Things to Make and Do, part 3b: Wallaby feet

I’m following up immediately on my last post because I am having so much fun with my wallaby carcass.  As you’ll recall, I was lucky enough to score a subadult male wallaby from a local farm park.  Today, we’re going to look at its feet.

Wallabies are macropods; together with their close relatives the kangaroos and Wallaroos, they make up the genus Macropus, literally “bigfoot”.  So wallabies got there long before cryptic North American anthropoids.  And indeed their feet are big.  Here are those feet, in dorsal view, from before I started doing unspeakable things to my specimen:

Bennett's wallaby, hind feet in dorsal view

From here they look pretty weird, but it’s only when we go round the back that we really see how odd they are.  Same feet in ventral view:

Bennett's wallaby, hind feet in ventral view

There are (at least) three things to notice here: first just that the feet are very long; second, the thick, scaly pad that runs all the way up to the heel; and third, the bizarre arrangement of toes.  At first glance, it seems that there is one main toe and a smaller one each side, but if you look more closely you’ll see that the medial “toe” is really two tiny toes closely appressed, so that they function as a single toe.  This condition is known as syndactyly, Darren tells me.  Also from Darren: it’s digit I that is missing in macropods, so the tiny-toe pair are digits II and III, the main toe is IV and the lateral one is V.

(By the way, seeing my patio in these photos reminds me of something I forgot to mention in the previous post: it’s surprisingly difficult to wash wallaby blood off paving slabs.  Remember that, kids, it’ll be on the test.)

Regular readers will remember from last time that I planned to prepare the skull and left fore- and hindlimbs by simmering and dissection, and let nature deal with the rest of the elements.  You’ve already seen the skull, so here goes with that foot.

After an initial simmer, I was able to skin the left pes, so here it is at that stage, in medial view:

Bennett's Wallaby, left pes in medial view, skinned and simmered

From this angle, you can clearly see the absurdly thin second metatarsal (MT II) that supports the innermost of those two tiny digits.  MT III is just as long and thin, but is fused proximally to the much larger MT IV, as we shall see below.  The simmering has resulted in the more distal phalanges breaking away from their more proximal brethren, and being pulled downwards and beneath them.  This is most apparent with the tiny digits, whose supporting phalanges are clearly visible poking out above the claws.  So the large lump of what looks like cartilage at top right is actually phalanx IV-I, with IV-II and IV-III (the ungual) beneath it.  Also note the significant amount of resilient tissue below the metatarsals.  I’ve cut most of it away, but you can get a good idea from the bits that are still attached distally.

Here is the metatarsus in ventral view after I had removed the phalanges:

Bennett's Wallaby, metatarsus in ventral view, skinned and simmered

Here you can clearly see the syndactyly (in those two closely appressed thin metatarsals II and III at the top of the picture) and the very sculpted distal ends of the  larger metatarsals IV and V.

Now let’s skip straight to to the completed stripped-down pes, now in dorsal view:

Bennett's wallaby, left pes in dorsal view, disarticulated and cleaned skeleton; ungual sheaths removed from bony cores.

It’s interesting that the phalangeal formula is so uniform: 0-3-3-3-3.  That is, all four digits have two normal phalanges and an ungual.  But the differences in proportions between them are quite something.

This is our first look at the tarsals — those seven bones on the left of the picture, before we get to the metatarsals.  The three big ones fit together very nicely.  At the back you see the calcaneum, where the achilles tendon attaches; next is the astragalus, which sits on top of the calcaneum and where the distal end of the tibia articulates. Next up is a bone whose name I don’t know, being pretty darned ignorant of ankles — might it be the cuboid?  Anyway, even after cleaning and cartilage-removal , this articulates very nicely indeed with both the calcaneum and MT IV.

Medial to these (i.e. below them in the picture) are four much smaller tarsal bones whose identity I can’t even guess at.  It’s not clear to me how they articulate with the big tarsals — they were all pretty solidly embedded in cartilage and gloop and I fear that they’re not going to fit neatly whatever I do.  Hints will be welcome.

One big surprise was the small bones between the metatarsals and their corresponding phalanges: one each at the ends of MT II and MT III, and two each at the ends of MT IV and MT V.  Because the proximal phalanges articulate so nicely with their metatarsals, it’s clear that these small bones were not positioned between them in life, but rather floated above them — rather as your kneecap, or patella, floats above your femur-tibia joint.  They are sesamoids.  Does anyone know whether this sesamoid formula of 0-1-1-2-2 is common?  Seems a bit weird to me.

Finally, I leave you with the entire left hindlimb: foot as in the previous picture, surmounted by the tibia and fibula, then by the femur, all in anterior view.  Just to the left of the femur-tibia joint is a small bone which I assume is the patella.

Bennett's wallaby, disarticulated left hind limb in dorsal view

Special bonus wallaby limb: over there on the right is the left forelimb.  As you can see, I’ve done the easy part (scapula, humerus, ulna and radius) but I still have to dissect out the bones from the wrist and hand — a picky, tedious job that to be frank I am not looking forward to.  The feet are much more exciting than the hands.

That’s all for today.  On Sunday evening I am off to London to spend a whole week in the company of the Archbishop.  The plan is to spend Monday to Wednesday taking final publication-quality photos (I finally have a proper tripod) and digging out field photos and suchlike from the museum archives, then take Cervical U to be CT-scanned at the Royal Veterinary College, courtesy of theropod hindlimb mechanics guru John Hutchinson.  Friday is emergency backup in case something crops up to delay the scanning, and also gives me a chance to retake any photos that didn’t come out as required.  The plan is that this visit should give me everything I need (pictures, measurements, observations, historical documents) to finish up the long-overdue Archbishop description.  Fingers crossed.

I leave you with a puzzle.  This is the jacket that I have designated “Lump Z”:

Brachiosauridae indet. BMNH R5937, "The Archbishop". Unidentified elements "Lump Z". Image copyright the NHM, since it's their material.

Can anyone offer a guess as to what this is, and which way up it should be?  It’s a jacket that was opened years ago — before I was involved with the specimen — but never fully prepared.  Matt and I have discussed it a little, but I don’t want to prejudice anyone with our guesswork, so I leave the floor open.  What is it?

SV-POW! Dollars are at stake!



How big were the biggest sauropod trackmakers?

You might have seen a story last week about some huge sauropod tracks discovered in Upper Jurassic deposits from the Jura plateau in France, near the town of Plagne. According to the news reports, the tracks are the largest ever discovered. Well, let’s see.

The Guardian (from which I stole the image above) says the prints are “up to 2 metres (6ft 6 in) in diameter”, but ScienceDaily says “up to 1.5 m in total diameter”. Not sure how ‘total diameter’ is different from regular diameter, but that’s science reporting for you. The BBC clarifies that, “the depressions are about 1.5m (4.9ft) wide”, which might be the key here (see below), but then mysteriously continues, “corresponding to animals that were more than 25m long and weighed about 30 tonnes.” I find it rather unlikely that a pes track 1.5 m wide indicates an animal only as big as Giraffatitan (hence this post).

So there’s some uncertainty with respect to the diameter of the tracks–half a meter of uncertainty, to be precise. But sauropod pes tracks are usually longer than wide, and a print 1.5 m wide might actually be 2 m long.

Not incidentally, Thulborn (1994) described some big sauropod tracks from the Broome Sandstone in Australia, with pes prints up to 1.5 m. Although the photos of the tracks are not as clear as one might wish, they do appear to show digit impressions and are probably not underprints.

I’ll feel a lot better about the Plagne tracks when the confusion about their dimensions is cleared up and when some evidence is presented that they also are not underprints. In any case, the only dimension with any orientation cited for the Plagne tracks is the 1.5 m width reported by the BBC, so we’ll go with that. So the Plagne tracks might only tie, but not beat, Thulborn’s tracks.

…Then again, Thulborn only said that the biggest tracks were up to 150 cm in diameter. What does that mean–length? Width? Are the tracks perfect circles? Does no one who works on giant sauropod tracks know how to report measurements? These questions will have to wait, because despite the passing of a decade and a half, the world’s (possibly second-) biggest footprints–from anything! ever!–have not yet merited a follow-up paper.

Nevertheless, for the remainder of this post we’ll accept that at least some sauropods were leaving pes prints a meter and a half wide. Naturally, it occurs to me to wonder how big those sauropods were. I don’t know of any studies that attempt to rigorously estimate the size of a sauropod from its tracks or vice versa, so in the finest tradition of the internet in general and blogging in particular, I’m going to wing it.

How Big?

First we need some actual measurements of sauropod feet. When Mike and I were in Berlin last fall (gosh, almost a year ago!), we measured the feet (pedes) of the mounted Giraffatitan and Diplodocus for this very purpose. The Diplodocus feet were both 59 cm wide, and the Giraffatitan feet were 68 and 73 cm wide. The Diplodocus feet are trustworthy, the Giraffatitan bits less so. Unfortunately, the pes is the second part of the skeleton of Giraffatitan that is less well known than I would like (after the cervico-dorsal neural spines). The reconstructed feet look believable, but “believability” is hard to calibrate and probably a poor predictor of reality when working with sauropods.

One thing I won’t go into is that Giraffatitan (HM SII) probably massed more than twice what Diplodocus (CM 84/94) did, but on the other hand G. bore more of its weight on its forelimbs. It would be interesting to calculate whether the shifted center of mass would be enough to even out the pressure exerted by the hindfeet of the two animals; Don Henderson may have done this already.

Anyway, let’s say for the sake of argument that the hindfeet of the mounted Giraffatitan are sized about right. The next problem is figuring out how much soft tissue surrounded the bones. In other words, how much wider was the fleshy foot–deformed under load!–than the articulated pes skeleton? I am of two minds on this. On one hand, sauropods probaby had a big heel pad like that of elephants, and it seems reasonable that the heel pad plus the normal skin, fat, and muscle might have expanded the fleshy foot considerably beyond the edges of the bones. On the other hand, the pedal skeleton is widest across the distal ends of the phalanges, and in well-preserved tracks like the one below the fleshy foot is clearly not much wider than that (thanks, Brian, for the photo!).

Bear in mind that a liberal estimate of soft tissue will give a conservative estimate of the animal’s size, and vice versa. Looking at the AMNH track pictured above, it seems that the width added by soft tissue could possibly be as little as 5% of the width of the pes skeleton. Skewing hard in the opposite direction, an additional 20% or more does not seem unreasonable for other animals (keep in mind this would only be 10% on either side of the foot). Using those numbers, Diplodocus (CM 84/94) would have left tracks as narrow as 62 cm or as wide as 71 cm. For Giraffatitan (HM SII) I’ll use the wider of the two pes measurements, because the foot is expected to deform under load and the 73 cm wide foot looked just as believable as the 68 cm foot (for whatever that’s worth). Applying the same scale factors (1.05 and 1.20) yields a pes track width of 77-88 cm.

These numbers are like pieces of legislation, or sausages: the results are more pleasant to contemplate than the process that produced them. They’re ugly, and possibly wrong. But they give us someplace to start from in considering the possible sizes of the biggest sauropod trackmakers. Something with a hindfoot track 1.5 meters wide would be, using these numbers, conservatively more than twice as big as (2.11x) the mounted Carnegie Diplodocus or 170% the size of the mounted Berlin Giraffatitan. That’s right into Amphicoelias fragillimus/Bruhathkayosaurus territory. The diplo-Diplodocus would have been 150 feet long, and even assuming a very conservative 10 tons for Vanilla Dippy (14,000L x 0.7 kg/L = 9800 kg), would have had a mass of 94 metric tons (104 short tons). The monster Giraffatitan-like critter would have been “only” 130 feet long, but with a 14.5 meter neck and a mass of 113 metric tons (125 short tons; starting from a conservative 23 metric tons for HM SII).

Keep in mind that these are conservative estimates, for both the size of the trackmakers and the masses of the “known” critters. If we use the conservative soft tissue/liberal animal size numbers, the makers of the 1.5 meter tracks were 2.4 times as big as the mounted Diplodocus or almost twice as big as the mounted Giraffatitan, in which case masses in the blue whale range of 150-200 tons become not just probable but inevitable.

Mike measuring Giraffatitan's naughty bits. Check out the hindfeet. Also note the sauropod vertebrae in the background--titular obligation fulfilled!

Too Big?

Going the other way, I can think of only a handful of ways that the “conservative” trackmaker estimates might still be too big:

First, the pes of Giraffatitan might have been bigger than reconstructed in the mounted skeleton. Looking at the photo above, I can image a pes 10% wider that wouldn’t do any violence to the “believability” of the mount. That would make the estimated track of HM SII 10% wider and the estimated size of the HM-SII-on-steroids correspondingly smaller. But that wouldn’t affect the scaled up Diplodocus estimate, and the feet of Giraffatitan would have to be a LOT bigger than reconstructed to avoid the reality of an animal at least half again as big as HM SII.

Second, the amount of soft tissue might have been greater than even the liberal soft tissue/conservative size estimate allows. But I think that piling on 20% more soft tissue than bone is already beyond what most well-preserved tracks would justify, so I’m not worried on that score. (What scares me more is the thought that the conservative estimates are too conservative, and the real trackmakers even bigger.)

Third, I suppose it is possible that sauropod feet scaled allometrically with size and that big sauropods left disproportionately big tracks. I’m also not worried about this. For one thing, when they’ve been measured sauropod appendicular elements tend to scale isometrically, and it would be weird if feet were the undiscovered exception. For another, the allometric oversizing of the feet would have to be pronounced to make much of a dent in the estimated size of the trackmakers. I find the idea of 100-ton sauropods more palatable than the idea of 70-ton sauropods with clown shoes.

Fourth, the meta-point, what if the Broome and Plagne tracks are underprints? I’ve seen some tracks-with-undertracks where the magnification of the apparent track size in the undertracks was just staggering. The Broom tracks have gotten one brief note and the Plagne tracks have not been formally described at all, so all of this noodling around about trackmaker size could go right out the window. Mind you, I don’t have any evidence that the either set are underprints, and at least for the Broome tracks the evidence seems to go the other way, I’m just trying to cover all possible bases.

Conclusions

So. Sauropods got big. As usual, we can’t tell exactly how big. Any one individual can leave many tracks but only one skeleton, so we might expect the track record to sample the gigapods more effectively than the skeletal record. Interestingly, the largest fragmentary skeletal remains (i.e., Amphicoelias and Bruhathkayosaurus, assuming they’re legit) and the largest tracks (i.e., Plagne and Broome) point to animals of roughly the same size.

It’s also weird that some of the biggest contenders in both categories have been so little published. I mean, if I had access to Bruhathkayosaurus or a track 1.5 m wide, you can bet that I’d be dropping everything else like a bad habit until I had the gigapod evidence properly written up. What gives?

Finally, IF the biggest fragmentary gigapods and the biggest tracks are faithful indicators of body size, they suggest that gigapods were broadly distributed in space and time (and probably phylogeny). I wonder if these were representatives of giga-taxa, or just extremely large individuals of otherwise vanilla sauropods. Your thoughts are welcome.

Epilogue: What About Breviparopus?

It’s past time someone set the record straight about damn Breviparopus. The oft-quoted track length of 115 cm is (A) much smaller than either the Broome or Plagne tracks, and (B) the combined length of the manus and pes prints together; I know, I looked it up (Dutuit and Ouazzou 1980). Why anyone would report track “length” that way is beyond me, but what is more mysterious is why anyone was taken in by it, since the width of 50 cm (pathetic!) is usually quoted along with the 115 cm “length”, indicating an animal smaller than Vanilla Diplodocus (track length is much more likely than width to get distorted by foot motions during locomotion) [This part is wrong; see the update below.]. But people keep stumbling on crap (thanks, Guiness book!) about how at 157 feet long (determined how, exactly?) Breviparopus was possibly the largest critter to walk the planet. Puh-leeze. If there’s one fact that everyone ought to know about Breviparopus, it’s that it was smaller than the big mounted sauropods at museums worldwide. The only thing super-sized about it is the cloud of ignorance, confusion, and hype that clings to the name like cheap perfume. Here’s the Wikipedia article if you want to do some much-needed revising.

UPDATE (Nov 17 2009): The width of the Breviparopus pes tracks is 90 cm, not 50 cm. The story of the 50 cm number is typically convoluted. Many thanks to Nima Sassani for doing the detective work. Rather than steal his thunder, I’ll point you to his explanation here. Point A above is still valid: Breviparopus was dinky compared to the Broome and Plagne trackmakers.

Parting Shot

You know I ain’t gonna raise the specter of a beast 1.7 times the size of HM SII without throwing in a photoshopped giant cervical. So here you go: me with C8 of Giraffatitan blown up to 170% (the vert, not me). Compare to unmodified original here.

References

• Dutuit, J.M., and A. Ouazzou. 1980. Découverte d’une piste de Dinosaure sauropode sur le site d’empreintes de Demnat (Haut-Atlas marocain). Mémoires de la Société Géologique de France, Nouvelle Série 139:95-102.
• Thulborn, R.A., T.Hamley and P.Foulkes. 1994. Preliminary report on sauropod dinosaur tracks in the Broome Sandstone (Lower Cretaceous) of Western Australia. Gaia 10:85-96.

What a 23% longer torso looks like

Just checking: no-one’s bored of brachiosaurs yet, are they?

Thought not.  Right, then, here we go!

Greg Paul’s (1988) study of the two “Brachiosaurus” species — the paper that proposed the subgenus Giraffatitan for the African species — noted that the trunk is proportionally longer in Brachiosaurus than in Giraffatitan due to the greater length of its dorsal centra. Paul (p. 7) stated that the difference is “25%-30%” on the basis of his figure 2.

Having seen the dorsal vertebrae of the type specimens of both species, my gut reaction was that the difference was nowhere near this great, so I recalculated it for myself (Taylor 2009:table 3).  Dorsal column length is the sum of the “functional length” of the centra of the dorsal vertebrae, where functional length is the length of the centrum not counting the condyle (which of course is nestled in the preceding vertebra’s cotyle when the column is articulated).  For Brachiosaurus, Riggs (1904) did not give this measurement, but did give total heights, and using these for scale I was able to measure the functional lengths from his plate LXXII.  For Giraffatitan, Janensch’s (1950:44) superbly comprehensive table supplied measurements for D4 and D8; for D11 and D12 I was able to determine the length by measuring from Janensch’s (1950:fig. 62) figure, knowing the height from his table; and for D5-D7, D9 and D10, I interpolated linearly between the measurements that I had.  Summing the functional lengths of D6-D12, I got 226 cm for Brachiosaurus and 183 cm for Giraffatitan.  So Brachiosaurus is 226/183 = 1.23 times as long as Giraffatitan — in other words, 23% longer, which is pretty much what Greg Paul said.  So I learned something there.

(Yes, brachiosaurs probably had 12 dorsals.)

So: is a 23% longer torso a big deal?  Back when I was trying to answer that question for myself, I figured it would help to take an image of a familiar animal and stretch it — so here is a horse, stolen from here and stretched:

Horse (top); and evil mutant horse with 23% longer torso (bottom).

To me, that second picture is wrong enough to hurt my eyes a little; your mileage may vary, but I suspect those among you who love horses will feel ill when you look at it.  This image was one of the reasons — one of many — that I concluded that generic separation was unavoidable.

But here’s an odd thing: tonight, for this blog post, I did the same thing to a human body, expecting it to seem even more horrible in light of how familiar we are with our own bodies.  Here it is:

Flayed Homo sapiens in orthograde anatomical position, from Vesalius (1543) "Tertia Musculorum Tabula". Modified from Wilson (2006:fig. 1). Left, as drawn; right, with torso elongated by 23%.

To my surprise, the elongated human doesn’t look appallingly wrong to me.  It doesn’t look right, of course, but it seems within the realms of, for example, what might appear as a representation of a human body in the early issues of Fantastic Four.  I am not sure what to make of that fact.  I don’t believe I have a more finely tuned sense of horse anatomy than human anatomy: it might be that I am more used to badly drawn humans than badly drawn horses; or that there is more variation in human proportions than in horse proportions; or maybe weirdness just looks less weird when it’s upright than when it’s horizontal.  I’ll be interested to hear in the comments whether the Long Horse or the Long Human looks most wrong to readers.

(By the way, I casually talk about the type specimens of both “Brachiosaurus” species: while the situation is simple in the case of Brachiosaurus altithorax, whose holotype is FMNH P25107, things are more complex in the case of Giraffatitan brancai.  Janensch nominated “Skelett S” as the holotype of his new species “Brachiosaurus” brancai, but that turned out to be a chimera, composed of the two skeletons which he subsequently designated SI and SII — but Janensch never designated one of these as the type, and so far as I’ve been able to determine, neither has anyone else done so.  SI is represented by cranial elements and the first seven cervicals, but that’s all; SII is a much larger animal and is represented by most of the skeleton, and has been informally treated as though it were the type specimen most of the while, so I formally proposed HMN SII as the lectotype of the species (Taylor 2009:788) — just a bit of housekeeping.)

Here’s our old friend, the 8th cervical vertebra of HMN II, in a rare posterodorsal aspect, showing just how thin and, well, lamina-like the spinopostzygapophyseal laminae are.  All that space in between them?  Filled with diverticula, mostly.  Amazing.

Giraffatitan brancai lectotype HMN SII, 8th cervical vertebra, in posterodorsal view

Meanwhile some good news:

Remember the good news and bad news about the all-dinosaurs special volume of The Anatomical Record?  Well, since we posted that, the entire issue has been made open access!  Fantastic stuff there: details from D. Schachne of the Wiley-Blackwell Communications Team.  It’s not clear why the articles were all paywalled when originally posted, but all’s well that ends well.

And finally …

There’s been a gratifying amount of discussion in the comments on recent articles.  It can be hard to keep track of, but it helped a lot when I found an RSS feed for comments, which is what I now use.  For anyone else who wants it, it’s at http://svpow.wordpress.com/comments/feed/

References

• Janensch, Werner.  1950.  Die Wirbelsaule von Brachiosaurus brancai.  Palaeontographica (Suppl. 7) 3: 27-93.
  Paul, Gregory S.  1988.  The brachiosaur giants of the Morrison and Tendaguru with a description of a new subgenus, Giraffatitan, and a comparison of the world’s largest dinosaurs.  Hunteria 2 (3): 1-14.
  Taylor, Michael P.  2009.  A re-evaluation of Brachiosaurus altithorax Riggs 1903 (Dinosauria, Sauropoda) and its generic separation from Giraffatitan brancai (Janensch 1914).  Journal of Vertebrate Paleontology 29(3):787-806.
  Vesalius, A.  1543.  Andreae Vesalii Bruxellensis, Scholae medicorum Patauinae professoris, de Humani corporis fabrica Libri septem [facsimile]. Ex Officina Ioannis Oporini, Basel, 659 pp.
  Wilson, Jeffrey A.  2006.  Anatomical nomenclature of fossil vertebrates: standardized terms or “lingua franca”?  Journal of Vertebrate Paleontology 26(3): 511-518.
• Janensch, Werner.  1950.  Die Wirbelsaule von Brachiosaurus brancai.  Palaeontographica (Suppl. 7) 3: 27-93.
• Paul, Gregory S.  1988.  The brachiosaur giants of the Morrison and Tendaguru with a description of a new subgenus, Giraffatitan, and a comparison of the world’s largest dinosaurs.  Hunteria 2 (3): 1-14.
• Taylor, Michael P.  2009.  A re-evaluation of Brachiosaurus altithorax Riggs 1903 (Dinosauria, Sauropoda) and its generic separation from Giraffatitan brancai (Janensch 1914).  Journal of Vertebrate Paleontology 29(3):787-806.
• Vesalius, A.  1543.  Andreae Vesalii Bruxellensis, Scholae medicorum Patauinae professoris, de Humani corporis fabrica Libri septem [facsimile]. Ex Officina Ioannis Oporini, Basel, 659 pp.
• Wilson, Jeffrey A.  2006.  Anatomical nomenclature of fossil vertebrates: standardized terms or “lingua franca”?  Journal of Vertebrate Paleontology 26(3): 511-518.

NHM 46870 Strikes Back: ASP

By now you’ll recognize this as NHM 46870, a minor celebrity in the world of pneumatic sauropod vertebrae. Darren has covered the history of the specimen before, and in the last post he showed photographs of both this chunk and its other half. He also briefly discussed the Air Space Proportion (ASP) of the specimen, and I’ll expand on that now.

People have mentioned the weight-saving properties of sauropod vertebrae from the very earliest discoveries of sauropods. But as far as I know, no one tried to quantify just how light they might have been until 2003.

That fall I was starting my third year of PhD work at Berkeley, and I was trying to think of everything that could possibly be investigated about pneumaticity in sauropod vertebrae. I came up with a list of four things:

• external traces of pneumaticity (foramina, fossae, tracks, laminae)
• form and complexity of internal spaces (camerae, camellae, branching patterns)
• ratio of bone to air space within a pneumatic element
• distribution of postcranial skeletal pneumaticity (PSP) in the body

That list of four things formed the outline for my first dissertation chapter (Wedel 2005), and for my dissertation itself. In fact, all of my papers that have anything to do with pneumaticity can be classified into one or more of those four bins:

• external traces: Wedel (2005, 2007)
• internal complexity: Wedel et al. (2000a, 2000b), Wedel (2003b)
• bone/air ratio: Wedel (2005)
• distribution in the body: Wedel (2003a, 2006, 2009)

That list is not exhaustive. It’s every aspect of PSP that I was able to think of back in 2003, but there are lots more. For example, I’ve only ever dealt with the internal complexity of sauropod vertebrae in a qualitative fashion, but the interconnections among either chambers or bony septa could be quantified, as Andy Farke has done for the frontal sinuses of hartebeests (Farke 2007). External traces on vertebrae and the distribution of PSP in the body can also be quantified, and were shortly after I drew up the list–see Naish et al. (2004) for a simple, straightforward approach to quantifying the extent of external pneumatic fossae, and O’Connor (2004, 2009) for a quantitative approach to the extent of pneumaticity in the postcranial skeletons of birds. There are undoubtedly still more parameters waiting to be thought of and measured. All of these papers are first steps, at least as applied to pneumaticity, and our work here is really just beginning.

Also, it took me an embarrassingly long time to “discover” ASPs.  I’d had CT slices of sauropod vertebrae since January, 1998, and it took me almost six years to realize that I could use them to quantify the amount of air inside the bones. I later discovered that Currey and Alexander (1985) and Casinos and Cubo (2000) had done related but not identical work on quantifying the wall thickness of tubular bones, and I was able to translate their results into ASPs (and MSPs for marrow-filled bones).

The procedure is pretty simple, as Mike has shown here before. Open up the image of interest in Photoshop (or GIMP if you’re all open-sourcey, like we are), make the bone one color, the air space a second color, and the background a third color. Count pixels, plug ‘em into a simple formula, and you’ve got the ASP. I always colored the bone black, the air space white, and the background gray, so

ASP = (white pixels)/(black + white pixels)

For the image above, that’s 460442/657417 = 0.70.

Two quick technical points. First, most images are not just black, white, and one value of gray. Because of anti-aliasing, each black/white boundary is microscopically blurred by a fuzz of pixels of intermediate value. I could have used some kind of leveling threshold thing to bin those intermediate pixels into the bone/air/background columns, but I wanted to keep the process as fast and non-subjective as possible, so I didn’t. My spreadsheet has columns for black, white, gray, and everything else. The everything else typically runs 1-3%, which is not enough to make a difference at the coarse level of analysis I’m currently stuck with.

Second, I prefer transverse sections to longitudinal, because most of the internal chambers are longitudinally oriented. That means that longitudinal sections, whether sagittal or horizontal, are likely to cut through a chamber wall on its long axis, which makes the walls look unnaturally thick. For example, in the image above the median septum looks 5-10 times thicker than the outer walls of the bone, which would be a first–usually the outer walls are thicker than the internal septa, as you can see here. I don’t think the median septum really is that thick; I strongly suspect that a very thin plate of bone just happened to lie in the plane of the cut. It takes some work to get used to thinking about how a 2D slice can misrepresent 3D reality. When I first started CT scanning I was blown away by how thick the bone is below the pre- and postzygapophyses. I was thinking, “Wow, those centrozygapophyseal laminae must have been way more mechanically important than anyone thinks!” It took me a LONG time to figure out that if you take a transverse slice through a vertical plate of bone, it is going to look solid all the way up, even if that plate of bone is very thin.

Even apart from those considerations, there is still a list of caveats here as long as your arm. You may not get to choose your slice. That’s almost always true of broken or historically sectioned material, like NHM 46870. It’s even true in some cases for CT scans, because some areas don’t turn out very clearly, because of mineral inclusions, beam-hardening artifacts, or just poor preservation.

The slice you get, chosen or not, may not be representative of the ASP of the vertebra it’s from. Even if it is, other elements in the same animal may have different ASPs. Then there’s variation: intraspecific, ontogenetic, etc. So you have to treat the results with caution.

Still, there are some regularities in the data. From my own work, the mean of all ASP measurements for all sauropods is about 0.60. That was true when I had only crunched my first six images, late on the evening of October 9, 2003. It was true of the 22 measurements I had for Wedel (2005), and now that I have over a hundred measurements, it’s still true. More data is not shifting that number at all. And Woodward (2005) and Schwartz and Fritsch (2006) got very similar numbers, using different specimens.

This is cool for several reasons. It’s always nice when results are replicated–it decreases the likelihood that they’re a fluke, and in this case it suggests that although the limitations listed above are certainly real, they are not deal-killers for answering broad questions (we are at this point seeing the forest more clearly than the trees, though).

More importantly, the mean 0.60 ASP for all sauropod vertebrae is very similar to the numbers that you get from the data of Currey and Alexander (1985) and Cubo and Casinos (2000): 0.64 and 0.59, respectively. So sauropod vertebrae were about as lightly built as the pneumatic long bones of birds, on average.

Naturally, there are some deviations from average. Although I didn’t have enough data to show it in 2005, brachiosaurids tend to have higher ASPs than non-brachiosaurids. And Early Cretaceous brachiosaurids from the US and England are especially pneumatic–the mean for all of them, including Sauroposeidon, ‘Angloposeidon’, some shards of excellence from the Isle of Wight, and assorted odds and ends, is something like 0.75-0.80, higher even than Brachiosaurus. So there’s probably a combined phylogenetic/functional story in there about the highly pneumatic, hyper-long-necked brachiosaurids of the Early Cretaceous of Laurasia. Another paper waiting to be written.

Here’s another shard of excellence, referred to Chondrosteosaurus, NHM R96. As Mike had discussed here before, there’s no good reason to believe that it actually is Chondrosteosaurus, and the internal structure looks considerably more subdivided than in NHM 46870. This is an anterior view, and normally you’d be seeing a nice hemispherical condyle, but all of the cortical bone is gone and the internal structure is revealed. The little black traces are bone and the brownish stuff is rock matrix filling the pneumatic cavities.

A few years ago, Mike asked me to look at that photo and guess the ASP, and then run the numbers and see how close I got. I guessed about 78%, then did the calculation, and lo and behold, the answer was 78%. So I’m pretty good at guessing ASPs.

Except I’m not, because as any of you armed with photo software can tell, that picture has 24520 black pixels and 128152 white ones, so the ASP is actually 128152/(128152+24520) = 0.84. The moral of the story is check your homework, kids! Especially if you seem to be an unnaturally good estimator.

ASP-ESP aside, I think ASP is cool and has some interesting potential at the intersection of phylogeny and biomechanics. But the method is severely limited by sample size, which is severely limited by how much of a pain in the butt preparing the images is. In most cases you can’t just play with levels or curves to get a black and white image that faithfully represents the morphology, or use the magic wand, or any of the other myriad shortcuts that modern imaging programs offer. Believe me, I’ve tried. Hard. But inevitably you get some matrix with the bone, or some bone with the matrix, and you end up spending an impossible amount of time fixing those problems (note that this is not a problem if you use perfect bones from extant animals, which is sadly not an option for sauropod workers). So almost all of my ASP images were traced by hand, which is really time-consuming. I could pile up a lot more data if I just sat around for a few weeks processing images, but every time I’ve gotten a few free weeks there has been something more important demanding my attention, and that may always be the case. Fortunately I’m not the only one doing this stuff now, and hopefully in the next few years we’ll get beyond these first few tottering steps.

Side Note: Does NHM 46870 represent a juvenile, or a dwarf?

This came up amongst the SV-POW!sketeers and we decided it should be addressed here. Darren noted that the vert at top is pretty darned small, ~23 cm for the preserved part and probably only a foot and a half long when it was complete, which is big for an animal but small for a sauropod and dinky for a brachiosaurid (if that’s what it is). Mike made the counter-observation that the internal structure is pretty complex, citing Wedel (2003b:fig. 12) and surrounding text, and suggested that it might be an adult of a small or even dwarfed taxon. And I responded:

I’m not at all certain that it is dwarfed. It matters a lot whether the complex internal structure is polycamerate or camellate. I was agnostic for a long time about how different those two conditions are, but there is an important difference that is relevant in this case: the two internal structures develop differently. Polycamerate verts really do get progressively more complex through development, as illustrated–there are at least two great series that show this, that I need to publish one of these days. But I think camellate vertebrae may be natively complex right from the get-go; i.e., instead of a big simple diverticulum pushing in from the side and making a big camera first, a bunch of smaller diverticula may remodel the small marrow spaces into small air spaces with no prior big cavities. At least, that’s how birds seem to do it. This needs more testing from sauropods–a good ontogenetic sequence from Brachiosaurus would be clutch here–but it’s my working hypothesis. In which case NHM 46870 may be a juvenile of a camellate taxon, rather than an adult of a polycamerate taxon.

The whole camerate-vs-camellate problem deserves a post of its own, and this post is already too long, so we’ll save that for another day.

References

• Cubo, J., and Casinos, A. 2000. Incidence and mechanical significance of pneumatization in the long bones of birds. Zoological Journal of the Linnean Society 130: 499–510.
• Currey, J. D., and Alexander, R. McN. 1985. The thickness of the walls of tubular bones. Journal of Zoology 206:453–468.
• Farke, A. A. 2007. Morphology, constraints, and scaling of frontal sinuses in the hartebeest, Alcelaphus buselaphus (Mammalia: Artiodactlya, Bovidae). Journal of Morphology 268:243-253.
• Naish, D., Martill, D. M., Cooper, D. & Stevens, K. A. 2004. Europe’s largest dinosaur? A giant brachiosaurid cervical vertebra from the Wessex Formation (Early Cretaceous) of southern England. Cretaceous Research 25:787-795.
• O’Connor, P.M. 2004. Pulmonary pneumaticity in the postcranial skeleton of extant Aves: a case study examining Anseriformes. Journal of Morphology 261:141-161.
• O’Connor, P. M. 2009. Evolution of archosaurian body plans: Skeletal adaptations of an air-sac-based breathing apparatus in birds and other archosaurs. Journal of Experimental Zoology DOI: 10.1002/jez.548
• Schwarz D, Fritsch G. 2006. Pneumatic structures in the cervical vertebrae of the Late Jurassic Tendaguru sauropods Brachiosaurus brancai and Dicraeosaurus. Eclogae Geologicae Helvetiae 99:65–78.
• Woodward, H. 2005. Bone histology of the titanosaurid sauropod Alamosaurus sanjuanensis from the Javelina Formation, Texas. Journal of Vertebrate Paleontology 25 (Supplement to No. 3):132A.

The hitherto hidden half of BMNH R46870

It’s no secret – at least, not if you’re a regular SV-POW! reader – that the Lower Cretaceous Wealden Supergroup of southern England includes more than its fair share of enigmatic sauropod remains (see Mystery sauropod dorsals of the Wealden part 1, part 2, part 3). Poor taxonomic decisions, a dearth of adequate descriptive literature, and (perhaps) the vague concept that sauropod diversity in the Lower Cretaceous of Europe must be low have combined to prevent adequate appraisal. Recent comments on Wealden sauropods have been provided by Naish et al. (2004), Naish & Martill (2007), Taylor & Naish (2007) and Mannion (2008).

One of the most interesting Wealden sauropods – and I mean ‘interesting’ in an entirely subjective, historiographical sense – is Chondrosteosaurus gigas. This taxon has a rather confusing history that I don’t want to repeat here. The type series consists of two cervical vertebrae: BMNH R46869 and BMNH R46870 (and it is BMNH R46870, despite the occasional use in the literature of ‘46780′). We’ve looked at BMNH R46869 before. This time round I want to briefly talk about BMNH R46870. Anyone familiar with the literature on Wealden sauropods will know that this specimen was sectioned and polished. However, to date, only half of BMNH R46870 has been published (Owen 1876, plate V; Naish & Martill 2001, text-fig. 8.4), on both occasions as a mirror-image of the actual specimen. Previously unreported is that both halves of the specimen were polished, and both are in the Natural History Museum’s collection today. And here they are, shown together for the first time ever. I screwed up on the lighting, so sorry for the poor image quality [images © Natural History Museum, London].

A little bit of science has been done on this specimen. Chondrosteosaurus has had a mildly controversial history: it’s been suggested at times to be a camarasaur, but its camellate interior show that it’s a titanosauriform. Because the exact ratio of bone to air can be measured, the specimen lends itself particularly well to an Air Space Proportion analysis of the sort invented by Matt. Indeed, Matt did some ASP work on the figured half of BMNH R46870 in his thesis, finding an ASP of 0.70 (Wedel, Phd thesis, 2007). The average ASP of sampled neosauropod vertebrae is 0.61, and an ASP of 0.70 for the mid-centrum (as opposed to the condyle or cotyle) is most similar to the values present in camarasaurs and brachiosaurs. Mid-centrum ASP values of titanosaurs seem to be lower (Wedel, Phd thesis, 2007).

Anyway, more on Wealden sauropods – hopefully, a lot more – in the future.

References

• Mannion, P. 2008. A rebbachisaurid sauropod from the Lower Cretaceous of the Isle of Wight, England. Cretaceous Research 30, 521-526.
• Naish, D. & Martill, D. M. 2001. Saurischian dinosaurs 1: Sauropods. In Martill, D. M. & Naish, D. (eds) Dinosaurs of the Isle of Wight. The Palaeontological Association (London), pp. 185-241.
• Naish, D. & Martill, D. M. 2007. Dinosaurs of Great Britain and the role of the Geological Society of London in their discovery: basal Dinosauria and Saurischia. Journal of the Geological Society, London, 164, 493-510.
• Naish, D., Martill, D. M., Cooper, D. & Stevens, K. A. 2004. Europe’s largest dinosaur? A giant brachiosaurid cervical vertebra from the Wessex Formation (Early Cretaceous) of southern England. Cretaceous Research 25, 787-795.
• Owen, R. 1876. Monograph on the fossil Reptilia of the Wealden and Purbeck Formations. Supplement 7. Crocodilia (Poikilopleuron). Dinosauria (Chondrosteosaurus). Palaeontographical Society Monographs, 30, 1-7.
• Taylor, M. P. & Naish, D. 2007. An unusual new neosauropod dinosaur from the Lower Cretaceous Hastings Beds Group of East Sussex, England. Palaeontology 50, 1547-1564.

Blogs, papers, and the brave new digital world: Matt’s thoughts

First off, thanks to everyone for reading, commenting on, and discussing the previous post. Seeing the diversity of opinions expressed has been interesting and gratifying for us, and we’ve learned a lot from you about how the blogosphere is changing science already. My own thoughts follow, Mike chimes in at the end, and Darren will probably have something to add soon, too.

The Intolerable Problem

Sometimes people push back on posts of mine they don’t like by telling me I’m out of bounds. Somehow, they say, I’ve crossed the boundary of what I’m allowed to write about. They are angry that I’m now writing about something outside my defined area.

I’m usually taken aback by this, because I didn’t realize I’d actually agreed to any boundaries.

Seth Godin, 2009, “Out of Bounds”

Several commenters have brought up what I call the Intolerable Problem, which is that people online can critique papers and present new evidence and arguments in a format that is impermanent and not peer-reviewed. It’s intolerable because on one hand such material is not currently (operative word) citable in most outlets, and on the other hand repeating it sans citation in peer-reviewed literature smacks of plagiarism (to some, but not to all). Although this material is potentially valuable it “doesn’t count” professionally (see exceptions below), which some professionals (not necessarily those who have commented here) regard as a fatal argument against posting it in the first place. But–and this is crucial–it’s only a problem for the tiny fraction of the audience who might want to cite the freely exchanged material. If you’re in that fraction, we value your attention and comments, but don’t assume we’re writing only for you, or to further our professional standing. We blog because we love this stuff, and even at a technical niche blog like SV-POW! the majority of readers probably don’t care at all whether the information is peer-reviewed or “counts” for professionals; they mostly care whether it’s right or not.

One obvious solution to the Intolerable Problem is to simply let people cite anything they want, including blog posts and DML posts. This is already starting to be implemented–see examples here and here and more discussion here. This runs into two problems: one is permanence (there is no guarantee that the cited post will be up forever, or that the author won’t revise it later in response to criticism [as I have done with this very post!]), which can already be solved using tools such as WebCite (thanks to Cameron Neylon for bringing this to our attention in a comment on the previous post).

The other problem is that citations serve two functions, which are to establish priority and to lend authority to an argument. Citing a blog post may establish priority, but some researchers will cavil at the idea that a blog post is an authoritative source (for varying combinations of researchers and blog posts). Whether they would be right to cavil I don’t know; in the end the market will decide. The market–that is, the desire to attain professional respect and avoid censure–will also dissuade authors from larding up their papers with citations to trivial or worthless online sources.

Those who are troubled by the free discussion of papers, evidence, and hypotheses online need to realize that:

• it’s been going on for a long time (15 years for the Dinosaur Mailing List);
• it’s only going to accelerate in the future;
• it’s not a problem for the vast majority of people participating in the discussions;
• any solution must involve accommodation to the reality of how people exchange information online (immediately, freely, globally, without prior filtering).

These discussions are not going to stop, and ignoring the output of such discussions (because they “don’t count”) will eventually become prohibitively expensive as those workers who insist on playing only by the old rules are outmaneuvered by others who find ways to use all available information regardless of its provenience or “respectability”.

Paper journals will die when online journals stop sucking

Most online publications are hampered by having to be identical to the dead-tree versions (no links, no embedded video, no rotating 3D PDF images, etc.). Eventually people will realize that it is counterproductive to keep hobbling the new medium to make it as slow, flat, and inefficient as the old medium. Once one journal takes the hobbles off, others will do the same rather than lose contributors to cutting-edge outlets. A few boutique journals may still produce flattened, gutted versions of the online publications on paper. People still fly biplanes, too. Paper-based journals will never be popular again and their existence will not stop people from doing whatever technology allows them to in the online venues.

Note that this does not even refer to the economic argument against dead-tree publishing, which has already relocated encyclopedias and newspapers from ubiquity to marginality or extinction.

I’m surprised that the revolution isn’t farther along already. The cage is open.

Whither peer review and editing?

This is all part of the Big Flip in publishing generally, where the old notion of “filter, then publish” is giving way to “publish, then filter.” There is no need for Slashdot’s or Kuro5hin’s owners to sort the good posts from the bad in advance, no need for Blogdex or Daypop to pressure people not to post drivel, because lightweight filters applied after the fact work better at large scale than paying editors to enforce minimum quality in advance.

Clay Shirky, 2003, “The Music Business and the Big Flip”

PLoS ONE is already going gangbusters, without peer-review prior to publication in many cases. The only holdup there is that the post-hoc review by commenters is not working out quite like they’d hoped, because few people are commenting. Not everyone agrees that there is a dearth of commenting at PLoS ONE; the larger point is that people publish there a lot and the community treats those pubs like they count, even though in many cases they are essentially un-reviewed.

[Update: I misunderstood peer review at PLoS ONE. Papers may be reviewed externally by people unconnected to PLoS, or by one or more unpaid Academic Editors, or by a combination. I had thought of the review by Academic Editors only, which accounts for 13% of papers, as a form of internal review, but according to Bora (down in the comments) it should count as external review. If you're happy with that--and the system is not without its critics--then all papers at PLoS ONE are externally reviewed prior to publication; even if you're not, pre-publication review by someone is still in place across the board at PLoS ONE, and 87% of papers are externally reviewed by people unaffiliated with PLoS. Post-publication commenting supplements rather than replaces pre-publication review.]

People do comment on blogs, all the time. Post-hoc review will work, in fact already does work, just fine on blogs. I predict that PLoS ONE clones of the future (PLoS TWO?) will emulate whatever features of blogs make people willing to comment on them but not on PLoS ONE v1.0.

Alternatively, the paucity of post-hoc commenting at PLoS ONE could be taken as further evidence that journal-mediated peer review, whether before or after publication, is dying just off to a slow start. I think that editorial control is not far behind. Both are locally extinct in some parts of the science publishing ecosystem, since people are already citing blogs.

Q: But–but–but? What about protecting the sanctity of the process? What about about guaranteeing respectability? What about prestige?

A: Hey, those questions would make a terrific opinion piece for your local newspaper–oops, too late.

I don’t deny that editors and peer reviewers often make significant contributions to the quality of published work. I just think that people will learn to get along without them if doing so allows faster and easier exchange of information. That was never possible on paper; it’s long been possible here.

A priori peer review and editorial control were invented because publications were scarce (in the Econ 101 sense of being limited) and there needed to be a barrier to entry. Now publication is instant, free, and global. Error correction and the assignment of value will still happen, but they’ll happen after publication rather than before, and they’ll be distributed rather than centralized.

Creeping blogification

Clay Shirky described the problem for newspapers and the recording industry as the existence of “cheap perfect copies”. An expanded but by no means exhaustive list for science publication includes:

• cheap perfect copies
• editable (but also archivable)
• sharable
• linkable (both incoming and outgoing)
• globally distributed
• instantly
• for free
• without pre-publication filtering
• with multimedia embeds (as opposed to including video etc. separately in the suppl. info.)

Online open-access journals currently take advantage of all of those capabilities except the last two. Newsgroup posts cover all the bases except the last one (so do tweets, despite the severe length limitations).

What covers everything? Blog posts. Which have the added advantage that people will comment on them without being asked.

But that’s not the whole simple story.

The center cannot hold–or can it?

So we’re looking at total chaos, right–a world where anyone posts anything they want, no one has any control, and no one knows how to find the good stuff? Well, two out of three, at least. I’m not worried about that last point, for two reasons.

First, thanks to search engines, aggregators, tags, tweets, links, etc., we already have pretty good tools for finding the good stuff. Those direction finders will get better even as the map gets more complicated.

Second, prestige will always be a motivator, so people will always compete to get into exclusive venues. Nature is not going away, although I think that in the near future they will decouple their online and print publications so that the former can take advantage of all the possibilities the web offers.

If I have a really good idea backed up with lots of data, I’ll keep trying to get it into the most prestigious outlet I can. I won’t put my best stuff on a blog just because it’s faster and less encumbered. Blogs probably won’t replace journals, at least not anytime soon. Rather, the spectrum of publishing possibilities will expand; below the category of Least Publishable Unit we’ll add Most Bloggable Unit and so on down to Least Tweetable Unit, and the new categories will interpenetrate with the old over time.

How nice for me

Well, what a striking coincidence that Mr. Paleo Blogger looks into the ole digital crystal ball and sees “bloggy with a 90% chance of exactly-what-he’s-already-doing”.

I can’t claim to be either uninterested or unbiased in all of this. But I am new to actually thinking about the implications. I hadn’t been to most of the above links or had any of these thoughts as of a week ago. When Casey first e-mailed me six days ago, I replied:

If you’re curious, here’s the short short version of my thoughts: science bloggers critique published papers and blog about unpublished observations all the time. Our post-paper run of posts might be an extreme or even vulgar example, and it might fire more discussion about “what counts?”, but I don’t see it as being different in kind from what many science bloggers do. Papers are papers and blogs are blogs, and I never intended to blur the lines. If people feel that all the blog posts only count as “crap some guys wrote on the internet” and that they can be safely ignored, that’s fine with me. If they think the blog posts deserve some higher level of recognition a la “what counts?”, then I’m honored, but that’s extra value that others are investing in our blog, and not anything that we’ve knowingly sought. I suppose you could turn around and say that I’m trying to have my cake and eat it, too, first with all the pro-paper blogging and now with this “I’m innocent” schtick. I don’t know what the answer is, but I know that I’m too tired to figure it out tonight. All the more reason to have an open conversation about this stuff.

Now I realize that the lines between papers and blog posts are blurring, and whether we mean to or not, we SV-POW!sketeers are contributing (Darren’s doing double duty thanks to Tet Zoo). I still think that the investment of blog posts with respectability, value, citability, or whatever rests entirely with readers, and always will. Options range from treating posts like papers to treating them like bar conversations to treating them like spam. You decide.

Also, I tried to keep the writing above value-neutral but probably failed. It’s hard not to get a bit evangelistic about the potential advantages of online publication and online everything else, a tendency I call DISSUADE: Da Internet Shall Save Us All Dead-trees Excepted. Getting published in science hasn’t always been easy up until now, but the process has been relatively clear and familiar. And stable, on decadal and even centennial timescales. Everything about scientific publication is about to get much more fluid and much less clear, and it will probably stay that way for a long time, and it may stay that way forever. Not all of the changes will be for the better, and it may be hard to decide what’s better and what’s worse until we look back with some perspective. Mechanical looms were bad for weavers but good for everyone else. I think many of the changes discussed in this post and the previous comment thread are likely, and some are inevitable.

Set against the shiny digital future is the inertia of the academy and those of us who roost there. I’m not going to stop publishing papers in dead-tree journals (although I will never publish in a journal that doesn’t provide PDFs to authors). Heck, I’m not even going to stop publishing in closed-access journals, some of which are run by societies I admire and want to participate in (after all, everything is open anyway). At the same time I will keep blogging, and while I will frequently bring up technical stuff I don’t want to publish more formally (at least not yet), I will try not to deliberately blur the lines any more than I already have. I don’t need to; the web is already blurring them faster than most of us can keep up.

Hang on.

Oh, about that mystery vert…

Metapophyses, I haz them

…at the end of the post Necks Lie. Nima called it–good spot on the split neural spine. It’s a mid-cervical of Barosaurus, AMNH 6341, in the big bone room (well, one of many big bone rooms) at the American Museum of  Natural History in New York. A cast of this vertebra makes up part of the neck in the awesome mounted skeleton in the museum rotunda. Here’s that skeleton, with Mike for scale.

Thanks for slogging through all this. We’ll get back to perforated postcentrodiapophyseal laminae, sacralized caudal transverse processes, and the air space proportions of pneumatic vertebrae soon.

Addendum (from Mike)

Matt is much more ready than I am to throw away peer-review, editorial control, and journals in general.  Sometimes, the reasons that things are the way they are, are good ones; it’s not in the interests of professional iconoclasts like Clay Shirky and Cory Doctorow to point that out or to discuss the strengths of how things are today, but that doesn’t mean we have to accept their arguments as uncritically as (say, to pick a name out of the air completely at random) Matt.

Anyway, happily, G. K. Chesterton foresaw the abolition of journals in favour of blogs, and commented thus:

Suppose that a great commotion arises in the street about something, let us say a lamp-post, which many influential persons desire to pull down. A grey-clad monk, who is the spirit of the Middle Ages, is approached upon the matter, and begins to say, in the arid manner of the Schoolmen, “Let us first of all consider, my brethren, the value of Light. If Light be in itself good–” At this point he is somewhat excusably knocked down. All the people make a rush for the lamp-post, the lamp-post is down in ten minutes, and they go about congratulating each other on their unmediaeval practicality. But as things go on they do not work out so easily. Some people have pulled the lamp-post down because they wanted the electric light; some because they wanted old iron; some because they wanted darkness, because their deeds were evil. Some thought it not enough of a lamp-post, some too much; some acted because they wanted to smash municipal machinery; some because they wanted to smash something. And there is war in the night, no man knowing whom he strikes. So, gradually and inevitably, to-day, to-morrow, or the next day, there comes back the conviction that the monk was right after all, and that all depends on what is the philosophy of Light. Only what we might have discussed under the gas-lamp, we now must discuss in the dark.

- Heretics (1905).

Necks lie

Since we’re spending a few days on neck posture, I thought I’d expand on what Mike said about bunnies in the first post: in most cases, it is awfully hard to tell the angle of the cervical column when looking at a live animal. Because necks lie.

Take this horse (borrowed from here). You can see that the external outline of the neck, which is what you would see in the living animal, is pointed in a different direction than the cervical column.

And here’s why. Many mammals carry their heads and necks so that the cranio-cervical joint is up high and the head is angled down from it. At the base of the neck, tall neural spines on the anterior thoracic vertebrae support the nuchal ligament, which lifts the body profile far above the cervical vertebrae. Basically, the cervicals run from the lower or middle part of the neck at its base to near the top of the neck at the head end.

This mismatch holds no matter how the neck and head are oriented. When the animal lowers its head to graze, the cervical column is still angled up relative to the apparent angle of the neck defined by its dorsal and ventral margins.

But if you think that’s bad, you ain’t seen nothin’ yet.

In most of the smaller birds, like this budgie (from Evans 1969:fig. 5-6) the neck is much longer and more flexible than you would think based on the external profile. And check out the mismatch between the cervical column (in front) and the trachea (behind). That’s not drawn incorrectly; the trachea is outside the bundle of neck muscles that encloses the vertebrae, and it is free to slide around all over the place, and does so in many birds.

Also note that while the neck is extended past vertical, the extension occurs in the middle of the neck, not at the shoulder. The neck actually goes down from the craniocervical joint, not up. My guess is that there is a lot of this in climbing taxa that hold their torsos elevated. Vultures come to mind here, too. A useful reminder that in natural history we are usually dealing with norms, not laws.

In the pigeon, note again the fact that the mid-cervicals are angled up much more sharply than is the external profile of the neck. In fact, the external profile of the neck is angled forward while the mid-cervicals are angled backward. This excellent reconstruction is from this page, which has several others which also show that necks lie.

Lest anyone think that the pigeon was either an outlier or a case of artistic embellishment, here’s yet another rabbit, this time from Vidal et al. (1986: fig. 5a). Again, the mid-cervicals–actually, almost all of the cervicals–are angled backward, but the neck as a whole is pointing slightly forward.

As an aside, I think possibly it has blown some people’s minds that we have used so many rabbits as examples, both in the paper and in our blog coverage. What can we say? Rabbits are awesome.

Of course not all necks lie. With flamingos, what you see is what you get.

Giraffes: 20 feet of reticulated irony

Let’s see here: necks not vertical.

Necks not vertical.

Trying . . . very . . . hard . . . and . . . just . . . getting . . . to . . . vertical!

(I know it looks like the neck is just slightly less than vertical, but remember that necks lie, and the cervical column is steeper. In this animal, you could drop a plumb bob from the ear and it would track the course of the cervical vertebrae just about perfectly.)

Cat, not trying at all: cervical column past vertical (Vidal et al. 1986: fig. 2).

Rat, taking its ease (top): cervical column vertical. Guinea pig, straight chillin’ (bottom): cervical column past vertical (Vidal et al. 1986: fig. 5 b and c).

Here’s the irony: for  practically as long as sauropod neck posture has been contentious, giraffes have been held up as THE example of the most extreme (dude!) elevated neck postures out there. But in fact giraffes have to really reach to achieve vertical cervical postures that “ordinary” animals like cats, rats, guinea pigs, chickens, and, yes, rabbits, reach or exceed all the time.

Good paleobiology has to start with good biology. It’s high time that the sauropod neck posture debate got a reality infusion. Giraffe necks are extreme in terms of length, but not in terms of posture.

Speaking of sauropods…

All right, you’ve suffered long enough. Here’s your sauropod vert. Care to guess what it is?

References

• Evans, H.E. 1969. Anatomy of the budgerigar; pp. 45-112 in Petrak, M.L. (ed.), Diseases of Cage and Aviary Birds. Lea and Febiger, Philadelphia.
• Vidal, P.P., Graf, W., and Berthoz, A. 1986. The orientation of the cervical vertebral column in unrestrained awake animals. Experimental Brain Research 61: 549­-559.

X-Men Origins: Pneumaticity

The respiratory system of a pigeon injected with pink latex. Click for the unlabeled gory version.

In case you’ve missed it, William Miller has been asking some great questions over in the comment thread for “Brachiosaurus: both bigger and smaller than you think“. Here’s his most recent, which is so good that the answer required a post of its own:

…in birds, the air sacs are obviously useful for flight, and they might have been useful for weight lightening in sauropods: but the common ancestor would have been flightless and too small to need the lightening. So what drove their evolution in the first place, I wonder?

To which I say: oh, Alice, the rabbit hole is a lot deeper than that.

Introduction to the Three Mysteries

First, in birds the diverticula that enter the bones are a comparatively small subset of all diverticula. Visceral, intermuscular, and subcutaneous diverticula run between the guts, between muscles, and under the skin, respectively. These are usually more numerous and more extensive than the diverticula that enter the bones, and with rare exceptions, like the subcutaneous “bubble wrap” in pelicans, we have no idea what they do. If, indeed, they do anything. All a character needs to do to be hereditarily propagated is not compromise the survival and reproduction of its bearer. Diverticula could be mostly functionless products of developmental processes that are usually invisible to selection but sometimes produce useful exaptations, like lightening the skeleton, insulating the body, etc. Sort of the evolutionary equivalent of the fire extinguisher in your kitchen: most of the time it does absolutely nothing, but once in a while it is really, really useful.

Second, postcranial skeletal pneumaticity (PSP) starts in the cervical vertebrae in basal theropods and sauropodomorphs, and possibly also in pterosaurs (Butler et al. 2009). The vertebrae adjacent to the lungs and air sacs are not the first to be pneumatized. Rather, the pneumatic diverticula must have gotten out of body cavity and traveled a ways before they started impacting the skeleton. Assuming that one thing had to come before another and it didn’t happen in one saltatory leap, diverticula must have evolved before they started pneumatizing the skeleton.

Third, in the earliest evolutionary stages of pneumatization in saurischians, the amount of bone removed is completely negligible. In Wedel (2007) I calculated that in Pantydraco (Thecodontosaurus caducus at the time) and Coelophysis the pneumatic spaces in the bones accounted for 0.0017% and 0.17%, respectively, of the body volumes. The fossae in the Pantydraco vertebrae are not absolutely diagnostic for PSP, but they’re in the right place and hard to explain otherwise. The holotype individual is a juvenile, and it is possible that PSP might have been more extensive in an adult, but it could increase one hundred-fold and still only be 1/500 of the animal’s volume, as in Coelophysis. Although I haven’t run the numbers, a similar result probably hold for the basalmost sauropods with definitive PSP.

Pneumatic fossae in the cervical vertebrae of Coelophysis

To sum up:

1. Most diverticula in birds are not involved with pneumatizing the skeleton, so PSP can’t be the reason for their existence.
2. In basal saurischians, the diverticula that pneumatized the skeleton must have evolved before they could start pneumatizing the skeleton, so PSP can’t be the reason for their existence, either.
3. In the early stages of the evolution of PSP in saurischians, the amount of mass saved was negligible and could not plausibly have influenced natural selection, so PSP didn’t initially evolve to lighten the skeleton.

Lighten Up, Fatso

There is a complication on that last point, which requires a little digression on fat.

In birds, pneumatic diverticula don’t just replace bone tissue, they also take up space that would be occupied by fat in mammals, for example in the spaces between muscles and around plexuses of nerve and blood vessels. Any of you who have had the misfortune to dissect the brachial plexus of a mammal know whereof I speak–you spend most of your time carefully picking fat out from around the nerves and blood vessels. This isn’t gross subcutaneous fat that means an animal or person is obese, this is adipose tissue doing its other job of being a lightweight packing material. Mammal bodies put fat in those spaces because they need to occupied by something light and squishy and fat is the cheapest thing your body can build.

That may seem backwards; we think of fat as an energy store and therefore energetically expensive. But it’s cheaper to build than muscule or cartilage or skin, and lighter than any other tissue or fluid in the body. It has been observed that even when mammals are starving, they do not use the fat in the yellow marrow that fills the marrow cavities of long bones. This is utterly unsurprising if you think about how bodies work. Nature really does abhor a vacuum, at least biologically (cosmically, it seems to be the biggest thing ever). If a starving body used the fat in the marrow cavity, it would have to replace it with something else, and all of the alternatives are heavier and more expensive to build. If the fat was not replaced, a partial vacuum would develop which would cause serous fluid to weep into the space, and that would also be heavier and more expensive, and a great site for infection to boot (ask someone who has an edema).

Birds cheat the system by replacing the lightest of tissues with something even lighter: air, held in diverticula that are basically super-thin layers of epithelium. Possibly diverticula had been running around replacing fat for a long time before they first entered the skeleton, in which case the earliest stages of pneumatization would have been a continuation of pre-existing function of replacing superfluous connective tissue (fat and bone are both forms of connective tissue, along with cartilage, ligaments, tendons, mesenteries, fascia, and blood; blood is connective tissue the way snakes are tetrapods).

Although that will be difficult or impossible to test, it actually makes quite a bit of sense. Getting fat out of the way ought to be easy; the lipids can be mobilized into the bloodstream and the flattened cells could either be pushed out of the way or resorbed. Getting bone out of the way requires increasing parathyroid hormone, mobilizing blood-born multinucleated osteoclasts, and convincing them to digest bone where it needs to be digested, which I assume is a more complicated process from a regulatory standpoint (physiologists or cell biologists, please correct me if I’m wrong!). So it seems plausible that diverticula might have acquired the ability to replace fat early on, and the ability to replace bone much later, and that by the time they got started on the skeleton diverticula could have been lightening the body for a long time by removing little bits of superfluous fat.

This does not contradict my statement above that by and large we don’t know what diverticula do. Some diverticula run where there is no fat to replace. And healthy birds do carry some fat, like any healthy tetrapod. One would think that this energy-reserve fat would need to be protected from diverticula that would otherwise resorb it, but I don’t know how or if that happens, and I don’t know if anyone else does either. The amount of research on diverticula is basically nil.

I also think that fat-resorbing diverticula don’t solve the third mystery, they just pushes it back a level. The amount of mass saved by replacing the “packing” fat with air is probably negligible in most animals, and it certainly would have been so in the earliest stages of replacement, so the third mystery still holds if it  is restated as:

3b. In the early stages of the evolution of diverticular replacement of connective tissue in saurischians, the amount of mass saved was negligible and could not plausibly have influenced natural selection, so PSP didn’t initially evolve to lighten the body.

A dorsal vertebra of Haplocanthosaurus in anterodorsal oblique view. It's pneumatic, sure, but not THAT pneumatic.

The Problem is the Solution

So, we seem to be stuck. We don’t know why diverticula evolved in the first place, and we don’t know what most diverticula do, and even the diverticula that lighten the body could not have initially evolved to do so.

One upshot of all this is that we need more research on possible  physiological functions of diverticula in birds. Oy! Ornithologists and avian physiologists! We’ve thrown you a bone, now throw us some data. Please?

Another upshot is that the erratic evolutionary pattern of PSP in Triassic and early Jurassic ornithodirans is maybe not entirely unexpected. Pterosaurs and theropods seem to have had PSP right out of the gate, but at least in theropods it was not enough to have done any good. Basal sauropodomorphs had little or no PSP, and not enough to have done any good below about the level of Eusauropoda. No non-dinosaurian dinosauromorphs have been found with PSP, but then we only have a handful of them and they’re all pretty dinky, so it’s possible it just hasn’t been recognized yet. Silesaurids, at least, had very pronounced, very thin laminae, which in derived saurischians are almost always associated with PSP. And ornithischians never had PSP at all, as far as we know.

My opinion is that an air sac system is probably primitive for Ornithodira, and that most of these lineages had pneumatic diverticula, but the speed with which they “discovered” extensive, skeleton-lightening PSP–ranging from “almost immediately” in pterosaurs to “after a while” in theropods to “after a long while” in sauropodomorphs to  “never” in ornithischians–varied because it was such an evolutionarily haphazard process. Basically, PSP had to evolve as a developmental accident, and in some lineages it got far enough to become visible to selection, and in others it did not, or took a long time to do so. That’s a pretty picture that makes a lot of sense to me. If I ever figure out a way to test it, I’ll let you know.

What's going on here? Why are ornithischians so lame?

The Solution is the Problem

The absence of PSP in Ornithischia is still a right sod. Pterosaurs, theropods, and sauropodomorphs all evolved some level of PSP in the Late Triassic, even if it wasn’t enough to significantly lighten their skeletons at first. Why not ornithischians? If air sacs are primitive for Ornithodira, then ornithischians had the gear for 160 million years and never exploited it, when the other three major lineages of ornithodirans discovered PSP pretty fast out of the gate. And if air sacs are not primitive for Ornithodira, three out of four ornithodiran lineages still discovered PSP on their own, so why not Ornithischia? It’s a big mystery, any way you slice it.

What do you think?

References

• Butler,  R.J., Barrett, P.M., and Gower, D.J. 2009. Postcranial skeletal pneumaticity and air sacs in the earliest pterosaurs. Biology Letters. doi:10.1098/rsbl.2009.0139
• Wedel, M.J. 2007.What pneumaticity tells us about ‘prosauropods’,
  and vice versa. Special Papers in Palaeontology 77:207–222.

OMG: MPT, PHD!

If you woke up this morning and thought, “Global warming is on the rise, amphibians are in a race to see who can go extinct first, the economy is in the toilet, any day now my boss will discover that I don’t actually do anything at work,  and my blog will never have the eclectic cachet of SV-POW!, but at least Mike Taylor doesn’t have a Ph.D.,” then it is my happy duty to ruin your day. Mike defended today, successfully.

Ladies and gentlemen, I proudly present Michael P. Taylor of Ruardean, Englishman, adventurer, raconteur, Doctor of Philosophy in the paleontological arts. Note that when recumbent he is approximately equal in length to 1.5 Sauroposeidon cervicals, and appears to be cradling an invisible wine glass. Don’t stare too long, or you might not be able to look away.

Congratulations, sir! Let the blogosphere ring with the happy news, and undescribed sauropods cry out for recognition.

Update (from Mike)

Thanks to Matt, and all commenters, for your kind words.  I wondered when the “Latin love god” photo was going to appear, and that day has finally come.  What Matt doesn’t know is that this photo was used for the cover of my forthcoming album:

Available wherever good music is sold

Off-topic: non-open academic publishing is dead

Because of my work on the recent Cetiosaurus petition, I’m on the ICZN mailing list.  Apart from the brutally technical threads on specific nomenclatural cases, the favourite topics of that mailing list are electronic publication and in particular the long-term preservation on anything not printed onto compressed plant matter.  In one such recent discussion, the LOCKSS system came up as possible solution, and I found myself replying with what quickly became a tangential rant.  Here it is, in lightly edited form, for your amusement.

LOCKSS is a complete red herring here.  Although the project acronym — Lots Of Copies Keep Stuff Safe — implies that it’s all about replication, the project really exists to keep published work locked up — to prevent people reading it, keeping it hidden away to be opened up only in the event of something catastrophic happening like the publisher going out of business.

The reality, as we surely all know from our interactions with our colleagues within our own subdisciplines, is that everything that gets published and made available in electronic form is already replicated in lots of copies; and those copies are distributed far more widely than a monolithic system such as LOCKSS could ever achieve.  Not only that, but the distribution requires (and has) no funding: individuals do it because it benefits them and their friends.

I know that for-profit publishers have reasons to pretend that closed-access publishing is still possible, but there is no reason for the rest of us to be blinded by that fantasy.  The ship has sailed, the genie is out of the bottle, the can is open and the digital worms are everywhere.  Everything is open access.  Whether a publisher makes a PDF freely available or not, is is freely available to anyone who wants it — that’s the way it is in 2009, and nothing that anyone does can change that.

We can and should plan on the basis of reality, not on the basis of either history or of a publishers’ delusions.

So: the PDFs are out there, and will stay out there.  Assuming that every personal computer in the world and every backup store isn’t simultaneously destroyed (which could only happen under circumstances that left us with much worse problems than nomenclature), what could happen to make us lose the accumulated literature available?  Software rot?

Some people worry that the software that reads PDFs will decay so that all our PDFs become useless. Sorry, but that is another red herring.  It is true that Adobe may at some point stop supporting their particular PDF-reading program, Acrobat.  But that really is not important: the specifications for PDF are open, and there are many, many implementations of those specifications, including half a dozen open-source PDF readers that I could name off the top of my head.  While there is a demand for them (i.e. while there are PDFs), these will never go away — and for the same reason the PDFs themselves will never go away: because they exist in hundreds, thousands of copies — quite likely millions, given that these readers tend to be distributed as part of operating systems.

Again, please understand: it simply does not matter if a particular proprietary PDF-handling program goes away, because the knowledge of how to read PDFs is itself distributed.  That knowledge is in the public domain.  (PDF was recently ratified as ISO 32000-1:2008).  Lots Of Copies really do Keep Stuff Safe, and they don’t need LOCKSS to do it.

So where are we?  We have PDFs, which will always be readable — and perhaps successor formats, which will also always be readable for the same reasons.  We have PDFs-reading programs, which will also always be available.  Both the publications and the software are distributed literally globally on a network which was designed to survive a direct nuclear strike.

Folks, it’s over.  The digital revolution has happened.  There is absolutely no rational reason in this day and age not to accept digital publication; in another ten years, the ICZN is going to look stupid for even having discussed this.  And let’s hope they’re still around in ten years to feel dumb — because if they’re still insisting on paper, they’ll be history long before then.  The Code is afforded legitimacy by the journals only because it serves them; if the Commission lets it become anachronistic the journals will desert it — or, if we’re lucky, they might pick and choose, following only those provisions of the code that suit them.

Let’s not be overtaken by the rush of events.  Eyes open, face into the wind.  Let’s go.

As it happens, Andy Farke has just published a list of Open Access Journals in Paleontology over on his Open Source Paleontologist web-site.  That’s ironic timing since we were just in the process of establishing such a list over here on SV-POW!, by importing Matt’s old lists from his Ask Doctor Vector site.  But better two lists than none, so we’re going ahead and published ours, too — not least because it contains links to individuals’ publication pages and miscellaneous collections as well as journals.  With three of us over here to work on it, hopefully we can keep it up to date: do let us know in the comments of anything we’re missing.  The lists are over here in the sidebar —->

Finally, here is Cervical U of Migeod’s Tendaguru brachiosaur BMNH R5973, informally known as “The Archbishop”, this time in anterior view.  Copyright the Natural History Museum.