in males. If she turns out to be a he, we’ll love him just the same, we’ll just keep him away from Easty.)

Speaking of her size, here’s an obligatory random-objects-for-scale photo. Baby turtle was closer in size to that US quarter when she hatched. You can tell that she’s grown a bit already because each scute on her shell has a outer rim of smooth new keratin. It’s a bit bittersweet, because I want her to grow big and strong and healthy, but I will miss the tiny turtle days when she is bigger. 

If you just want to die of cuteness, watch this video of her trying to eat some banana. She got it all down eventually, but with a little more adventure than either of us expected. If you turn up the volume, you can hear me talking her through it. That was entirely for my benefit, because I’m a big ole softy who talks to animals a lot, and she got through just fine on her own.

Full bulletins as events warrant.

The early armored fish Bothriolepis, which Yara Haridy affectionately refers to as a “beetle mermaid”. Art by Brian Engh, dontmesswithdinosaurs.com.

If I had to sum up my main research program over the past 20+ years, it would be, “Why pneumatic bone?” Or as I typically put it in my talks, most bone has marrow inside, so if you find bone with air inside, someone has some explaining to do (f’rinstance).

One of the reasons I like hanging out with Yara Haridy is that she is interested in an even more fundamental question: “Why bone?” And also “How bone?” And she has a paper out today that gives us new insights into the form and function of bone cells — osteocytes — in some of the earliest vertebrates that had them (Haridy et al. 2021; if you’re in TL;DR mode, here’s the link). 

Bones have multiple functions in vertebrate bodies: they’re a mechanical framework for our muscles, and a mineral reservoir, and form armor in many taxa, and are involved in hormone regulation, and doubtless other things that we are still discovering, even now. To fulfill those functions, bone tissue has to be formed in the first place, it has to be maintained, and it has to be able to be reshaped as an individual grows. Derived extant vertebrates, including humans, have an impressive array of cellular machinery to make all those things happen. Central to most of those operations are osteocytes, the cells inside living bone, which maintain intimate connections to extracellular bone tissue and to other osteocytes via fine, tentacle-like processes.

Individual osteocytes look something like the Flying Spaghetti Monster. The central portion of the FSM, with the meatballs, is the osteocyte body, and the noodly appendages are the processes.

Now imagine that you cloned the FSM many, many times, and the resulting array of FSMs stayed in physical contact with each other via their noodly appendates, forming a network.

Then imagine that you entombed all of the cloned FSMs in concrete. This is more or less what cellular bone — the kind you find in humans, dinosaurs, and even some jawless fish — looks like on the microscopic scale: osteocytes (the FSMs) and their processes (the noodly appendages) embedded in space-filling stuff (the bone matrix). Some critters, including teleost fish, have acellular bone, but I don’t have time for those unbelievers today.

When an animal dies and decomposes, the osteocytes and their processes decay away, leaving behind the spaces that they used to occupy. The big spaces that hold osteocytes are called lacunae, and the little tunnels that hold the osteocyte processes (noodly appendages, in this metaphor) are canaliculi. Collectively, the lacunae and canaliculi form the lacunocanalicular network or LCN.

Those spaces can then be filled by matrix — not extracellular bone matrix, but future rock matrix, like mud and clay. In point of fact, not all of the spaces are filled with matrix. Even in their 420-million-year-old fish, Yara and colleagues found some osteocyte lacunae that had not been filled with matrix, and were filled by air instead. Whether the lacunocanalicular network is filled with matrix or air, its preservation in fossil bone has turned out to be a boon for paleontologists, because we can ‘see’ the sizes and shapes of osteocytes, and their level of connectivity, by studying the lacunae and canaliculi they left behind. 

Histological thin section of bone in the osteostracan Tremataspis mammillata (MB.f.TS.463), imaged with transmitting light microscopy showing osteocyte lacunae (osl) and canaliculi (ca); scale bar, 100 microns. Haridy et al. (2021: fig 2A).

Traditionally osteocyte lacunae and canaliculi in fossil bone have been imaged by taking thin sections of the specimens and looking at them under microscopes.

Synchrotron tomography of bone of Bothriolepis trautscholdi (MB.f.9188a) with the vasculature and osteocytes segmented; scale bar, 0.4 mm. (D) Close-up of tomography in (C) showing the resolution of the osteocyte lacunae volumes; scale bar, 10 microns. bs, bone sample; vs, vasculature channels. Modified from Haridy et al. (2021: fig. 2C-D).

If you’re fancy, you can also do synchrotron tomography, which is fine enough to show osteocyte lacunae — the colored blobs in the image on the right, above.

Those methods have their limitations. Light microscopy will reveal both lacunae and canaliculi in 2D, but it’s hard to get a 3D understanding of the lacunocanalicular network that way (at least in fossils; in modern samples it can be done with confocal miscoscopy). Synchrotron tomography can resolve lacunae in 3D, but not canaliculi, sort of like a map that shows only cities but not the highways that connect them.

Enter FIB-SEM: focused ion beam scanning electron microscopy. An ion gun blasts the specimen with a beam of gallium ions, which vaporizes a slice of the specimen that is less than 1 micron thick, and an SEM images the freshly exposed face. If you do this over and over again, you can build up a 3D model of the stuff that once occupied the volume that got zapped. 

FIB-SEM tomography imaging and processing of the fossil jawless vertebrate Tremataspis mammillata (MB.f.9025). (A and B) FIB-SEM setup showing the FIB in relation to the SEM both aimed at the region of interest. (C) Bone surface with an excavate area made by the FIB. (D) Internal wall of the excavated area lined with small black dots that are the fossil osteocyte lacunae. (E) Single osteocyte lacuna from the surface that is scanned; the single SEM image shows the lacunae and canaliculi in black and the mineralized bone in gray; scale bar, 5 microns. (F and G) An image stack is obtained, and 3D made of fossil LCN can be made. Haridy et al. (2021: fig 3).

FIB-SEM is fine enough to resolve both osteocyte lacunae and canaliculi — the lacunocanalicular network or LCN — in three dimensions, in fossil specimens where confocal light microscopy doesn’t always work very well. And the resolution is pretty insane. The rough edges on the 3D models of the LCN aren’t sampling artifacts, they’re accurately reflecting the real morphology of the walls of the lacunae and canaliculi as they were preserved in the fossil bone.

But wait — that’s not all! Not only can FIB-SEM show us osteocyte lacunae and canaliculi in incredible detail in three dimensions, it can also help us figure out at least some of what osteocytes were doing. Together, osteocytes and their processes can sense mechanical strain in bone, trigger bone remodeling, and resorb and lay down bone from the walls of the lacunae and canaliculi. That last process starts with osteocytic osteolysis — the resorption of bone matrix (= osteolysis) from the lacunae and canaliculi by the osteocytes themselves (as opposed to the more familiar destruction of bone at a larger spatial scale by osteoclasts), which is typically followed by the replacement of new matrix where the old bone used to be. Lots of extant vertebrates do osteocytic osteolysis, especially those that have a high demand for calcium and phosphorus in physiologically challenging times. Examples including migrating salmon, lactating mice, and lactating humans. But when did that capacity evolve — did the earliest osteocytes already have the ability to resorb and replace bone? As Yara said to me when she was telling me about her new paper, “We think we know how things work by looking at extant animals, but we’re looking at this highly pruned tree, and we can’t just assume that things worked the same way earlier in our evolutionary history.” 

Yara wanted to investigate when osteolytic osteolysis first evolved when she started her dissertation in 2018, but she didn’t know that FIB-SEM existed. Then she was visiting a neutron tomography facility in Berlin and she saw a poster on the wall about people using FIB-SEM to image corrosion in batteries on ultra-fine scales. She thought, “Wow, the corrosion pits in the batteries look like osteocytes!” The rest you probably figured out faster than it’s taking me to write this sentence: together with her collaborators, she got some samples of bone from the jawless fish Tremataspis and Bothriolepis and zapped them with the FIB-SEM.

Osteocytic osteolysis as a mechanism for early mineral metabolism. (A to C) Illustrations depicting the process of osteocytic osteolysis; the phases are stasis phase, dissolution phase, and redeposition phase, respectively. (D) Single SEM image from the FIB-SEM acquisition showing the air-filled osteocyte lacunae and canaliculi of T. mammillata. (E) Same SEM image as in (D) with contrast shifted to show the demineralized zone surrounding the lacunae. (F and G) 3D render of the stack of images from (D and E) T. mammillata (MB.f.9025). The 3D model shows several osteocytes and their canaliculi, with the red areas showing where the “areas of low density” were found. ald, area of low density; os, osteocyte. Scale bar, 5 microns.

And, wonder of wonders, some of the osteocyte lacunae in Tremataspis were surrounded by a halo of less-dense bone, which is evidence for osteocytic osteolysis. Now, Yara and colleagues can’t be sure whether the bone is less dense because it was being resorbed when the animal died — the actual lytic or bone-destructive phase — or because new bone was being laid down after the old bone had been resorbed; naturally the new bone is less dense as it being formed than it will be when it is complete. They also can’t be sure why the process was occurring in that one individual Tremataspis. Mice only do osteocytic osteolysis when they’re lactating, and salmon only do it when they’re migrating, so the presence of osteocytic osteolysis might indicate that the Tremataspis in question was doing something stressful related to its ecology or life history — both topics we know almost nothing about.

Yara and colleagues didn’t find any evidence of osteocytic osteolysis in their Bothriolepis sample, but this is one of those ‘absence of evidence is not evidence of absence’ things — you wouldn’t find evidence of osteocytic osteolysis in my skeleton either, despite a long ancestral history, because I’m skeletally healthy, not fasting or migrating, and not lactating. Possibly other Bothriolepis individuals that were going through a rough patch, metabolically speaking, would show osteocytic osteolysis. So far, as a species, we’ve only looked at the one sample, from the one individual.

I asked Yara what she wanted people to take away from her new paper. Her response:

  1. We have technology can image fossil bone cells at the same resolution that we can see modern bone cells.
  2. Bone metabolism was going on 420 million years ago, in the earliest osteocytes, the same way it happens in modern mammals, including humans. 

I expect that we will see a lot more FIB-SEM papers on fossils in years to come. That research program started today, with the publication of Haridy et al. (2021). I often sign off posts with “stay tuned”, and this time I really mean it.

Reference

Yara Haridy, Markus Osenberg, André Hilger, Ingo Manke, Donald Davesne, and Florian Witzmann. 2021. Bone metabolism and evolutionary origin of osteocytes: Novel application of FIB-SEM tomography. Science Advances 7(14): eabb9113. DOI: 10.1126/sciadv.abb9113.

Matt dropped me a line midweek about the catalogue of complete sauropod necks, with some interesting thoughts. He broke down the necks as listed across a basic phylogeny of sauropods, and counted the occurrences:

Simplified phylogeny of Sauropoda, showing counts of complete and near-complete necks. Captions: C, complete and described; U, complete but undescribed; –1, missing the atlas but otherwise complete; O, other near-complete necks; T, total.

Matt and I were both surprised to see that non-neosauropods are quite well represented, both inside and outside of Mamenchisauridae — although it’s a pity that two of those ten specimens are of Jobaria, for which we have next to zero information.

Diplodocoids are surprisingly poorly represented, with essentially just one each in Dicraeosauridae and Diplodocidae that are complete. And brachiosaurids are a black hole, with absolutely no representation — see the 2015 preprint for details on how unconvincing the neck of Giraffatitan is.

But camarasaurids are crushing it, probably just by being the most abundant sauropods of all time in terms of individual specimens in museums. (Of course when we say “camarasaurids”, we just mean Camarasaurus, which is the only named sauropod currently considered to belong to Camarasauridae unless you follow Mateus and Tschopp (2013) in considering Cathetosaurus to be generically distinct. But Matt and I both suspect that Camarasaurus is way over-lumped, so we’ll see how this pans out over the next decade or two.)

It’s surprising, though, that the second and third best represented sauropods in museums, Diplodocus and Apatosaurus, are both barely represented in terms of complete necks. And while it’s encouraging to see quite a few complete and nearly-complete necks among somphospondyls, including titanosaurs,it’s disappointing that about half of them are not yet described.

References