Another call from another science to replicate experiments.

The gist for this post came from:
“Research, Report, Repeat“– an article from Discover Magazine (Yong 1/14).

The story interviews psychologist Brian Nosek, at the University of Virginia, who is at the forefront of the fight to make psychology more transparent. While you’re reading this, delete in your mind the word, “fraudulent” and put in its place “incomplete.” In place of “charlatan” put “traditionalist” in its place.

From the article:
“In 2011, Dutch social psychologist Diederik Stapel was revealed as a charlatan who had published dozens of fraudulent scientific papers. The shocking thing was that no one in his field had noticed until courageous students in his lab reported their suspicions. This spate of misconduct happened in tandem with many failed attempts to replicate some of the field’s classic results, prompting acolytes to question whether psychology was being polluted by quirky and attention-grabbing findings that might not actually be true. This issue applies to every field of science, from physics to medicine.“

The key point to the article is reproducibility.

Hypotheses, phylogenetic trees, reconstructions that fit footprints—all of these things in paleontology must be reproducible and tenable. Unfortunately, as I’ve reported here, replication often fails, typically due to an incomplete inclusion set. Sometimes, as in deep chord wing membrane papers, to wishful thinking.

We’ve seen this in phylogeny following attempts at nesting pterosaurs with archosaurs, at nesting mesosaurs with pareiasaurs, at nesting caseasaurs with pelycosaurs. All that was fine, but now that the repair is available (see www.reptileevolution.com) there is less excuse for continuing phylogenetic errors based on incomplete inclusion sets.

The pterosaur heresies blog is here to reproduce and verify or falsify the work of other paleontologists. Just as other paleontologists are doing all the time.

Testing is key.
Did they include the proper inclusion set? Too often they did not. Did they find sisters that provide a tenable evolutionary path that provides a gradual accumulation of traits? Too often they did not. Did they invent excuses for soft tissue not behaving in situ according to their traditional hypotheses? Too often this is so. Did they really try to pull details out of the specimen or did they draw a crude circle around the crushed skull and call it a day?

Unfortunately,
all these were done with the best intentions following established procedure with no intention to defraud. Rarely, as in Bennett’s 2008 imaginary protopterosaur, hypotheses can appear that are completely imaginary with no basis in reality, no thought to untenable evolutionary scenarios, and no testing or review of prior published studies and specimens.

Back to the Discover article:
In 2011 Brian Nosek and colleagues launched the Reproducibility Project, in which a team of about 200 scientists are carrying out experiments to replicate findings published in psychology journals. They want to examine the problem of false-positive results.

Nosek reports, “There is an ethic that science is self-correcting, but replication is often a pain the in butt, and since scietists’ career success doesn’t depend on exactly replicating a study that’s already been published, they usually don’t do it. As a result, mistakes end up hanging around longer than they need to.”

The same can be said of paleontology.
Most of paleontology is on an even track. But there are still problems out there, like “modular evolution” and the exclusion of tiny (sparrow-sized) pterosaurs and fenestrasaurs from analyses.

Nosek built the “Open Science Framework” a web application where collaborating researchers can put all their data and research materials so anyone can easily see them. The same thing is happening for paleontology at ResearchGate.org and Morphobank.org.

Nosek concludes, “Replications are so rare that people perceive them to indicate a lack of trust. I want it to be very ordinary for people to say, “I’m not sure about this, so I’ll replicate it,” and for that to be a compliment, not a threat.”

I heartily agree.

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The Sericipterus mandible reconstructed – new insights using Photoshop

I love it when this happens.
I made a mistake here earlier today, and within just a few hours, I am able to correct it. So what you are about to read here has been thoroughly rewritten to reflect the latest thinking.

Earlier I misidentified what looked like a too gracile mandible (relative to the other skull parts) on the pterosaur, Sercipterus (Figs. 1-3), as a tibia and fibula. Here is the illustration in which I made the mistake (Fig. 1). And made a further mistake by calling out the original interpretation as an error.

Figure 1. From Andres et al. 2010, where they misidentify a tibia/fibula and call it a mandible with surangular.

Figure 1. Click to enlarge. From Andres et al. 2010, where they identify a mandible and surangular. I thought it odd that it would be preserve narrow edge up, and where are the teeth or their alveoli? But now i see the reason for this. Read on.

At the time I overlooked the left mandible. It’s easy to do. There’s not much that makes it look like a mandible. The back half is all that is preserved. The left mandible appears to be a little deeper, which it needs to be according to phylogenetic bracketing.

This is the key. 
Allthough the fossil had been thoroughly stirred during preservation so that nothing is where it was in the living pterosaur, there are two bones that are indeed in their original configuration: the two posterior mandibles (Fig. 2, in pink). How can this be??

Figure 2. When you use your imagination, and a little Photoshop, you can retire the front of the mandible. What we're seeing is the ventral view, so no teeth are visible. The reason why the mandibles remain in their original configuration is the front of the fused mandibles, now vanished. And that's why the right mandible is preserved narrow end up.

Figure 2. When you use your imagination, and a little Photoshop, you can restore the front of the mandible. What we’re seeing here is the ventral view, so no teeth are visible. The reason why the posterior mandibles remain in their original edge-on configuration is due to the front of the fused mandibles, now vanished. The entire mandible was originally preserved in its flattest plane. And that’s why the right mandible remains narrow end up.

Restoration of the missing parts clears up all the confusion.
When you extend the lines of the posterior mandible, the anterior portion becomes plainly visible. Now we have a mandible that is the proper length for the skull parts (actually it elongates the earlier restoration of the skull and suggests a larger antorbital fenestra than in other dorygnathids, Fig. 3). And now the narrow mandible makes sense because it is not preserved in lateral view.

Figure 3. New reconstruction of Sericipterus with restored mandible in lateral view based on the related MBR 1920 specimen, in color at right.

Figure 3. New reconstruction of Sericipterus with restored mandible in lateral view based on the related MBR 1920 specimen, in color at right.

Colleague [name deleted] was kind enough to drop a note on this (see below) that prompted a review of the situation. Later Mike wrote, “Sometimes it is better to trust people who have spent many hours with the specimen in front of them and read the descriptions.”

That’s a common notion,
but that’s not the thought you should take-away from this exercise.

Science doesn’t work on trust.
It works on testing. Having never seen a mandible preserved edge-on in the matrix, without obvious alveoli and too gracile for the skull, I sought another explanation for the questionable portion of the fossil. The tibia/fibula seemed to be a good fit.

But I was wrong. The mandible was not preserved edge-on, but flattened along its widest dimensions, like most fossils are. Then the anterior half of the fused mandible was lost leaving the posterior parts edge-on. Now it makes sense.

It would have helped if the above restoration was made prior to publication. I’m sure you can see how well it illustrates the situation here. Making mistakes is one way to shed new light on a problem. I never would have arrived at this solution and explanation had I merely trusted the original authors.

When something doesn’t make sense, keep working on it until it does makes sense.

It’s a process. And I’m always glad to accept any help that is offered. Getting it right is the ultimate goal.

References
Andres B, Clark JM and Xing X 2010. A new rhamphorhynchid pterosaur from the Upper Jurassic of Xinjiang, China, and the phylogenetic relationships of basal pterosaurs, Journal of Vertebrate Paleontology 30: (1) 163-187.

Revision to earlier mistake on Darwinopterus pelvis

Earlier I misinterpreted the pelvis and prepubis of Darwinopterus robustodens (since revised). Here (Figs. 1-5) I want to take you through the DGS process that more accurately identifies the elements present. Here (Fig. 1) is the in situ fossil. The original reconstruction, you might recall (Fig. 5) found a very deep pubis and a very shallow ischium opening, hardly enough to squirt out a turd, let along an egg!

Figure 1. The pelvic area of Darwinopterus robustodens in situ.

Figure 1. The pelvic area of Darwinopterus robustodens in situ. The ilium is easy to see. The ventral pelvis can be confusing at first glance. Here’s where DGS really shines.

First we’ll colorized the sacral verts (Fig. 2).

Figure 2. Darwinopterus robustodens sacral vertebrae in red.

Figure 2. Darwinopterus robustodens sacral vertebrae in red.

Then we’ll find the left and right pelvic and prepubic elements (Fig. 3). Note how the rear prepubis provides the illusion of a continuous ventral pelvic rim. The left pubis is folded back onto the medial left ischium, thickening it. Compared to other Darwinopterus specimens, the prepubes are flipped here.

Figure 3. Darwinopterus robustodens pelvic and prepubis elements. Note the left pubis is folded back on top of the left ischium. The rear prepubis fills a nice gap that makes the elements look like a single element.

Figure 3. Darwinopterus robustodens pelvic and prepubis elements. Note the left pubis is folded back on top of the left ischium. The rear prepubis fills a nice gap that makes the elements look like a single element.

Finally, we’ll colorize the two femora.

Figure 4. The two femurs of Darwinopterus robustodens

Figure 4. The two femurs of Darwinopterus robustodens

Pulling the elements out of the tracings (Fig. 5) provides a more plesiomorphic pelvis with an ischial opening large enough to pass a Darwinopterus-size egg.

Figure 5. Darwinopterus robustodens pelvis as originally reconstructed (gray scale) and as recovered using DGS (color).

Figure 5. Darwinopterus robustodens pelvis as originally reconstructed (gray scale) and as recovered using DGS (color). I wonder whether the present orientation of the prepubis is correct. but it seems to fit better both here and to match with sister taxa when flipped like this.

Cleaning up mistakes is the process of Science.

References
Hyder ES, Witton MP and Martill DM 201X. Evolution of the pterosaur pelvis. Acta Palaeontologica Polonica 5X (X): xxx-xxx. http://dx.doi.org/10.4202/app.2011.1109

Short hiatus – hdd crash

Apologies to faithful followers of the Pterosaur Heresies.

Over the weekend while trying to download Maverick (the latest OS from Apple) I had a hard drive crash. All files were backed up. So the inconvenience will only last 3-5 business days.

I’m at the public library at the moment.

This is a good time to send in requests, by the way. If you have any phylogenetic mysteries you want some discussion about (please keep it in the range of basal reptiles (avoid higher mammals and higher dinosaurs, please, as these have been adequately covered in the literature).

Thank you for your patience.

Some interesting reports are “in the hopper.”

BTW
For followers of the Dinosaur Mailing List, they are also experiencing computer problems, according to Mary Kirkaldy (per. comm).

Wukongopterus – with a broken leg

Pterosaur fossils can get pretty messed up over 150 million years. Most of that happens during their lifetime or shortly thereafter as they sink into sediments.

Wukongopterus (IVPP V15113 , Wang et al. 2009) is a not-quite complete specimen that preserves a broken leg (Fig. 1). The Daohugou Bed of the Tiaojishan Formation was originally described as Early Cretaceous, but is now dated to the Middle/Late Jurassic boundary. This makes more sense with regard to phylogenetic order.

Figure 1. Wukongopterus with a broken tibia (in pink).

Figure 1. Wukongopterus with a broken tibia (in pink). It looks like the tibia was kept in place by tendons and dermis after the break, whether before or after death. Compare the broken tibia to the unbroken one. Even the foot was twisted medial to lateral.

References

Wang X, Kellner AWA, Jiang S and Meng X 2009. An unusual long-tailed pterosaur with elongated neck from western Liaoning of China. Anais da Academia Brasileira de Ciências 81 (4): 793–812.

wiki/Wukongopterus

Second egg in Momma Darwinopterus?

Figure 1. Darwinopterus pelvic area in situ.

Figure 1. Darwinopterus pelvic area in situ.

Mrs. T, the AMNH specimen of Darwinopterus (Lü et al. 2011a, Figs. 1-3), preserves a well-defined egg just past her  fossilized cloaca, oddly on top of the tail in ventral view. This is the fourth pterosaur egg recognized by paleontologists. The other three, the IVPP specimen, the JZMP specimen and the MHIN specimen (embryo Pterodaustro), preceded it and preserve embryos with well-defined bones and a bit more leathery eggshell.

Figure 2. Pelvic elements colorized. Red-prepubes. Magenta-femora. Green-ilia. Blues-ventral pelvis. Yellow-vertebrae.

Figure 2. Pelvic elements colorized. Red-prepubes. Magenta-femora. Green-ilia. Blues-ventral pelvis. Yellow-vertebrae.

While trying to colorize the pelvic elements (Fig. 2), I came across a smaller oval that did not leave the body (Fig. 3).

Figure 3. Darwinopterus egg (lower left), and possible egg (upper right). What is it really?

Figure 3. Darwinopterus egg (lower left), and possible egg (upper right). What is it really?

I wondered if it was a younger egg? There’s little reason for this. The eggshell, never substantial even in full term embryos, would not have formed at the early stage this size would represent. And the contents of the egg are mostly goo. Nevertheless, the larger more mature and verified egg, has little more substance than the small one.

So, if anyone out there can help with this  I.D., let me know.

References
Lü J, Unwin DM, Deeming DC, Jin X, Liu Y and Ji Q 2011a. An egg-adult association, gender, and reproduction in pterosaurs. Science, 331(6015): 321-324. doi:10.1126/science.1197323

Looking for the Darwinopterus bits’n’pieces

This is a short trip through DGS using the YH2000 specimen of Darwinopterus (more completed than the holotype, but with a poorly preserved skull, (Lü et al. 2009). Crushed flat and spread eagle, one wonders whether this is a ventral or dorsal view. Without a prominent sternal complex and with such dark bones, it’s hard to tell at first glance (Fig. 1).

Figure 1. Darwinopterus as published in Lu et al. 2009.

Figure 1. Darwinopterus as published in Lu et al. 2009.

The first thing we’ll do is play with the exposure to bring out the bones better (Fig. 2). Now we can see the scape are below the ribs.

Figure 2. Darwinopterus again with pelvic and pectoral regions brightened.

Figure 2. Darwinopterus again with pelvic and pectoral regions brightened.

Next we’ll add a layer in Photoshop and colorize the elements we’re interested in.

Figure 3. Bones colorized. Here the left scapulocoracoid is lavender/purple, the right one is magenta.

Figure 3. Bones colorized. Here the left scapulocoracoid is blue, the right one is magenta. Sternal complex in two parts in yellow. Where is the rest of it? For that matter, where is the right coracoid? I think it has drifted below the left scapula. 

The final step ghosts back the original image to bring out the tracings better. There’s the sternal complex, broken in two and tiny. Maybe parts are missing here. Prepubes in pink. One broken. A few drifted ventral pelvis parts here.

Figure 4. Ghosted image to bring out the tracing better. If bones are broken, you have to find both ends.

Figure 4. Ghosted image to bring out the tracing better. If bones are broken, you have to find both ends. One prepubis in pink is complete. The other is broken in two. I think that’s a right ischium beneath the broken prepubis above and a pubis below the proximal prepubis below. Second sacral has a broken tip. 

 

 

The final step is to apply your tracings to a reconstruction.

Figure 5. In situ and reconstruction of the YH2000 specimen of Darwinopterus.

Figure 5. In situ and reconstruction of the YH2000 specimen of Darwinopterus.

Earlier we looked at Darwinopterus here.

References
Lü J, Unwin DM, Jin X, Liu Y and Ji Q 2009. Evidence for modular evolution in a long-tailed pterosaur with a pterodactyloid skull. Proceedings of the Royal Society London B  (DOI 10.1098/rspb.2009.1603.)