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

Chytrid fungus in plethodontid salamanders

Posted by tigerhawkvok on December 18, 2009 16:47 in General , biology , research , misc science , herpetology

Yes, I know I failed on the Tuesday Tet. I know what it will be (and will be a double-feature next week), but I couldn't bring myself to do a short entry without some research first.

Also, the entry on the basal theropod (DOI 10.1126/science.1180350) will be coming. More importantly though, I wanted to note that my good friend Sara Weinstein had her first paper published in Copeia today. You can view the abstract at asihcopeiaonline.org ("An Aquatic Disease on a Terrestrial Salamander: Individual and Population Level Effects of the Amphibian Chytrid Fungus, Batrachochytrium dendrobatidis, on Batrachoseps attenuatus (Plethodontidae)" DOI: 10.1643/CH-08-180). I'll post a nice summary of it in an few days, also. Hopefully that will be somewhat illuminating, as I've known about this project (and helped a little bit) for 3-4 years now!

Now, I just need to get myself in gear and get *my* paper out. 9 months is just embarassing.

Perils of Non-FOSS

Posted by tigerhawkvok on December 08, 2009 18:41 in research , programming

Poking around my archives, I find that I've somehow managed to lose my IDL installation backups, while keeping my carefully configured startups and such. Of course.

Seeing as I had a bout of inspiration to do work on my research and, well, finally re-submit it (It's been nine months!), I suddenly find that my customized scripts to churn out quick calculations and the nice eps plots are useless, as I can run IDL for all of 15 minutes.

Damn. I need to see what Python's plotting options look like. Look for a tetrapod post later tonight.

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.

Journals and Publishing

Posted by tigerhawkvok on June 08, 2009 13:37 in research

I have some ideas for blog posts on the docket, but I've had a bit of writer's block the past few days. As journals have been high on my mind recently, I thought I'd just link off to SV-POW about "LOCKSS" and choosing a journal to publish in. I'm working with JVP for my paper, and they've been incredibly helpful, and definitely have some prestige that I'm looking for — I wish that they were open access officially, but most importantly to me, I keep copyright on my work. Or, as the case will be — "copyleft".

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.

Late Kepler Post

Posted by tigerhawkvok on March 10, 2009 20:16 in kepler , astronomy , news , research , IYA

So, I composed most of a post on the Kepler launch, then, well, forgot to post it. Belatedly, here we are:

So, Kepler. I mentioned it a little while ago, what was I talking about? Well, I was talking about the Kepler mission (kepler.gov) being sent up by NASA, set to launch on 3/6/09 (This is one of those "Whoops, posted late" parts).

Kepler is a sattelite that will observer one portion of the sky for its entire mission, looking for transit events. To understand a transit event, consider a lightbulb. When something passes in front of it, it obscures part of the surface from your view, and thus reduces the amount of light you observe. So, by observing the same starfield for its mission duration, Kepler can detect any minute changes in stellar flux, thus detecting a planet. The amount of flux change then gives you the planetary size (since color/spectral profile -> temperature -> size -> flux ).

However, there is a caveat here. Sunspots can often be regular, long lasting, or otherwise look like planets. So, my own impact on the Kepler project came with my research work with Gibor Basri, in which we wrote routines in IDL to analyze our own star for the influence of magnetograms on stellar luminosity profiles (IE, where are sunspots? How big? etc).

Various identification methods picking out
umbrae and penumbrae

A particularly good example can be seen in the figure to the left, where various versions of the algorithms pick out different features in a sunspot group. It is important to note that the differences are exaggerated -- the sun is very bright, so the "dark" spots are valued about 0.85 on an absolute scale. you can also see on the right an early version of the algorithm picking out by far most of the major solar features, including the harder-to-discern faculae, or unsually bright areas (which are, of course, very hard to observe in photos such as these).

Early feature identification

The detection and automation algorithms we developed were actually fairly robust and accurate, though CPU intensive (running through about 100 photos took about 3-4 hours on my now-deceased laptop Liz), though our funding ran out over here before I could complete an algorithm to reverse-construct a star from its magnetic profile. Thus, by also observing the long-range magnetic profile of the stars (particularly Sun-like stars) we can rule out some categories of false positives. Looking at some more "final" algorithm photos, you can see why this could be relevant:

light contrast

Solar feature identification with
later versions of the algorithm

If a dark spot such as that passed along the star, it is enough of a brightness dip that it could register as a false positive — that is to say, it could look very much like a planet. While prolonged observation is one way to get around this, feature identification is another way. And I had a part in it! Nifty!


Updated: 3/13/09

IYA Entry


Posted by tigerhawkvok on February 23, 2009 18:04 in biology , research

I've become increasingly interested in birds — particularly ratites — as of late. Posts like this over at TetZoo just make me more interested. Their evolution and morphology is fascinating, as well as the divergence in the group.

I wonder how much of this has to do with the unusually saurian characteristics of ratites (even the mammal-like kiwi)? I wish I would just pick something to be interested in and stick to it! My current list of "I'd like to do research in this some time" fields include:

  • Galactic evolution
  • Ratites
  • Stellar magnetograms on surface microstructure
  • Saurischian biomechanics
  • Compact object dynamics
  • Sauropsid evolution


Fun fact for everyone: Did you know ostriches have the best feed:weight-gain ratio among land animals? They're actually by far the most efficient source of meat, as well as being rather healthy apparently. I'd like to try some ....