Friday, October 31, 2014

I'm back...

After a long, long hiatus, I'll be slowly getting back to blogging, hopefully more on palaeo, R and data analyses (and the occasional scribbles and doodles - I won't call them palaeoart!).

I shan't go into detail in this post but I spent about 18 months away from academic research, doing data analyses in the private sector as a 'data scientist', a buzz-word profession which has been all the rave for some time now. It was an 'interesting' experience, and one that gave me a lot of opportunities to acquire new skills in the big data arena.

But I missed research too much, and I'm now at the University of Reading as a Postdoctoral Research Assistant, doing phylogenetic modelling of trait evolution, primarily using Bayesian approaches (e.g., MCMC).

So, this blog will still feature old familiar topics like dinosaurs, sabre-toothed cats, and R, but also a bit more on modelling.

Tuesday, July 10, 2012

Cat skull shape evolution across phylogeny and through time

I have a new paper out in PLoS ONE (coauthored with Marcello Ruta) on the variation and evolution of skull shape in extant and fossil felids. Below, I'll outline a few key points:

1) We analysed the relationships of some extinct sabre-toothed cats, and their interrelationships with modern conical-toothed cats and basal (ancestral) cats using maximum parsimony analyses in PAUP* and TNT.

Our results show that all sabre-toothed cats (Machairodontinae, including species with shorter canines, intermediate in form between conical- and sabre-like morphologies) are more closely related to each other than any of them are to modern conical-toothed cats (Felinae).

Phylogeny of Felidae (doi:10.1371/journal.pone.0039752.g001)

2) We quantified skull shape using traditional linear measurements (but adjusted for size, or isometric scaling) from over 300 cat skull specimens and:

A) We performed a linear discriminant analysis (LDA) to assess the ability of the linear morphometrics in distinguishing and correctly classifying group delimitations. For the taxonomic groups we used 'lineages': the eight extant lineages, 'Bay Cat', 'Caracal', 'Domestic Cat', 'Leopard Cat', 'Lynx', 'Ocelot', 'Panthera' and 'Puma' lineages; and three fossil lineages, 'Homotherium', 'Metailurus', and 'Smilodon' lineages. The three sabre-toothed cat (machairodontine) lineages are widely cited as being tribes, i.e. Homotheriini, Metailurini, and Smilodontini, in the palaeontological literature, but we opted to follow the practice observed in neontological literature and treated these groups as lineages. I'm just being pedantic here.

LDA revealed really high classification accuracy (overall 88.2% accuracy), which shows that traditional measurements can still be very powerful discriminators of taxonomic identity: this is really useful for museums where there may be specimens of as yet unknown identity (or suspicious identity).

B) We performed a principal components analysis (PCA) to construct a morphospace (shape-space) to investigate the patterns of variation in cat skull shape. PCA captures the major axes of variation in a multivariate dataset, each axis perfectly orthogonal (at right angle) to each other, so the resulting morphospace (e.g. a scatterplot of PC1 against PC2) is a proper 'space', unlike a scatterplot of two variables; a bivariate plot arbitrarily has orthogonal axes,  but PC axes are mathematically orthogonal.

Felid skull morphospace (doi:10.1371/journal.pone.0039752.g004)

Our results show that there is a general size trend across morphospace distribution, but also that there is a notable separation between the modern small-medium (feline cats excepting 'Panthera' lineage cats) and modern large cats ('Panthera' lineage cats). Sabre-toothed cats generally plot out on the periphery of the 'Panthera' lineage  distribution.

3) We investigated patterns of skull shape evolution across phylogeny and through time. This was achieved through estimating ancestral positions through shape-space and time, an extension of the phylomorphospace approach (Sidlauskas 2008) by the addition of a time axis.

Below is a normal two-dimensional phylomorphospace, with a phylogeny superimposed onto a morphospace delimited by the first two principal components axes. The internal nodal positions are estimated using maximum likelihood ancestral character estimation (Schluter et al. 1997).

Phylomorphospace (doi:10.1371/journal.pone.0039752.g005)

We basically then simply added a time axis to this plot as a third axis. This is easier said than done, especially when you're trying to code this in R. But I did manage to get it plotted the way I wanted and we decided to call the plot, chronophylomorphospace (CPMS):

Chronophylomorphospace (doi:10.1371/journal.pone.0039752.g006)

I wrote a R function called chronoPTS (short for chronophylotraitspace, because this method is not limited to morphospace), which outputs something like the one above, but this one is retouched for publication so the raw output looks a bit rougher. I used the rgl R package to accomplish this, so the neat thing is, you can save a spinning gif animation:

Spinning CPMS! (Supplementary VideoS1 accompanying the paper.)

Inspection of the CPMS shows that there was an early and conspicuous divergence between the conical-toothed cats and sabre-toothed cats. It is evident that these two major cat groups diverged early in their evolutionary history and followed separate evolutionary trajectories.

Within the modern group of conical-toothed cats, the separation between the small-medium and large cats is also deeply rooted, with a divergence in skull shape early in their evolutionary history. This means that small-medium cats and large cats followed different evolutionary trajectories with respect to skull shape.

Large conical toothed cats ('Panthera' lineage cats) have moved into regions of morphospace that were previously occupied by sabre-tooth cats. Thus, there is a form of sequential morphospace filling, whereby sabre-toothed ancestors first occupied the ‘large-cat’ region of morphospace, followed by a migration out of that region by the descendant sabre-toothed species into a new and unique region of morphospace, and finally by the subsequent filling of the now empty ‘large cat’ region by conical-toothed cats.

Our new paper:
  • Sakamoto M. & Ruta M. 2012. Convergence and divergence in the evolution of cat skulls: temporal and spatial patterns of morphological diversity. PLoS ONE 7(7): e39752. doi:10.1371/journal.pone.0039752
  • Schluter D., Price T., Mooers A.O., Ludwig D. 1997. Likelihood of ancestor states in adaptive radiation. Evolution 51(6), 1699-1711.
  • Sidlauskas B. 2008. Continuous and arrested morphological diversification in sister clades of characiform fishes: a phylomorphospace approach. Evolution 62(12), 3135-3156.

Tuesday, February 21, 2012

On the word, 'theory'

The Japanese language has two separate words equivalent to the two usages of the English word, 'theory'.

理論 [RI-RON]
A system of knowledge built on logic to systematically and uniformly explain individual phenomena. In addition, a purely logical knowledge corresponding to practice.

説 [SE-TSU]
1. A principle (belief) or claim for certain things.
2. Rumor.

I tried to translate the Japanese definitions as faithfully as I can into English. The first word, 'ri-ron', is equivalent to the scientific usage of the English word, 'theory' (as in 'the theory of evolution' or 'the theory of relativity'), while the second word, 'se-tsu', is equivalent to the common usage (more like 'I have a theory!'). Setsu doesn't need to be substantiated and can be wild claims.

It's a shame the English language doesn't have two separate words; we can avoid a lot of confusion.

Friday, October 14, 2011

Baryonyx walkeri skull

Following on from my previous post, here is another one of my theropod skull line drawings. However, this time, it's a little bit more original than the last one. At least a bit more effort went into it.

This is my 'reconstruction' of the Baryonyx walkeri skull and mandible. I based this on photos of various skull elements (Charig & Milner, 1997; Rayfield et al., 2009) and published reconstructions (Sereno et al., 1998; Rauhut, 2003) all scaled appropriately. I also base this on some personal observations of the specimen at the NHM. The arrangement of the postorbital portion of the skull is largely based on Rauhut (2003) (but ultimately on Irritator) but adjusted so that it fits with the braincase and quadrate. So overall, it looks slightly different from Rauhut's (2003) reconstruction.

Thursday, October 13, 2011

My first impressions of Star Wars Episode II: Attack of the Clones

When I first saw posters and merchandising for Star Wars Episode II: Attack of the Clones, I was immediately confused by the weird-looking stormtroopers, which I later found out to be the clone troopers. I was confused by two things: first, I had thought that stormtroopers were a uniquely Imperial thing; and second, I didn't understand why the clone trooper helmets resembled the Mandalorian helmet.

I've been a big Star Wars fan since even before I can remember, but I really got into the Expanded Universe when I was in my early teens, starting with Kevin J Anderson's Jedi Academy Trilogy and going on to Timothy Zahn's Thrawn Trilogy, I was pretty into the Star Wars Universe. I even had an encyclopaedia; Bill Slavicsek's A guide to the Star Wars Universe. And in it was an entry on the Clone Wars, which stated that it was a galactic conflict where the Jedi fought evil forces. And under the entry for Boba Fett it was stated that his armour was that of Mandalorian warriors, evil warriors that were defeated by the Jedi during the Clone Wars.

By the time Attack of the Clones came out, I had completely lost interest in the Expanded Universe so my impression of the Clone Wars and Mandalorians were pretty much based on Slavicsek's limited entries. So when I saw Mandalorian-looking stormtroopers, I immediately thought that these stormtroopers were the foot soldiers of the Mandalorians, and they would be the antagonists of the film. But what I didn't get was, why the stormtroopers would be fighting the Republic, which was obviously going to become the Empire. Stormtroopers are completely loyal to the Empire and to Emperor Palpatine, so how could they have been on the other side of the Clone Wars?

Having stormtroopers be clones as strongly suggested by their nearly identical appearances to clone troopers also nullified the purpose of the faceless stormtrooper masks of the original trilogy. Each stormtrooper is identical to the next one because they're wearing the armour and have their identity wiped out by Imperial Army propaganda and training. You don't need to be a genetically bred clone to be completely loyal and complacent to authority. Besides, it was amusing to see personality in the small talk between two stormtroopers in Star Wars. I know that clones are just like twins but the in-your-face message you get from stormtroopers=clones was that stormtroopers are not only identical in their uniform and ideology but also in their breeding and genetics. How lame is that? We're not all idiots that need to be told that stormtroopers don't have individualities, that was established in the original trilogy without any explanation about their backgrounds.

On top of that, I really disliked the idea that stormtroopers are derived from Mandalorian warriors. It gave too much credence to Boba Fett and I didn't like it. Sure Boba Fett is cool and all, but stormtroopers could be cool in their own unique way; they are the pinnacle of loyalty. Not everything has to be connected, you know. I guess the prequels kinda sucked in that it gave too much meaning to secondary characters like Darth Vader and Boba Fett; I mean why does the Universe have to revolve around these two characters?

But I digress

I hadn't seen any trailers for Attack of the Clones for some reason so I absolutely had no idea that the clones were going to be led by the Jedi. So imagine my surprise at the cinema…. Well, actually, I must confess, I was pretty impressed. Not by the story but by a swift efficient army of clone troopers; it was like seeing stormtroopers actually hit something!

As much as I like the clones (especially how they've been depicted in The Clone Wars TV series), on hind sight, it was a pretty lame idea to have the Grand Army of the Republic be completely composed of clones. As I mentioned above, my expectations for the Clone Wars was that Mandalorians were going to be featured heavily as one of the Jedi's primary adversaries. And I had this vague notion that clones may be part of the bad guys. Let's face it, clone armies in fiction are almost always used by bad people. So it fits with convention that a brutally evil force possibly led by Mandalorians would be breeding clone super soldiers to wage war on the Republic. And the Jedi have to fight them. So I was immensely disappointed when I found out that the evil forces threatening the Republic were none other than the retarded droid army that was only good for comic relief for five year olds (I shouldn't have to say more than, 'uh, uh, that doesn't compute, you’re under arrest' and 'roger roger').

Finally, the name Clone Wars suggests that the Republic fought clones. It is kind of odd to call a full scale war after your own soldiers, especially if that war was a galactic conflict that pretty much threatened the existence of the Republic. You don't call the Zulu Wars, the Red Coat Wars. No, it's called the Zulu Wars. Why? Because the British Empire fought the Zulu! So the Clone Wars is thus called because the Republic fought the Clones.

I really wish George Lucas had consulted me before he wrote the script…

[Note 04 Jan 2012: I must give credit where credit is due, I had forgotten about my thoughts about the Republic fighting clones until I saw the Plinkett Reviews on Red Letter Media. If you have not seen Plinkett Reviews, then I urge you to go watch them!]

Wednesday, October 5, 2011

Tyrannosaurus rex skull

A while ago, I created some line drawings of several theropods for a talk I was giving. One of those drawings was a Tyrannosaurus rex based on Stan, BHI-3033. It's a simple drawing so I haven't bothered with drawing out all the individual bones, but what I did do was to push the teeth into the sockets so that only the crowns are exposed. It's evident that a lot of the teeth have shot out of the sockets after the animal had died so that much of the roots are exposed. Presumably, this version should be closer to what the tooth row would have been like in life; I don't suppose roots would be exposed too much in life... The result is rather stunning in that the teeth are not as long as you typically see in T. rex skull restorations. And of course, the tips of the teeth form a more uniform and even biting surface. Perhaps I pushed them in too much and maybe the teeth were poking out a bit more, but it shows how much of a difference it makes.

Tuesday, June 21, 2011

Teaching kids to question things

Not palaeo or art I'm afraid, but kind of along the lines of critical thinking. When I was a kid, I lived in the United States. I also went to elementary (primary) school there. I forgot which grade it was or what class it was in, but one day, my teacher showed a video about the possibility that the Earth could be flat and how we can perceive it to be round; i.e. explanations on why the Earth looks round from outer space when it is really flat (something to do with light bending due to gravity). I was shocked, but apparently, our teacher's aim was to try and engage the kids to question established ideas, which in and of itself is fine. However, to this day, I fail to understand how she thought it would be appropriate to teach kids to question something that is observational, and present an alternative idea that has repeatedly been falsified. Fortunately (and perhaps surprisingly), our class was smart enough, and the video was met with the appropriate scepticism. However, I now wonder how many of my classmates were affected by this video...

Understandably, my father was enraged when I told him that evening during dinner.