Scientia Pro Publica 32: Biology Overload

Posted by tigerhawkvok on June 07, 2010 03:01 in General , evolution , physics , biology , astronomy , news , anti-science , medicine , paleontology , sci-fi , public science , climate , scientia pro publica

Welcome to Scientia Pro Publica, 32th edition!

Scientia Pro Publica logo

Scientia Pro Publica logo (C) by Flickr user jmarcx via loryresearchgroup. (Hotlinked by my usual policy)

This round, it seems that the name of the game is biology. Submissions really ran the gamut in biology, including some delightfully from-left-field posts. Bryan Perkins having some fun with embryological development, and Amanda Morti shows us why we have actinomycete bacteria to thank for that fresh rain smell (and for throwing off Latinate intuition - anyone else read "actinomycete" and think muscley whale?). Speaking of whales, David "WhySharksMatter" Shiffman does a great bit of ResearchBlogging and reminds us why not all fish (fine, non-sarcopterygian gnathostome) stock are created equal - sandbar sharks (Carcharhinus plumbeus) are closer in population dymanics to bowhead whales and other balaenids than cod.

That wasn't the only bit of ResearchBlogging this time around (Hey! ResearchBlogging! Stop hating my feeds!). Kelsey has a great post about the intraspecific male competition among red-eyed treefrogs. Sure, they amplex for dear life, but what about before that? Turns out that ... they shake their butt (Does that mean that the frog Sir Mix-a-Lot is a lady?). Madhu R-Blogs over at Reconciliation Ecology takes the opportunity to do a great smackdown on a pet peeve of mine — evolution is not a "ladder" or any such silliness. It is blind and targetless. It was a statement from a Stanfurd professor, though, so what can you expect (Go Bears!)? But before we get ranty, Luigi diverts our attention from critterland and the rivalries of my alma mater to teach us about why Kibale's Wild Coffee Project didn't get off the ground, concluding that scientists, once again, just can't do "messaging".

Illustration: Peter Trusler for Wildlife of Gondwana/NOVA (PBS). From Grrlscientist's post.

Thonoir continues to take us down our diversion away from Critterland, showcasing two sets of endangered non-metazoans, and my total ignorance of plant/photosynthizing phylogenies. We don't stray from Critterland for long, though, as John at Kind of Curious details a very interesting ponderous borer. Emily talks about sensationalism, mountain lions, and that Fox, even as they get extirpated from areas densely populated by a certain primate. Which, as Amanda points out, is no good thing, and there are difficulties restoring predators to ecosystems that they have been extirpated from (trust me, a one sentence synposis does not do that entry justice). The great Grrlscientist brings us some aborignal rock art possibly depicting Genyornis newtoni (Dromornithidae, incomplete phylogeny link (Anseriformes)). This is both the oldest paintings in Australia at 40,000 years (predating the earliest European cave paintings) and is of something that can be loosely imagined as an ostrich-sized duck, which simply can't be awesome.

Now, we don't end here. Oh no. That was just organismal biology and evolution. How about a dose of medicine? Michelle Dawson is better than Mary Poppins, because her post about circadian rythyms certainly doesn't need any sugar for you to take it down (and introduces you to an interesting side effect of autism-spectrum disorder). Scientific Chick writes about cell phones improving mental performance in Alzheimered mice. Meanwhile, Wendy at Bioloser gives us the physiological background of shock, and a shocking description of shock in a man nearly severed in half.

The larger constructs of medicine were not neglected, either. Bradley Kreit discusses the fact that we need to accept our intellectual limits, while Luke examines the crazy in large groups, looking at HIV denialism and Ryan looks at child mortality.

Bisected men and child mortality? Lets get a bit more lighthearted. Jessica Drake at Soilduck ponders what makes a scientist a scientist, and Romeo Vitelli tells us how subliminal messaging was an advertising gimmick (how many levels of fake-out is that?). Adam Park redeems some sci-fi stories with various predictions made therein that have come true today. Of course, Asimov gets a mention for the mention of pocket calculators in Foundation, but Asimov also nailed our reliance on them as time went on in The Feeling of Power (psh, arithmetic).

BP, the Gulf, and the utter dismaying farce of the spill have been in the news, and oil makes its showing in Scientia this time around. Scienceguy238 gives us a history leading up to the spill, and Grrlscientist looks at the ethics involved with oiled seabirds. Jeremy at The Voltage Gate writes about how the Saudi coast has recovered, 20 years later, from the 11-million-barrel (1.2 GL, or 1.2e6 m3) spill. A decade afterwards, 1 million cubic meters still persisted. Every spill is different, though, so hopefully ours won't be as bad.

You know you love it.

Finally, we round out with the physical sciences, which didn't get much love this time around. Lab Rat talks about bacteria and climate change, while Matt Wills talks about the more metaphorical breathing Earth, Charles Lyell, and mollusk damage in Greek columns. Finally, Sarah Kavassalis gives a great article on one of my favorite subjects: special relativity, astronomical distances, and the meaning of "now". After all, if a star (super)nova's in the distance, but you don't see (E&M) or feel (gravity) it, has it gone? She even does it without the inevitable jargoning I'd go into!

That does it for this round of Scientia Pro Publica! This was my first blog carnival, so I more than welcome suggestions. Hope you all enjoyed it!

If you want to learn more about this carnival, head over to the carnival's website. Be sure to check out the next round hosted by Andrew over at Southern Fried Science, on June 21st. And remember — this is a blog carnival! Submissions and hosts are wanted! If you're interested in hosting, check out the current schedule on the official schedule thread and drop Grrlscientist a line (or leave a note in the comments). If you find a cool article, submit it! Send a link via this submission form. Thanks again all!

Dinosaurs and Extinct Feather Morphotypes

Posted by tigerhawkvok on May 28, 2010 00:19 in evolution , paleontology

Dinosaurs and feathers. The story has gone from scaly lizards to that of animals strikingly similar to birds. Now, a recent paper in Nature (doi:10.1038/nature08965) further muddies the picture with dinosaurs demonstratedly showing development of feathers as the animal aged.

The paper in question is one describing the find of a Similicaudipteryx in the limestone of the Yixian formation in the Liaoning province in China. It describes how in addition to a marked developmental sequence in the feathers (implying moulting), it also indicates a currently extinct line of feather morphologies and developmental pathways. The authors introduce the term "proximally ribbon-like feathers", best typified by the tail feathers in male Confusciousornithes. These are feathers that are long ribbons until the distal end, where they become pennaceous (like modern feathers).

In Similicaudipteryx, two specimens are compared; a early and late juvenile form (STM4-1 and STM22-6). STM4-1 has pennaceous feathers attached to the hands and rear of the skeleton (tail and rear back vertebrae), but the rest of the feathers are "plumaceous" (think down feathers, like chicks). STM22-6, on the other hand, has had anterior feathers on the head replaced with non-plumaceous varieties and (if it is not a preservation artifact) has gained secondary remiges. Futher, the plumaceous feathers are different from true down, indicating that feather types changed several times during the ontogenetic development of these animals, unlike modern birds.

A nice touch is a passing mention in the paper to feathered-dinosaur-haters; many dissafected with the idea of feathered dinosaurs claim they are remnants of dermal collagen, it is true (and it is brought up) that dermal collagen would lack the melanosomes present in the feathers of fossilized animals.

Fossilized Melanosomes and Extinct Dinosaur Colors

Posted by tigerhawkvok on February 14, 2010 16:24 in dinosaurs , evolution , research , paleontology


I may have fallen off the face of the planet, but it doesn't mean science stopped going. So, beginning with a bit of admittedly old news — we've determined the color of a few coelurosaurian theropod dinosaurs' plumage. It's the subject of a few papers that came out in Science and Nature two weeks ago (DOIs 10.1126/science.1186290,10.1038/nature08740, summary: 10.1126/science.327.5965.508). The trick, it turns out, was to use a scanning electron microscope (SEM) to look at the microstucture of the preserved melanosomes in the feathers.

Figure 2, DOI 10.1038/nature08740

a, Optical photograph. b, Strongly aligned, closely spaced, eumelanosomes preserved as solid bodies. c, Mouldic (that is, preserved as moulds) eumelanosomes (at arrow) a short distance above a layer in which the eumelanosomes are preserved as aligned solid bodies. d, Area (at arrow) comprising more widely spaced mouldic phaeomelanosomes surrounded by less distinct, aligned eumelanosomes (top of image). e, Gradational boundary between areas dominated by eumelanosomes (longer arrows) and phaeomelanosomes (shorter arrows), both preserved as solid bodies. Scale bars: a, 50 mm; b—e, 2 µm.

If you can work your way through this paragraph, you can also see why this discovery is not just a novelty, but scientifically interesting (I don't think I can phrase it better):

Integumentary filaments occur both in non-avian theropods that possessed true pennaceous feathers (for example, Caudipteryx) and in those in which the latter are absent, such as Sinosauropteryx, Sinornithosaurus and Beipiaosaurus. The report of superficially similar unbranched filaments in the ornithischian dinosaurs Psittacosaurus and Tianyulong suggests that such structures might be common to all dinosaurs. Many investigators have accepted that these various filamentous to feather-like structures are epidermal in origin and represent feathers; others have disputed this view, arguing, for example, that in the theropod dinosaur Sinosauropteryx they represent degraded dermal collagen fibres, part of the original strengthening materials of the animal's skin. Resolving this fundamental difference in interpretation is important for our understanding of the biology of the taxa in which they occur, but also has wider implications; if epidermal in origin, these structures will inform models of the evolutionary origin of modern feather and the timing of steps in the acquisition of this evolutionary novelty.

Wikified for your convenience

Figure 4, DOI 10.1126/science.1186290

Anchiornis huxleyi, as rendered in Li et al..

Well, it turns out that the preserved microfeatures of the integument on Sinosauropteryx and Sinornithosaurus bear strong resemblance to modern microstructures in feathers known as melanosomes, which are responsible for giving color to feathers. Further, they are located inside the preserved feathers in physical locations analogous to those in living dinosaurs (ie, birds). The Nature paper thus conclusively demonstrates that they are epidermal features of the animals, ie, not degraded bits of skin, collagen, and scales that merely resemble feathers. As a fun fact, it showed that the animals they looked at had black, white, and russet feather colorations, and even color variations along single feathers and colored crests. The Science report suggests that Sinosauropteryx even had banding along its' tail.

Figure 5, DOI 10.1126/science.1186290

Cladogram of feather coloration, from Li et al..

In side-news related to the series of dino discoveries, the discovery of an early alvarezsauroid pretty much once and for all deflated the arguments of Alan Feeduccia. He had essentially resorted to temporal arguments (i.e., Archaeopteryx was older than the oldest found non-avian eumaniraptoran dinosaur) to state that Aves must have had a seperate, basal archosaurian/avesuchian ancestory, not nested within Dinosauria. Goodbye, so-called "temporal paradox". Now I just need to get people to stop saying the K-Pg event wiped out dinosaurs, and get them to insert non-avian in there. Remember, encourage evolutionary/cladistic thinking whenever you can!

Zhang, F., Kearns, S., Orr, P., Benton, M., Zhou, Z., Johnson, D., Xu, X., & Wang, X. (2010). Fossilized melanosomes and the colour of Cretaceous dinosaurs and birds Nature DOI: 10.1038/nature08740

Basal theropod, with interesting implications

Posted by tigerhawkvok on December 10, 2009 15:35 in dinosaurs , evolution , paleontology

Now, this is actually an interesting piece. according to LiveScience, a new basal theropod dinosaur, Tawa hallae has been found in lower Triassic New Mexico rocks, dated at ~213 MYA. The paper is due to be published in the December 11th issue of Science, after which I'll post more.

However, LiveScience implies that there is reason to believe that T. hallae was covered in filamentary integumentary structures, adding to the evidence suggesting filamentary integument was at least basal to dinosauria (interesting blog post on that topic, though this find, if LiveScience's implications are correct, would invalidate his point (5).)

To avoid needless speculation, though, I'll avoid talking more about it right now, and instead post a longer entry on it in the next few days when I can look at the actual paper. But I'm looking forward to it!

Crowdsourcing Science

Posted by tigerhawkvok on September 10, 2009 19:37 in dinosaurs , research , paleontology , internet

Mike Taylor, Matt Wedel, and a bunch of other folks have gotten together with an ambitious project: to crowdsource science. While this may seem bizzare at first glance, the idea is that there are many, many papers out there, with all sorts of information that can be useful — and in this case, they're looking for measurements on ornithischian limb bones. So, enter the Open Dinosaur Project. For science, for acknowledgements, or for possible co-authorship, just head on over, give it a quick read, and start contributing!

If you want to dive right in, just go straight to the page for contributors.

On a more personal note, this project has re-invigorated me to start looking at the last bits of data for my paper ... it's been sitting idle for too long, it's time for it to get out! It means I need to do some more proofing of it, in addition to filling in the empty bits — if anyone is interested in proofing, let me know.

Too True

Posted by tigerhawkvok on August 31, 2009 15:03 in General , news , paleontology , misc science

Click on the picture to see the whole thing.

Click for whole comic. Via Saturday Morning Breakfast Cereal.

Alas, too true. Also, read today's comic. Also, far too true. That and "feature creep" on papers.

To make this a bit more substantial, how's this for some interesting news: scientists have found microstructures on a fossil feather (40 MY old) that indicate it was iridescent. Nifty!

Tuesday Tetrapod (1 of 2): Fishapod?

Posted by tigerhawkvok on July 28, 2009 17:27 in paleontology , tuesday tetrapod

For today's first Tuesday Tetrapod, I present ... an unidentified "fishapod" fossil.


Basal tetrapod (?) fossil find.

Fossil anterior portion

Anterior portion of the fossil. Penny for scale.

Fossil posterior portion

Posterior portion of the fossil.

Whole fossil, rotated

This find was located by Sara's aunt and uncle (though I won't disclose the location — things are in process to get it into the proper hands for museum care). Since this is unidentified, it'll be a walk through the features we can currently see in the rock — though it is actually not wholly clear if it is actually a tetrapod yet (via discussions with UCMP contacts)!

So, here are some nifty features I think that lend toward identification as a basal tetrapod, or what is sometimes jokingly called a "fishapod":

Ribs on fossil tail

Note the ribs on the fossil tail. These are commonly found on animals with fleshy tails used for swimming.

  • Looking at the anterior portion of the fossil, there are obvious ribs along the caudal vertebrae. While these are apparently in the transverse direction, they could easily just be distortion from the process of fossilization.
  • There are structures adjacent to a large mass on the posterior half of the animal. While not quite clear in the photographs, it seems to be fairly robust and narrow element, and possibly two other connected elements near the midline. I postulate that these could be the pelvic girdle, femur, and a fibia/tibula
  • The pelvic structure appears mirrored across the vertebral column, though perhaps not strongly joined, indicated a basal state.
Fossil pelvic girdle

Region around the presumed pelvic girdle of the fossil. Light outline is one hypothesized articulation for the detached bone.

Finally, the anterior portion of the fossil has a well developed jaw that appears not exceptionally "fish-like" and more like early tetrapods. In addition, the cervical vertebrae have well-developed bones by them (processes?) that could be hyoid bones / remnants of gill arches, and well-developed hyoids are also seen in modern amphibians for feeding — though this part of my analysis is admittedly more sketchy, as I am not up on my fish anatomy.

So perhaps this entry is a week late -- but hopefully it was worth the wait!

Please note that all photos in this blog post were taken by Sara Weinstein, and copyright (or copyleft or any other form of release) belongs wholly to her. Please visit her blog and drop her a line there if you'd like to use the photos!

Compiled Phylogenies

Posted by tigerhawkvok on July 27, 2009 19:23 in biology , paleontology

I've finally ported over my work on phylogenetics that I did for the UCMP to its own dedicated site: http://phylogeny.revealedsingularity.net. I've tried to compile this with sources from multiple papers and college levels textbooks, which gives even it's current status a unique place on what I've found on the internet. As a tetrapod phylogeny, it is complete (excepting avilae and rodentia), but my goal is to eventually have all extant organisms down to family, and include important extinct outgroups.

This is a very very tall order, and a planned multi-year project, but I encourage anyone running across it to contribute or to comment.

While there are other places on the internet with phylogenies, this is different than most of those. It is more complete in certain respects than the Tree of Life, but lacks accounts at the various levels. On the other hand, it is all contained on a single page which allows comparisons not possible on other pages, and the citations provide the ability to double-check the phylogeny posted.

Finally, I've published the source code, so people can contribute more to the phylogeny, and improve functionality in a crowdsourcing effort. My goal? Reach a tentative family level completion in five years. Lets see if we can do it. Share, help out, and encourage others to help!

Sauropod Postures, and Low-Slung Diplodocids

Posted by tigerhawkvok on May 31, 2009 17:08 in biomechanics , sauropods , biology , research , paleontology

Recently, Taylor, Wedel, and Naish published a paper on sauropod postures (SV-POW, TetZoo), which challenges a paradigm established by Stevens and Parrish's paper on DinoMorph modeling which states that based on the way the cervical vertebrae articulate together, certain postures are prohibited and thus you get the current model of low-slung necks for the majority of diplodocids. This works out nicely with authors who worry about the blood pressures required to pump blood up to a neck that is elevated so high off the ground. Now, given that only a few posts ago I talked about phylogenetic bracketing and its usefulness, it's appropriate that I talk about the problems in overusing it, and step into dangerously clichéd territory while talking about the paper I am working on.

< !-- Sauropod up image --> Neck held up

First, right off the bat, I want to say that I think this is an excellent piece of work. I think it has a good place in the literature, and that more than studies of giraffe blood pressure is needed to be convincing about the blood supply issues for diplodocids (I am pretty sure I've talked about this before, but if nothing else, let me reiterate that mammals are not necessarily a good model for archosaurs). The crux of Taylor et al's argument is that extant tetrapods from all groups have strongly inclined cervical vertebrae, and that in modern animals, yes, the most favorable position is in fact a horizontal neutral one. However, soft tissues mean that this is actually not the most neutral position, and only using the vertebrae is misleading. Absolutely true, good work, and I'm amazed this hasn't been looked at before. I've even worked with Matt Wedel in writing up my paper (though I'm sure he doesn't recall by now), and I value his opinion.

So, the argument goes, based on phylogenetic bracketing, you would expect sauropod necks to not be held horizontal, regardless of what the cervical vertebrae show. While this might be largely true, I will attempt to briefly, in this blog entry, illustrate why this doesn't have to be true, and give a bit of a preview into my work-in-progress (post-editor revisions) to demonstrate why I don't think this is true for diplodocids (without spoiling my paper. Sadly, something I must take care not to do).

First, it is important to note that phylogenetic bracketing can never tell the whole story. We are the only extant tetrapod that is fully bipedal with an entirely erect vetebral column, and possibly the only one that has yet evolved. No number of examining outgroups will tell you that Homo sapiens bones should be this way; this has to be inferred from our morphology. This is a fact of essentially all novel traits. Just relying on phylogenetic bracketing prohibits you from inferring novel postures based on morphology that have no extant representatives. Second, it's possible that there was something completely bizzarre going on that we just don't know about. As Matt's SV-POW entry very clearly demonstrates, finding the fossil of, say, a budgie 200 MY from now, with no birds, you might guess it has a crazy neck like a flamingo. Sometimes, you just can't tell. That is not to say it is a very good guideline, that is very often right and instrumental in a lot of work; but it is not perfect. They even address this fact:

Can the habitual posture of extant amniotes be expected to apply to sauropods? Phylogenetic bracketing strongly supports this hypothesis as the neck posture described by Vidal et al. (1986) is found in both Aves and Crocodylia, the nearest extant outgroups of Sauropoda, as well as in the increasingly remote outgroups Squamata, Testudines and Lissamphibia.

However, some authors have postulated that the necks of sauropods, rather than representing an extreme development of mechanisms found in other vertebrates, were anomalous structures maintained using novel mechanisms. If this were so, then it would not be surprising if the habitual posture of sauropod necks was different from that of other vertebrates.

Now, it is my personal opinion that Taylor et al. is probably right in the majority of the cases. Among other things, the construction of, say, Brachiosaurus would suggest strongly inclined necks, and I suspect that all sauropods would be able to list their heads like this, at least for moderate periods — it seems the obvious, niche-opening thing to do. Even in diplodocids, it seems that a completely flat neck is not necessarily correct, and I personally favor a slightly cantilevered position (this partially addresses their comments about the orientation of semicircular canals, by coincidence). However, according to their paper:

In all four sauropodomorphs figured by Sereno et al. (2007: fig. 1G), the occipital condyle is directed postero-ventrally when the HSCCs are horizontal. If the HSCCs were inclined upwards, as in most birds and mammals, the down? ward tilt of the occipital condyles would be even greater. Therefore, even if the cranio-cervical joints were held in ONP, the anterior part of the neck would be inclined in all four taxa.If the cranio-cervical joints were flexed as in extant terrestrial amniotes, the anterior portion of the neck would need to be even more steeply inclined in order to hold the HSSC horizontal, and would possibly have approached vertical in Camarasaurus and Diplodocus (Fig. 4B, C). Taylor et al. 2009

< !-- My image --> Suspension Model

My own paper works on estimating the sizes of diplodocids, with biomechanical parameters based on the assumption that they held their necks roughly horizontal, as estimated by Stevens and Parrish's work in line with the accessible ranges in Stevens and Parrish's work. Most accurately, the level of the "bridge" is the same as the level of the acetabulum (thanks to Matt for pointing out the error in this statement). The upshot of this is, when you assume this for diplodocids, you get the correct length popping out of the math. This is very strong evidence, in my opinion, that for at least that clade the neutral position was holding the neck horizontal. This model, in fact, pulls within 4.3% of of current restoration lengths.

Now, I really want to write more — but it probably lives somewhere in that mystical realm where Bad Ideas come from. I'm slowly working on an extensive rewrite of my opening, which does not lead to quick work! But with luck, the pace will pick up soon. I should talk to Matt and see if he is interested in taking a look at what I have so far — and if Darren or Mike is interested, as well. Hopefully I can revisit this in a few months, and talk about it more!


Teaser Post

Posted by tigerhawkvok on May 28, 2009 21:15 in biomechanics , sauropods , biology , research , paleontology

A teaser post ....

Suspension Model

Image from a preprint of my paper. CC-BY-NC-ND 3.0


Neck held up

Copyright Taylor, Wedel, Naish 2009.

Via TetZoo and SV-POW. Amusingly, I know one of the authors personally, and I am really interested in what his feeling will be when my paper gets to review.

Dinosaur Proteins

Posted by tigerhawkvok on May 04, 2009 18:45 in dinosaurs , biology , paleontology


So, a quick read over the Science news this week led to an interesting news brief (DOI: 10.1126/science.324_578) about a paper that expanded on the 2007 claim that T. rex collagens were recovered (DOI: 10.1126/science.1165069 ; 2007 article DOI: 10.1126/science.1137614). [Edit: And my lagging on my Nature RSS also shows that Nature also had a very similar report (DOI: 10.1038/news.2009.422) ]

Brachylophosaurus composite image

Composite picture of Brachylophosaurus. Color pictures from Wikipedia, reconstruction copyright Scott Hartman.

So, a refresher for those who don't remember: Back in 2007, Science published a paper that stated proteins from collagen fibers were recovered from a T. rex sample. While fascinating, the paper received much skepticism over the method, and this paper attempts to address that issue with a new genus and much more strictly controlled procedures.

By demineralizing the bone matrix of the fossil, and comparing it to a Struthio sample, the authors identified protein fragments with FESEM analysis and then checked for reactivity with antibodies to avian collagen I, ostrich whole bone extracts, and a specific epitope. The first two showed reactivity, but the last did not, indicated that this was either a novel epitope or simply not preserved. There were further antibody test against elastin, laminin, and hemoglobin (all associated with blood vessels), with were all also positive.

One of the more interesting points brought up in the article that wasn't really addressed in the news brief (though it certainly need much more research and a larger sample size) was that the antibodies (to ostrich bone extracts) used in the preparation to test binding to the proteins bound more strongly to the hadrosaur proteins than to G. gallus (chicken) proteins. If this result is consistent across more testing, it actually provides another reference point to the (uncontroversial) status of Paleognathene birds being basal to Neognathae.

Another big issue with the 2007 paper was the mass spectrometry. Its results were considered to be possibly contaminated with bacteria, and too close to noise level. In this experiment, the machine used was more sensitive, and analysed at two labs. The authors still found collagen peptide sequences.

< !-- Clade Image --> Cladogram from the paper

Cladogram from the paper. Copyright the authors.

When phylogenies were inferred from the collagen sequences, the results were consistent with inferences based on genetics and the fossil record. The sampled onithodirans ended up collapsing into a three-way polytomy, with Brachylophosaurus and Tyrannosaurus resolving as related to each other closely, but the relationship between the non-avian dinosauria and the sampled neornithines remained unresolved. This problem remained even with the removal of T. rex from the phylogeny, still leaving a three-way polytomy. The authors point out that there was, for obvious reasons, a fairly low resolution in Dinosauria, but B. canadensis still resolved as a derived archosaurian, more closely related to birds than to Alligator.

< !-- Ideal Clade --> Ideal cladogram

The predicted clade, based on extensive fossil evidence.

Now, its important to note that though this is incredibly cool, this is a far cry from Jurassic Park. The proteins recovered from the collagen fragments are incomplete, and it is highly unlikely that even an egg of an ostrich would provide a suitable oocyte for cloning. That said, however, this certainly has the promise of making paleontology gain a genetic basis for phylogenetics to complement the fossil record. Though, as this study showed, there's a way to go yet.

As an aside, does anyone think it'd be useful for me to put in a DOI search box on the right hand panel?

Schweitzer, M., Zheng, W., Organ, C., Avci, R., Suo, Z., Freimark, L., Lebleu, V., Duncan, M., Vander Heiden, M., Neveu, J., Lane, W., Cottrell, J., Horner, J., Cantley, L., Kalluri, R., & Asara, J. (2009). Biomolecular Characterization and Protein Sequences of the Campanian Hadrosaur B. canadensis Science, 324 (5927), 626-631 DOI: 10.1126/science.1165069

Commentary on Sauropod Neck Posture

Posted by tigerhawkvok on April 30, 2009 00:24 in biomechanics , dinosaurs , sauropods , biology , paleontology

If you look at a (yikes! month old) Science "Letters", there an interesting, if brief, back-and-forth about sauropod neck posture between RS Seymour and PM Sander.

Up front, I'd like to say like Sander, I don't necessarily disagree with Seymour's conclusion; my own work (still undergoing revision that is halting its review process) strongly suggests that the necks were mostly held laterally, due to energetics and biomechanical concerns. However, I do take issue with the blanket scaling argument used on several points.


Ara ararauna (Blue and yellow macaw), Hawaii

First, it is important to note that the work done by Seymour is based on mammalian modeling. I have no comment as to whether it strengthens or weakens his argument this way; however, as a saurischian dinosaur, a bird would be a much more convincing model point. Second, their morphology is wildely divergent even from birds, the closest living species to them. The anology, even to birds, would be as problematic for me as the biomechanical study that based T. rex on Gallus gallus (chicken). Merely being a close relative does not ensure analogy; the musculature distribution, posture, and body shape in both cases are significantly different from the model animal. The results might very well be interesting, but they are not sure be relevant at all.

While I also have some issue with the "plug and chug" nature of the blood pressure calculations, those you can't really get around — though I'd at least like to know if it was based on mammals or birds.

Well, that's my 2 cents for now. More later.

More on Hesperonychus

Posted by tigerhawkvok on March 17, 2009 15:03 in dinosaurs , paleontology


A little bit on Hesperonychus...

I managed to get a hold the paper on PNAS (DOI: 10.1073/pnas.0811664106), and I thought I'd flesh out what I thought was the most interesting report yesterday. First, a bit of clarification: I mentioned that it is the smallest, non-avian North American dinosaur yet found, but "small" is relative. Most people, thinking of carnivorous non-avian theropods, think of superpredators such as Allosaurus fragilis or tyrannosaurids.

Size Chart

Relative sizes of North American theropods

Now, for many reasons, smaller specimens are not likely to be fossilized, despite being much more numerous than their superpredator bretheren. Being light of frame, they are more prone to scavanging, or direct physical damage to their remains. Thus, the fossil evidence becomes much more scant at lower mass ranges, and Hesperonychus is the first animal found in North America under 10 kg, under-massing Sauronitholestes langstoni.

Pelvic girdle

Hesperonychus pelvic girdle

Hesperonychus is further an interesting find in that it is a microraptorine dromaeosaurid (first one in North America), unlike other Dinosaur Park Formation dromaeosaurids found to date. The holotype pelvic girdle was discovered in 1982, but remained unidentified for a number of years (UALVP 48778, figure at right), but like many specimens, remained unstudied for a long time (25 years in this instance!). In addition to the holotype pelvis, Longrich et al. discovered a number of toes, including the typical sickle claw of basal dromaeosaurids. While superficially similar to the more infamous ones of Deinonychus, Utahraptor, and Velciraptor, the claw is less blade-like and resembles on close inspection (including on cross-section) that of microraptorines such as Rahonavis. The claw was quite small, only about a 1.5 cm long (projection, not along curve), but well-preserved. The precise cladistic placement of Hesperonychus is not particularly well defined, residing in a polytomy of various members of Microraptorinae. The number of phalaxes found (particularly phalanx II-3) suggest that there at least ten speciments in the TMP collections — when recognizing species by that element, for comparison, only 2 Dromaeosaurus specimens have been found, suggesting that Hesperonychus might have in fact been quite common in its day. This is especially true in light of how difficult preservation would have been!


Hesperonychus "sickle claws"

It is finally worth noting that even though this is a tiny dinosaur at 1900 g, it outmasses the largest metatherian (early marsupial mammal) Eodelphis by 150% (600 g). Yep, mammals — still puny!

Longrich, N., & Currie, P. (2009). A microraptorine (Dinosauria-Dromaeosauridae) from the Late Cretaceous of North America Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0811664106

Please respect image copyright of the authors, and contact them for permission if you plan to use their images. Thanks!

Fossil finds, oh my!

Posted by tigerhawkvok on March 17, 2009 03:24 in dinosaurs , sauropods , news , paleontology

Seems that the news has been an bit heavy on the fossil finds! How about a rundown.

Hesperonychus claw, hotlinked via National Geographic. The claw is on a Canadian penny.

First up is Hesperonychus ("western claw") — as yet, the smallest theropod found in North America. At the time of this writing, the PNAS paper isn't up yet, but in particular PhysOrg has a pretty good synopsis. As the name suggests (via a linguistic kinship to Deinonychus), Hesperonychus elizabethae is a diminuitive dromaeosaurid, approximately 2 kg and 50 cm tall "beating" Albertonykus borealis for title of "smallest North American non-avian dinosaur". It retains the trademark "sickle claw" of the dromaeosaurids, and the hip configuration was one of the primary diagnostic traits used to pin it to dromaeosauridae. The pelvis is also fused, suggesting that this was a mature adult. It's dated to about 75 million years ago (which the PhysOrg article accidentally writes as 45 million years ago, obviously in error at 20 MY after the K-T event).

Picture of the Svalbard excavation, from the New York Times.

The next big find announced today was of an unnamed, massive pliosaur found in the Svalbard region. I'm outright going to say I wish Kit had something to say about this, as I vaguely recall him mentioning this almost a year ago, and he knew some basics about it already. Never mind how he knows, considering it hasn't been published yet — the NYT article is already a pre-publishing press release.

At any rate, this guy was massive. This pliosaur had a skull measuring over 3m long, and the entire animal was probably longer than 15m at over 40 tonnes. Its "nickname" for now is "Predator X". Particularly novel about this find is that it might represent a new family of pliosaurs, which would be rather significant, paleontologically. Initial biomechanical work suggests its bit force would be 2-4 times that of T. rex and more than 10 times that of any extant animal. It was estimated to live about 150 MYA.

Figure 1 from Mud-trapped herd captures evidence of distinctive dinosaur sociality by Varricchio et al. 2008. (property of the authors)

Sinornithomimus dongi (Chinese bird mimic)is the next guy to hit to press. It has the slightly dubious distinction of being discovered when a large immature herd got stuck in a mud trap. It is siginificant in that the herd was apparently all juveniles, and in the number of animals found. With 25 individuals found (aged 1-7), this promises to make Sinornithomimus particularly well described. This was a bit of a late reporting on a December 2008 paper by Varricchio et al., which I've not had a chance to go over yet. I might update this with more detailed information once I get the chance.

Finally, SV-POW has an interesting piece up on Brachiosaurus. I'd strongly suggest you read it. And, for kicks, I adapted Matt's image into something nice and widescreen-background sized:

I swear, I will post Higgs and the mouse post ...

Nature: Chixulub impact did not create global wildfires

Posted by tigerhawkvok on February 23, 2009 17:06 in dinosaurs , news , paleontology

An interested news update from Nature today: apparently, the K-T impact's (Chixulub event) [wiki, UCMP] global soot layer was not caused by vegetation, and was probably due to hydrocarbons. That is to say, the impact probably burned sequestered gas and oil.

Impact, artist rendition

The writing was on the wall for the vegetation idea for a few years, since 2003 studies showed a comparative lack of charcoal, which one would expect for global wildfires. This was supplemented by research done by Belcher et al in a PNAS paper showing that polycyclic aromatic hydrocarbons (PAHs) ratios match that of burnt hydrocarbons better than that of vegetation. So, no global wildfires. However, it *is* important to note that the massive amount of soot produced itself had a global environmental impact. No matter how you dice it, the K-T event was not a fun time to be around.

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