Raptor's Nest

Baryonyx walkeri skull

2011-10-14T09:00:00.000+01:00

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.

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

2011-10-13T05:26:00.000+01:00

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!]

Tyrannosaurus rex skull

2011-10-05T18:35:00.003+01:00

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.

Teaching kids to question things

2011-06-21T14:05:00.002+01:00

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.

My Google Sites page

2011-06-12T12:06:00.000+01:00

I've set up a new Google Sites page for my research associated stuff, including some basic introductions into my research interests and current projects, but also a section for R tutorials. I've put up my three R tutorials that I've posted here with slight updates. The good thing about a website as opposed to a blog is that pages are easier to navigate (i.e. they don't get lost as time goes by and more and more posts are added as it does in blogs). I'll probably directly post my R tutorials over there from now on and limit my blog here for palaeoart and other palaeo-related posts. In time, I will also add R functions and scripts to my website for anyone wanting to replicate some of the things I do.

Palaeoart: Pachyrhinosaurus

2011-05-03T19:15:00.000+01:00

Finally, I have completed my Pachyrhinosaurus! I started it around October of 2008, but with the subsequent job hunt and pushing papers out I hardly had time to make progress with it, and it ended up taking more than two years.

Anyway, here it is.

This is mostly done by referencing some photos given to me by Traumador Tyrannosaur... well, mostly the skull that is; the body is a generic ceratopsian. My fiancée asked me "why do you keep drawing the same dinosaur?" to which I replied "...but they all have different horns". I'm not sure I convinced her but that's essentially centrosaurs in a nutshell; very diverse cranial morphology in an otherwise conservative body plan. I even read somewhere that Greg Paul lumped all centrosaurs into the genus Centrosaurus in his newest book The Princeton Field Guide to Dinosaurs (but I haven't read it yet).

When I draw dinosaurs, I usually just draw rough outlines of the animal with very limited skeletal reconstructions (but I do draw the skull), and I completely draw over the rough sketch to flesh out the creature on the same paper. I just draw on inspiration and mental imagery (while referencing skeletals to get the proportions about right), so I don't draw proper skeletals (as seemingly most palaeoartists do as I found out about two years ago). But this time, I actually drew a skeletal (but very rough) and used a tracing paper to flesh out the creature on a separate layer. I was initially planning on drawing successive layers of muscles and skin and whatnot but I got extremely lazy and ended up drawing just one layer of life restoration. For reference, the following is my rough skeletal:

As you can see, it is really a rough skeletal.

Back to the finished drawing. I thought it would be kind of neat to have some patterns, but my fiancée didn't like it, saying they look like scars. Anyway, I kept the patterns mostly to the face and a big one on the frill since I thought that's probably where ceratopsians would mostly want colours and shocking patterns; to intimidate male competitors and woo the ladies! So the patterns along the body kind of fade out towards the tail.

Thinking back, I've been drawing mostly centrosaurs when it comes to ceratopsians so maybe I should tackle a chasmosaurine for my next ceratopsian. Or I might try out a hadrosaur as a late entry to the Art Evolved thing. Or maybe I'll just get back to my non-avian and avian theropods...

Orange Microraptor

2011-04-25T20:01:00.001+01:00

Today, I bring you the third instalment of my perching dino/bird series...my orange Microraptor.

I was originally trying to draw Archaeopteryx but realised halfway through that the face was too theropod-looking and decided that I was going to convert it into a Microraptor. Actually, this one is even drawn before my blue Archaeopteryx, so I'm posting things counter-chronologically. But that's not strictly true because I only coloured this sketch in today, so it is technically my newest drawing.

I tried to pose this Microraptor with a half-folded wing; kind of like a bird folding up its wings after either landing on the branch or just extending them out for whatever reason birds extend their wings from time to time. Aside from the obviously interesting point of having tarsal "flight" feathers, Microraptor also is quite interesting in that it has really long primary feathers on the wings proper.

Colouring is as suggested to me by my fiancée, who apparently doesn't like my blue Archaeopteryx, but this one is approved. I used WHSmith colour pencils again. I don't know if anyone will find this amusing as I do, but having lost the original packaging, I keep these colour pencils in a Ziploc bag...

Blue Archaeopteryx

2011-04-20T08:10:00.001+01:00

This is another rendering of Archaeopteryx, one I'd done before I'd done my red Archaeopteryx. Just like my red Archaeopteryx, I made this guy's head and neck quite fluffy. The colouring is loosely based on a blue jay because I really like blue jays. But also corvids in general; corvids are cool!

...but then in hind sight, it looks a bit too much like a corvid than an Archaeopteryx, I must admit, but this is all in an attempt to make Archaeopteryx look more birdlike rather than a feathered reptile; I think most of the artistic reconstructions out there are too reptilian. I wrote in my red Archaeopteryx post as well but I kind of like the idea that Archaeopteryx and other early birds had more fuzziness about them than widely depicted.

Before anyone says, "How is this an Archaeopteryx, it just looks like a bird?", look at the fluff on the tarsals. And look at the external nares at the tip of the premaxilla. Also, do look at the claws poking out from under the wing (maybe not so obvious but they are there). On the other hand, I didn't particularly make the claw on the second pedal digit noticeably bigger but it is just ever so slightly bigger.

I drew his picture with a mechanical pencil (B, 0.5) and coloured it using a cheap set of colouring pencils that I got at WH Smith about eight years ago.

Red Archaeopteryx

2011-04-19T10:00:00.009+01:00

After a very prolonged hiatus in palaeoart, today I bring you Archaeopteryx, the 'first' bird. I've recently been drawing various interpretations of fossil birds, primarily Archaeopteryx and Confuciusornis, but this rendering is one of my favourites so far.

A red Archaeopteryx perched on a branch.

I've come to notice that Archaeopteryx is most frequently reconstructed with very short feathers along the head and neck. Indeed in the Berlin specimen, there seems to be a general lack of long feathers around the head and neck other than faint striations (Christiansen & Bonde, 2004). Christiansen & Bonde (2004) offer two hypotheses regarding the preservation of contour feathers in Archaeopteryx: 1, the fossil is an accurate representation of plumage in life; and 2, feathers were present but lost during fossilisation. The authors seem to prefer hypothesis 1 and suggest that Archaeopteryx had mixed coverings of large pennaceous feathers and short simple proto-feathers but even regions without feathers (apteria).

I haven't seen any Archaeopteryx specimens other than a couple of really good cast replicas, but I think it is entirely possible that Archaeopteryx actually had more feathers around its head and neck, and that it is just not preserved very well in the fossils. The degree of feather preservation in other feathered dinosaurs and early birds seems to be quite variable, so preservation could be a reasonable explanation. Some exceptionally preserved specimens do offer insights into the head and neck of these fossil creatures. For instance, the "fuzzy raptor" specimen of Sinornithosaurus seems to have some fuzziness about its head with longer feathery integuments, while Anchiornis seems to have a crest or a tuft on its head. Confuciusornis specimens also seem to be associated at times with feathers around its head and neck. Further, I personally think that feathers in preflight maniraptorans functioned primarily as display items, so it wouldn't be all that surprising if the head and neck were also covered in long feathers, instead of short proto-feathers like that of Sinosauropteryx.

When it comes to palaeoart I think there is a lot of room for creativity. Amidst all the recent ramblings and discussion on good/reliable palaeoart and whether or not skeletal reconstructions should be art or science, I opt for art. Now, there are two meanings to the word "art". One is "art" as in "creativity" (like the head and neck feathers in my Archaeopteryx above), while the other is "art" as in "artform" or "craftsmanship". Palaeoart I think can either be one or both forms of "art". Palaeoart has room for creative art because there is still a lot that is unknown from the available evidence; for instance body plumage in fossil birds and maniraptorans or just simply colour of dinosaur skin. On the other hand, palaeoart can be an "artform" or a "craftsmanship" because life restoration relies a lot on experience. An experienced palaeoartist/morphologist may be able to "see" muscles bulging over bones because he/she'd seen enough dissections to just simply visualise how big a muscle should be in relation to a bone. But I think this is more an artform or craftsmanship than hard science because each experienced palaeoartist/morphologist would visualise life restorations in their own various ways. For reconstructions to be purely scientific we'd need to have some numerical/statistical model (like some form of linear/nonlinear regression) that would predict the size, orientation, location, colour, etc of each soft tissue (e.g. muscles, feathers) based on some osteological predictor variable(s).

References:
P. Christiansen, N. Bonde, C. R. Palevol 3 (2004).

R for beginners and intermediate users 3: plotting with colours

2011-02-04T11:30:00.001Z

For my third post on my R tutorials for beginners and intermediate users, I shall finally touch on the subject matter that prompted me to start these tutorials - plotting with group structures in colour.

If you are familiar with R, then you may have noticed that assigning group structure is not all that straightforward. You can have a dataset that may have a column specifically for group structure such as this:

B0 B1 B2 Family
Acrocanthosaurus 0.308 -0.00329 3.28E-05 Allosauroidea
Allosaurus 0.302 -0.00285 2.04E-05 Allosauroidea
Archaeopteryx 0.142 -0.000871 2.98E-06 Aves
Bambiraptor 0.182 -0.00161 1.10E-05 Dromaeosauridae
Baryonychid 0.189 -0.00238 2.20E-05 Basal_Tetanurae
Carcharodontosaurus 0.369 -0.00502 5.82E-05 Allosauroidea
Carnotaurus 0.312 -0.00324 2.94E-05 Neoceratosauria
Ceratosaurus 0.377 -0.00522 6.07E-05 Neoceratosauria
Citipati 0.278 -0.00119 5.08E-06 Oviraptorosauria
Coelophysis 0.351 -0.00921 1.63E-04 Coelophysoidea
Compsognathus 0.165 -0.00160 1.44E-05 Basal_Coelurosauria
Daspletosaurus 0.276 -0.00272 1.98E-05 Tyrannosauroidea
.
.
.

and you'd hope that there is an intuitive and easy way of specifying colour or grouping structure based on this last column. The short answer is, yes, there is. But when I was a novice, it was not necessarily easy to grasp.

But before we go into that, let's review simple plotting in R.

Let's say we want to plot the first 2 principal components from a principal components analysis (PCA) based on the complete dataset introduced briefly above. I just wanted to show PCA plots instead of the original variables because I wanted to represent all three variables in two dimensions. So assuming that we have the PCA results and we call the scores along the first two PCs, PC1 and PC2 respectively, then we can plot them like this:

plot(PC1, PC2)

and it would give you a default plot that looks like this:

The default plot setting is as shown above, with simple open circles. If you don't like the symbols then you can use the pch argument to change it the way you like it:

plot(PC1, PC2, pch=19)

Here, I use pch=19 which is just a filled circle:

Now let's start adding group structure using colour.

First, we must assign the group structure. Let's say that the data table above is called data, then the column containing group information is either data[,4] or data$Family. We need to use this information to assign grouping structure to the plot. One way of achieving this is to assign the contents of this column (or vector in R) as a "factor" and call the R object something like family:

family <- as.factor(data[,4])

A factor in R is basically like categorical data so each unique entry, like "Allosauroidea" or "Tyrannosauroidea", is not just a random line of text but is treated like categories within a factor variable. Now family is an R object of class factor with 12 levels, i.e, the individual clades. So the object family acts as our grouping structure. We can use this grouping structure to assign colours with the col argument to our plot like this:

plot(PC1, PC2, pch=19, col=family)

and the resulting plot is as follows.

In this plot, the data points have been separated into 12 levels each with a corresponding colour. However, if you look closely, there are only eight colours in the above plot, black, red, green, blue, cyan, magenta, yellow and gray. This is because the default colour palette in R is set at these eight colours, and any new colour assignment exceeding this number would just recycle these eight colours in order. For instance, in our case, the first to the eighth clades in family Allosauroidea to Ornithomimosauria get assigned the colours from black to gray, and again for the ninth group onwards, i.e., outgroup = black, Oviraptorosauria=red, Therizinosauroidea=green, and Tyrannosauroidea=blue. We can resolve that problem by using a different palette.

There are several built-in colour palettes that can give your plot quite different looks. You can have a look at some of these by typing help(palette) or help(colors) in R. A few examples are: rainbow, heat.colors, topo.colors, and terrain.colors. In order to change the palette from default to any of these colour palettes, we have to first create a colour palette by one of the following:

  col.rainbow <- rainbow(12)
  col.topo <- topo.colors(12)
  col.terrain <- terrain.colors(12)

where the "12" within the parentheses indicates the number of colours in the palette. And to assign one of these colour palettes for instance col.rainbow as the global colour palette just type:

  palette(col.rainbow)

Once you've done that, you can retype the plotting function:

  plot(PC1, PC2, pch=19, col=family)

but this time, the colour scheme would be different:

Next, if we use palette(col.topo) instead:

and palette(col.terrain):

All these different colour palettes are pretty and useful in different ways, but maybe they're not exactly what you're looking for, or maybe you want to control what colours to use for each group. For that, you'd have to specify your own colours. To specify the colours you want, you can just directly specify colour in the plotting function:

plot(PC1, PC2, pch=19, col="red")

which gives a plot like this:

But this shows just one colour, which is not bad if you're going to overlay each group using different colours every time, for instance using points()- maybe I'll expand on points() on a later post. You can also specify a vector of colours if you want to use more than one colour.

plot(PC1, PC2, pch=19, col=c("red","black"))

and the resulting plot would look like this:

It's not readily obvious, but this plot just alternates between red and black throughout the whole data set; Acrocanthosaurus = red, Allosaurus = black, Archaeopteryx = red, Bambiraptor = black, and so on. Here's the same plot with taxa names superimposed using text():

The same thing would happen if you provide a vector of 12 colours to reflect our 12 clades; the 12 colours would alternate through the list of 42 taxa instead of through the 12 clades. There are two ways of resolving this (maybe there are more, but I know of two).

First, you can prepare a vector of colour names such as "red", "black" or "burlywood" so that members of the same clade are assigned the same colour, for instance Allosauroidea = red and Tyrannosauroidea = blue. Naturally, you'd have a vector of length 42 (or number of taxa) with 12 different colour names (corresponding to the number of groups). You can view all the available colour names in R by typing colors(). Instead of typing all 42 colour assignments straight into the plotting function, we can create an R object in advance. The simplest way to do this is to create an extra column in your dataset in Excel containing the appropriate colour names. If this column is called Colours within your dataset data then you can call it up as data$Colours, or if it was the fifth column, then data[,5]. And because we'd want R to recognise the colour names as characters it's probably best if we use the as.character( ) function:

  colour <- as.character(data$Colours)

If you don't use as.character( ) for instance like this:

  colour <- data$Colours

then colour is not a character vector but a factor vector. Plotting using this factor vector will not produce a plot of your preferred colours but based on whatever your palette setting is. So if it is set on default, then you'd just get eight colours.

Using the character vector instead of the factor vector as the colour argument we can plot again:

  plot(PC1, PC2, pch=19, col=colour)

and get this plot:

and with text superimposed:

You can now clearly see that each clade has its own colour and every single member of a given clade is of a same colour. For instance, all tyrannosauroids are in blue, while allosauroids are in red.

The second way of getting this plot is to create a character vector of 12 colour names:

  col.list <- c("red","slategray","seagreen",....,"blue")

and set this vector as the colour palette:

  palette(col.list)

If you plot using the factor vector family as the grouping structure:

  plot(PC1, PC2, pch=19, col=family)

you should get the same plot as the one using the character vector colour for col=colour shown above.

I think that is about it for colour plotting, and I hope I did not make it too confusing. In summary, you can specify colour schemes either 1) by referring to a character vector (containing the colour names; e.g., colour) in the plotting function, or 2) by setting a character vector (e.g. col.list) as the colour palette and specifying a factor vector (e.g. family) as the col argument in your plotting function.

In a future post, I plan to expand on the points( ) function I briefly mentioned, but also touch on how to superimpose text using the text( ) function

R for beginners and intermediate users 2: extracting subsets of data

2011-01-19T14:55:00.002Z

For my second post on R, I think I will address how to extract subsets of data based on some selection criterion like taxon names. For instance, I have a huge dataset of morphometric variables for at least 36 species of cats (living and fossil). Sometimes I'd like to do some stats on a subset of this dataset, like all the living cats or just on the Panthera lineage species (Panthera and Neofelis). Till recently, I've been doing most of my dataset manipulation in Excel by filtering out certain taxa from the spreadsheet and copy-pasting to a text file, which I read into R. However, you can select subsets of data in R based on taxon names.

In my dataset that I call cat, I have a column labelled Taxa which contains all my taxon names. So typing cat$Taxa would be the way to call up my taxon names.

Let's say I want to extract from my dataset cat just the data for the lion Panthera leo. The associated taxon names in cat$Taxa would be Panthera_leo. So to extract that portion of the dataset, we can type something like:

leo <- cat[cat$Taxa=="Panthera_leo",]

and I've called the extracted subset leo. This command is very similar to some data manipulation I covered in my previous post (e.g. data[2,]) with the exception that I've specified leo to be the rows ([row,]) in the dataset cat that have the Taxa column equalling 'Panthera_leo', i.e. cat$Taxa=="Panthera_leo". In fact, typing cat$Taxa=="Panthera_leo" would return a list of TRUE/FALSE statements, where TRUE indicates those with cat$Taxa=="Panthera_leo".

Typing leo would now return a smaller subset of the dataset containing only the lion data.

Conversely, we can also select all the non-lion data like this:

not.leo <- cat[cat$Taxa!="Panthera_leo",]

Typing not.leo should now return all the data excluding the lion data.

My original dataset cat had 361 rows, leo has 17 rows and not.leo should be 361 - 17 = 344 rows.

To take this a bit further, we can even extract a subset of a dataset that overlaps with another dataset. For example, I have two datasets on theropod dinosaurs, one on morphological variables and another on biomechanical model parameters. My morphological dataset is larger than my biomechanical dataset, encompassing more taxa and specimens, for the simple reason that biomechanical modelling can only be done on specimens meeting certain criteria. But nonetheless, some specimens overlap. So we can first determine the specimens that are in both datasets using the match() function also expressed as data1 % in % data2.

Let's call the morphological dataset morph and biomechanical dataset biomech. Let's also say that the row names are the unique specimen numbers that we want to match up in the two datasets. We also want to determine the observations within the bigger dataset morph that is also present in biomech.

rownames(morph) %in% rownames(biomech)

This command compares and determines if the row names of morph are present in the row names of biomech, and returns a list of TRUE/FALSE statements. Observations in morph that are present in biomech will come back as TRUE while those absent in biomech would be shown as FALSE. Now to extract the common observations as a subset of morph, we can do something very similar to what I showed for the cat dataset above:

morph.common <- morph[rownames(morph) % in% rownames(biomech),]

The new dataset morph.common should now be a subset of morph comprising of specimens present in biomech. If morph had 92 rows and biomech had 34, and all 34 specimens in biomech were present in morph, then morph.common should have 34 rows. On the other hand, if only 20 of the specimens in morph (n rows = 92) were also present in biomech (n rows = 34) then morph.common would only have 20 rows.

These commands are proving very useful as I don't particularly have to go back to Excel so much for simple data comparison and extraction, but was a bit difficult to find. So I hope my attempt to summarise this bit of information would also be useful for someone else.

For my next post in my R 'tutorials', I'll finally try and address my original blog idea from all those months ago, i.e. how to plot in R using colours according to groupings.

Old drawings: Allosaurus, ambush predator

2010-11-16T22:28:00.000Z

I was flipping through an old sketch book yesterday (only because I was looking for spare large-sized sketch paper for some possible figures in preparation for a manuscript I'm currently working on) and I came across a few old dinosaur drawings that I had completely forgotten about. I present one here.

It's an Allosaurus squatting behind some foliage waiting for the right moment to burst out to attack the group of Stegosaurus. It's even inching forward little by little to get to the perfect position. I wouldn't be surprised if Allosaurus was an ambush predator; lying in wait till the right time to attack, then sprinting up to its prey and delivering a slashing bite to inflict serious wounds to its prey.

With it's relatively small teeth, Allosaurus doesn't fit the bill for an average theropod (even though it is frequently cited as being the quintessential theropod). However, Allosaurus had an incredible gape and very strong neck muscles. So Bakker (1998) suggested 'that the entire upper jaw of allosaurs functioned as one huge, saw-edged Samoan war club, with each small, individual tooth acting as a mega-serration' (Pp. 152-154, Bakker, 1998). Rayfield et al. (2001) independently arrived at a similar suggestion, based on the relatively weak muscle-driven bite force compared to it's extremely strong skull, that 'Allosaurus generally used a high velocity impact of the skull into its prey; an analogue would be a person wielding a large, heavy hatchet' (p. 1035, Rayfield et al., 2001). While disagreeing with the war club/hatchet analogue, Anton et al. (2003) also agreed that Allosaurus probably drove its small teeth into the flesh of its prey using the strong neck muscles, much in the same fashion that has been suggested for sabre-tooth cats (Akersten, 1985).

It's a bit of an old drawing and my skills aren't that great (maybe not that great even now...) but you can tell that I'm trying to play with a bit of perspective, in that the Allosaurus isn't exactly drawn from profile but at a bit of an angle; the head's supposed to be facing away from the viewer just slightly (note the slightly squished kind of look of the skull - I'm trying to get a perspective here, I think). Otherwise, maybe it's a young allosaur and it's got a bit of a short face...

I think I was also trying something with the scaly look along the back and tail but kind of failed with the hip region. But the skin texture around the face is definitely influenced by Greg Paul's illustrations in his Predatory Dinosaurs of the World.

A bit of anatomical inaccuracy, I guess, is the way the hand's being held.

References:
Akersten, W.A. 1985. Canine function in Smilodon (Mammalia; Felidae; Machairodontinae). Contributions in Science 356: 1-22.

Bakker, R.T. 1998. Brontosaur killers: Late Jurassic allosaurids as sabre-tooth cat analogues. Gaia 15:145-158.

Rayfield, E.J., Norman, D.B., Horner, C.C., Horner, J.R., Smith, P.M., Thomason, J.J., Upchurch, P. 2001. Cranial design and function in a large theropod dinosaur. Nature 409:1033-1037.

How to test if your milk is about to go off

2010-11-14T15:43:00.002Z

I just 'discovered' this morning that there is a way to test if your milk is about to go off even if it still looks, smells and tastes normal, although you know it's pretty old already. If that's the case and you're worried your milk is about to go off, then here's something you can do to see if it actually is close to going off:

Take some of the milk and microwave it for about 30 seconds. If it's actually pretty old then the milk should curdle; if not, you've got yourself a nice cup of warm milk. Alternatively, you can pour some of the said milk into a cup of hot tea or coffee and see the same effect but you'll end up wasting a perfectly good cup of tea or coffee!

Quick update - two year old Pachyrhinosaurus project

2010-09-28T16:16:00.000+01:00

I don't know if anyone remembers this ancient post and this follow-up on my Pachyrhinosaurus reconstruction, but I've just yesterday pulled out my half-finished drawing and started my process of finishing it. I just realised that my original post was about 2 years ago; it's about time I finished the darned thing. I've completely abandoned layering by anatomy (e.g. layers of muscle, skins) and reverted to my comfortable method of just fleshing it out the way I like. I've realised it's the only way to get it finished!

I also have to make my post on plotting in R...

R for beginners and intermediate users: reading and manipulating data

2010-09-10T04:05:00.003+01:00

I had been preparing a comprehensive tutorial on how to plot in R (The R Project) with different groups differentiated in different colours, but Blogger stupidly erased my post and decided to automatically save my empty draft at that precise moment. Since I cannot reproduce the original post, I decided to break it up into a series of smaller topics.

There are plenty of R resources available in various places but I found that they are frequently one of two extremes; either too basic or too advanced. I think of myself as an intermediate user (i.e., I can comfortably handle canned packages but want a bit more control than the default settings allow) so the type of info I find are not too helpful. So I thought it would benefit others like me if I summed up some of the simple things I learned over the last year or two.

As a first of such posts, I will deal with reading in and manipulating data. These may be very simple and basic, but some of the things I wanted to do required a bit more than reading a manual. I will try and explain things as simply as I can so that beginners can also find some use from these posts.

So here we go.

First, we should set up the working directory. This is the directory (or folder) where you want R to read in data from and write out results to. You don't have to do this but it's sometimes useful to do so.

In Windows, you can find a drop down menu "Change dir..." under the "File" menu. In Mac's this would be under the "Miscellaneous" menu. This prompts you to select a directory. I don't particularly like this approach because it takes time to navigate through many levels of directories to get to the one you are looking at; e.g. select "C Drive", select "Users", select "YOUR USERNAME", select "Documents"… etc… or whatever your pathway is.

An alternative is to use the setwd() function, for instance like this:

setwd("C:/Users/User Name/Documents/FOLDER")

Note that the pathway (C:/…) has to be within quotes (“…”) and the pathway separators are slashes (/) instead of backslashes (\) as in Windows pathway displays. If you are unsure if you have set your working directory correctly, then you can check by getting working directory, getwd().

Now that you have set your working directory we can start reading in our data. This would require that you have your data stored as a tab delimited txt file or something similar like comma delimited csv file for instance. For this example, I will use my published dataset of theropod biting performance measures. The txt file looks roughly as follows:

  Taxa   B0   B1   B2    Family
  Acrocanthosaurus     0.307931296   -0.00329298   3.28E-05   Allosauroidea
  Allosaurus       0.302008604   -0.002847656   2.04E-05   Allosauroidea
  Archaeopteryx   0.142338967   -0.000870802   2.98E-06     Aves
  Bambiraptor   0.181541103   -0.001606   1.10E-05  Dromaeosauridae
  Baryonychid   0.189377202   -0.00237557   2.20E-05  Basal_Tetanurae
  Carcharodontosaurus 0.368623687   -0.005015715   5.82E-05   Allosauroidea

The first column contains the names of the theropods, second to fourth the data and the fifth column the family names, as evident from the first row. We want to keep this structure so we will read in the data telling R to acknowledge the first row as the header and the first column as the row names:

data <- read.table("FILENAME.txt", header=T, row.names=1)

Here the data is read in and stored as an object called “data”. The FILENAME has to be within “”. The bit “header=T” or “header=TRUE” specifies that the first row is a header and “row.names=1” specifies the first column as row names. You can review your data by typing in “data” which would print out your data table, or you can type “str(data)” which will show you a compact description of the structure of your object “data”. The latter will return a list that looks like this:

  > str(data)
  'data.frame': 42 obs. of 4 variables:
   $ B0 : num 0.308 0.302 0.142 0.182 0.189 ...
   $ B1 : num -0.00329 -0.00285 -0.00087 -0.00161 -0.00238 ...
   $ B2 : num 3.28e-05 2.04e-05 2.98e-06 1.10e-05 2.20e-05 ...
   $ Family: Factor w/ 13 levels "Allosauroidea",..: 1 1 2 6 4 1 8 8 11 5 ...

This tells us that object “data” is of the class “data.frame” with 42 observations (our 42 dinosaurs) and 4 variables (B0, B1, B2, and Family). Variables “B0”, “B1”, and “B2” are numerical data but “Family” is a factor. For some analyses like principal components analysis, non-numerical variables like “Family” cannot be included, so we will have to exclude this variable (more on this later). The variables (or any other content of an object) are indicated by a “$” and you can always call up an individual variable within an object, e.g. “data$B0”. This is useful when you want to use specific components of an object for analyses (for instance a regression of B0 against B1) or plotting (e.g. B0 against B1) (more on plotting in my next post).

Next, I’d like to explain briefly the structure of R data tables. For instance, “data” is a 42 by 4 data matrix in terms of rows vs columns, which is how R handles tables; the format that R understands tables is [rows,columns]. So if you want to see the B2 value for Allosaurus then you would type “data[2,3]” because Allosaurus is the second row and B2 is the 3 column and R will return that value which is “2.04e-05”. Similarly, if you want to review all the values for B0, then you would type “data[,1]” to call up the entire first column (or alternatively you can type “data$B0” as I’ve described above). If you want to review all the values for a given taxon (row), let’s say Allosaurus, then you would type, “data[2,]”, which returns:

  > data[2,]
   B0 B1 B2 Family
  Allosaurus 0.3020086 -0.002847656 2.04e-05 Allosauroidea

Now we can move on to manipulating data in the simplest ways. As I’ve mentioned above, some analyses don’t like non-numerical data and we would have to eliminate the column “Family” from “data” for these analyses. One way to do this is to compile a new table using the cbind() function like this:

data2 <- cbind(data$B0, data$B1, data$B2)

This will bind the vectors “data$B0”, “data$B1”, and “data$B2” together into a table. Unfortunately, the row names and column headers are stripped in the process so we have to assign them again. For row names we can simply take them from “data”:

rownames(data2) <- rownames(data)

Column names on the other hand are a bit more troublesome as there are four columns in “data” and only three in “data2”. We have to directly name them like this:

colnames(data2) <- c(“B0”, “B1”, “B2”)

The function cbind() also seems to create a object of class “matrix” so if you want a “data.frame” instead (which is useful if you want to use the $ operator to call individual columns) then we’d need to reassign “data2” as a data.frame object:

data2 <- data.frame(data2)

Using cbind() to create a data table of desired columns is fine just as long as the number of variables is manageable. In many cases (such as large multivariate data sets) this is not possible, so we need to resort to an alternative, which is to delete columns or rows. This simple procedure of deleting rows/columns is not straightforward in R and it took me a bit of searching before I found how to do it. Let’s start with deleting a variable, in our example, the non-numerical variable “Family”. Since family is the fourth column in “data”, we have to somehow eliminate data[,4]. It turns out that it is actually quite simple; just put a “-“ in front of the column (or row) number:

data3 <- data[,-4]

By typing in “length(data3[1,])”, which shows you the number of items in the first row in the new data set “data3”, R should return a value of “3” . The command “str(data3)” should also give a short list with three variables.

The same can be done for rows; just put a “-“ in front of the row number you wish to eliminate. For instance, if we want to delete Allosaurus from “data3”, then we would type:

data4 <- data3[-2,]

We can also delete multiple rows (or columns) at once. I will give an example first:

data5 <- data3[-c(2,7),]

Here, I specified the second and seventh rows to be deleted from “data3”. The “c(2,7)” combines values “2” and “7” into a vector or a list; this is the format that R likes for lists of values. So our row specification of data3[row,column] is a vector (list) including the values “2” and “7”. And there is a “-“ in front of it to tell R to delete the values within this list. Of course, you can always simply repeat the code to produce “data4” (see above) and eventually get the same thing as “data5” but that involves some tedious coding if you have a lot of rows to eliminate.

Multiple columns can also be deleted simultaneously in a similar manner:

data6 <- data[,-c(3,4)]

This removes columns 3 and 4 from the original data set “data” (which incidentally is still stored within R’s memory as a separate object because all the data manipulation has been stored under new names each time, i.e. “dataN”). The resulting “data6” should now have two columns, “B0” and “B1”.

I think that’s enough for now. In my next post I will either explain how to deal with missing data or how to plot basic X-Y plots but with colours (families plotted in different colour).

I hate Blogger autosave!

2010-09-09T07:04:00.001+01:00

Until now, I quite liked Blogger's auto save feature. Not any more. I was hitting Ctrl Z to undo things until for some reason the whole post disappeared, and then at that moment, Blogger decided to auto save.... I lost a whole evening's worth of blogging and I can't remember the phrasing I used which I really liked.

Man-eater!

2010-09-05T18:00:00.034+01:00

I have been meaning to write about this for the longest time, but things kept getting in my way. Now, I have the perfect opportunity, as Paolo at Zygoma has coordinated with me to write a post on this very topic. When Paolo was at the Bristol City Museum, I used to go bother him a lot, and together we'd go through their extensive cat skull collection. One day, we came across a very interesting tiger skull specimen. The box kind of said it all; it was labelled 'TIGER' on one end and 'MAN-EATER' on the other. So we excitedly opened the box and found an isolated skull with no mandible but with a handwritten label. The label read:

So this tiger was hunting humans for two years (how regularly, no one knows) until someone shot it dead. Upon examining the skull it was apparent why this tiger was preferentially hunting humans; its canines are heavily worn down.

The canines even look like they could have broken and were subsequently worn down from continued use. With its teeth so worn down this tiger must have found hunting large game difficult, so it resorted to hunting easy prey, i.e. humans. It's a pretty neat specimen, and we admired it for a while, but after our initial excitement wore down, we moved on to other specimens.

However, this specimen was yet to give us all its surprises. After I had gone through quite a few of the cat skull boxes, I came across a number of isolated mandibles; some lion, but others tiger. I noted that the specimen numbers on these mandibles matched those of isolated skull materials that I had previously measured so I got pretty excited. What's more, I found the mandibles to the 'man-eater' tiger skull:

As you can see, it is totally messed up (yes, that is the technical term). This tiger had fractured its right mandible and survived long enough (at least two years judging from the label) for it to heal. However, obviously the bones had not set right and so this tiger probably couldn't bite properly. Combined with the worn-down canines it must have made hunting extremely difficult.

A further shock is how the teeth occlude.

A keen observer may have noticed an odd hole in the palate of the ventral view photo above, but I had completely missed that when I saw the isolated skull specimen and I had not noticed it until I found the mandible. It turns out the hole was caused by the lower molar biting into the palate. It looks almost as if the bones in the palate gave way over a period of time, so this tiger was probably biting and chewing at a regular interval for quite some time after the fracture had healed. Although I am not a pathologist so I don't know for sure that's what happened...

Aside from the obvious job satisfaction of studying specimens in museum collections, the occasional specimen like this 'man-eater' makes it that much fun to work with historical museum collections. Most of the cat specimens in the Bristol Museum are trophy specimens but some have unique histories. There are a couple of more specimens from the Bristol Museum that are quite interesting so I may post something about them in the future.

Thanks to Rhian Rowson of the Natural History Collection at the Bristol Museum for encouraging me to write this post.

And last but not the least, be sure to check out Paolo's post for more man-eater tiger specimens: http://paolov.wordpress.com/2010/09/05/maneaters/

Old drawings: Cars

2010-07-30T23:26:00.000+01:00

Next in my line of old drawings is a non-palaeo one. I always liked drawing cars but was never good at it. So I'd doodle and try to practice from time to time. Here, I've got a selection of cars; a Subaru Impreza, some Japanese pick-up truck, a sedan, and another Japanese-style truck with a kind of near-future Sci-Fi anime feel. Incidentally, Smarty Pants is a product idea I had as a joke (though the technology isn't available to make it happen).

Old drawings: Spinosaur!!!

2010-07-26T09:50:00.005+01:00

These are really old, from when I was doing my Masters; one of them is actually dated, 6 June 2004. I was really into spinosaurs back then and I would spend some evenings drawing spinosaurs. One particular evening, instead of drawing life restorations or skull reconstructions, I had decided to draw all the known fossil materials - well, whatever figured material I could find at that time.

The above are my drawings of the preserved cranial and mandibular elements of Baryonyx walkeri and Suchomimus tenerensis that I could see from published figures. ~~I based~~ ~~Baryonyx~~ ~~on a figure in Charig & Milner's chapter in the book~~ ~~Dinosaur Systematics: Approaches and Perspectives~~ ~~(Carpenter & Currie, eds) rather than the description, so the identification of the bones are according to that chapter. By that time I had already had a chance to observe the real~~ ~~Baryonyx~~ material at the NHM, the "jugal" of which is accompanied by an updated label identifying it as an angular. So even though it is shown in the position of the jugal here (as it was in Charig & Milner, 1990), I marked it as "?". [Oops...I just realised I made a mistake...Charig & Milner (1990) actually figure this bone as a surangular, so this drawing is obviously not based on their figure...] Suchomimus here is basically just a copy of the figure in Sereno et al. (1998), but I did have to kind of make up to what extent each bone is preserved because Sereno et al. (1998) only figured the cranial and mandibular elements as part of a reconstruction. That's the drawback of Science or Nature papers; they are limited in space for detailed descriptions. And till this day I haven't had the chance to examine the real materials of Suchomimus, although I did have a chance to compare the cast replica of the premax-maxillary complex at the NHM to that of Baryonyx. I've never really appreciated the size difference until that moment; despite the similar morphology (some people even say they are congeneric) Suchomimus is indeed larger.

Now onto this next drawing. As evident from the caption, the top is the partial (but well preserved) skull of Irritator challengeri. I really like how the species name is a homage to Professor Challenger from Arthur Conan Doyle's The Lost World; I suppose one of the earliest depictions of a palaeontologist (or maybe a generic all-round scientist) in popular fiction. As an aside, it is well known that Professor Challenger was in fact Doyle's favourite character instead of Sherlock Holmes. The genus name Irritator is from 'irritation, the feelings the authors felt (understated here) when discovering that the snout had been artificially elongated' (p.5, Martill et al., 1996). Irritator has by far the most complete postorbital region of any spinosaur.

Which leads me to the second drawing above; a direct copy of the 'generalised baryonychid' from Rauhut (2003). Unlike the very famous and widely popularised image of Sereno et al. (1998), Rauhut's skull reconstruction of a 'baryonychid' (Baryonyx + Suchomimus) has the postorbital region based primarily on Irritator. Rauhut regarded the status of Spinosaurus aegyptiacus ambiguous and cautioned the use of Spinosauridae and instead preferred to use Baryonychidae. Dal Sasso et al. (2005) however regard Spinosaurus aegyptiacus as a valid genus and use the family name Spinosauridae instead of Baryonychidae.

This last drawing is my skull reconstruction of Spinosaurus ('04 version) - pre Dal Sasso et al. (2005). I can't remember how much of it is my original interpretation and how much of it is ripped off of someone else's work. But it is obvious that I was heavily influenced by an article by Berislav Krzic in the now out of press Japanese dinosaur magazine Dino Press. This is most evident in my depiction of the external nares and the antorbital fenestra; they are similar to those depicted in Krzic's illustration. Of course this reconstruction of the antorbital fenestra is probably not correct in light of more recent evidence. The postorbital region looks like I just took Irritator and changed the proportions a bit...so ends up with a more gracile looking Spinosaurus than that reconstructed recently.

I don't think any of my other old dinosaur drawings are good enough to be featured on the web, lest I humiliate myself ;) So my next post will be on another old drawing that I thought was kind of funny but it won't be a dinosaur nor will it be anything palaeo, I'm afraid. But should be fun nonetheless...

References:
Charig, A.J. & Milner, A.C., 1990. The systematic position of Baryonyx walkeri, in the light of Gauthier's reclassification of the Theropoda. in Carpenter, K. & Currie, P.J. (eds), Dinosaur Systematics: approaches and perspectives. Pp. 127-140.

Dal Sasso, C., et al., 2005. New information on the skull of the enigmatic theropod Spinosaurus, with remarks on its size and affinities. Journal of Vertebrate Paleontology 25: 888-896.

Martill, D.M., et al., 1996. A new crested maniraptoran dinosaur from the Santana Formation (Lower Cretaceous) of Brazil. Journal of the Geological Society, 153: 5-8.

Rauhut, O.W.M., 2003. The interrelationships and evolution of basal theropod dinosaurs. Special Papers in Palaeontology, 69: 3-213.

Sereno, P.C., et al., 1998. A long-snouted predatory dinosaur from Africa and the evolution of spinosaurids. Science 282: 1298-1302.

Old drawings: Allosaurus

2010-07-22T21:09:00.005+01:00

Recently, I came across a stash of old drawings that I had completely forgotten about. I'll try and upload them in the next week or two. Some are palaeo, others are not, but still quite interesting nonetheless...

Here is the first.

I think it is an Allosaurus head. At least the skull looks like an Allosaurus and it has lacrimal horns like an Allosaurus, so it must be an Allosaurus. Nothing special I guess...

Spinosaurus - biomechanical profile of biting

2010-07-16T12:58:00.009+01:00

In a comment to a post on my paper, Andrea Cau suggested I use his reconstruction of Spinosaurus to run my analysis and compare it to the one I used in my paper (the reconstruction from Dal Sasso et al., 2005).

So here is the result. The plot above shows all the mechanical advantages from my 41 taxa as grey dots. The black line is the Spinosaurus from Dal Sasso et al. (2005) while the red line is Andrea's reconstruction. There is an obvious difference, with Andrea's showing higher mechanical advantages overall. However, in the whole scheme of things, the difference is quite small. There isn't a drastic difference in the profile either. So all in all, this is good news, both to me and to those that reconstruct skulls.

New paper: media response

2010-06-25T00:37:00.005+01:00

I was originally going to post more on the science in my new paper on theropods, but I thought it would be a good opportunity to present my observations on the media response to my paper (or whatever media coverage there was).

The Proceedings of the Royal Society releases their own press materials before the official online release, the abstract for which, I actually wrote myself (200 words) when I submitted the final corrected version of the manuscript. Following the said press release (but before the online release) I got contacted by two journalists, one for Discovery News and another for Australia's ABC News. I was quite impressed by both journalists' questions; they were very good questions. So I did my best to answer as much as I can in the limited time I had (I was in London visiting the Natural History Museum).

The resulting articles that came out on the day of the online release of the paper were quite good. I was pleasantly surprised. If you haven't already, you should have a look at both articles (Discovery News and ABC News). They are quite accurate in the science reporting.

However, having said that, there were a couple of things that amused me; like the phrase 'ripping the heads off of prey'. But annoyingly (though very mildly), I am misquoted in one to have claimed Velociraptor is an ostrich dinosaur. I was actually listing theropod groups and Velociraptor just followed ostrich dinosaurs, separated by a comma. And I don't particularly understand the relevance of mentioning the bite force of Carcharodon megalodon.

All other news stories following these two were just basically copy-paste jobs, with a few minor changes; like me apparently being a British palaeontologist...

There were a few nice blog pieces on this too (here, here and here). So thanks to those bloggers that picked up and commented on my study.

I must say, I was a bit disappointed in the somewhat pervasive phrasing 'unsurprisingly' or 'confirms what palaeontologists have already suspected'; this makes it look like my study was a waste of funding (BTW if you do think this, then you are so wrong about funding...or pretty much a lack thereof). But more importantly, just because everyone thought so, doesn't mean you shouldn't test it. In fact, this type of analysis has never been done before; that's why Proc B thought it was worth their page space. Furthermore, Allosaurus has previously been considered to have weak muscle driven bites, so unique biting strategies have been suggested (Bakker, 1998; Rayfield et al., 2001; Anton et al., 2003), but my results would indicate that Allosaurus and other allosaurs actually had very efficient biting. Of course, the sizes of the jaw adductors are ignored in my study but the it remains that allosaurs are not inefficient biters. One of the other surprises I had was the tendency in allosaurs (especially in the carcharodontosaurs) to have extremely high-efficiency biting at the back of the toothrow. Carcharodontosaurus and Giganotosaurus have always been compared to Tyrannosaurus and people commonly said, 'well Giganotosaurus may have been bigger but T. rex would have ripped its head off!'. Now my study confirms that Tyrannosaurus is a high-efficiency biter but it also shows that carcharodontosaurs had higher efficiency at the back of the tooth row than Tyrannosaurus. That's kind of contrary to what a lot of people have suggested in the past; for instance, Carcharodontosaurus doesn't have strong enough dentition for powerful biting (don't ask me for the source because I don't know; it's one of those 'what palaeontologists have long suspected' type statements that I really don't know where it originated). So personally, I think we should be putting more focus on carcharodontosaur functional morphology.

Anyway, enough of the rant, and thanks to the journalists at Discovery News and ABC News for their quality reporting and also to all that blogged about it!!!

References:

Anton., M., Sanchez, I.M., Salesa, M.J., & Turner, A. 2003. The muscle-powered bite of Allosaurus (Dinosauria: Theropoda): an interpretation of cranio-dental morphology. Estudios Geologicos 59: 313-323.

Bakker, R.T. 1998. Brontosaur killers: Late Jurassic allosaurids as sabre-tooth cat analogues. Gaia 15: 145-158.

Rayfield, E.J., Norman, D.B., et al. 2001. Cranial design and function in a large theropod dinosaur. Nature 409: 1033-1037.

New paper: jaw biomechanics and the evolution of biting performance in theropod dinosaurs

2010-06-12T12:40:00.026+01:00

My new paper on theropod jaw biomechanics was finally published as an early online edition of the Proceedings of the Royal Society B. It became available on Wednesday, 9th June, but I was busy studying cat skulls at the NHM in London and I didn't have much time to comment on it until now. It is a modified version of the study I presented at SVP 2009; although I don't know how many people remember my talk. I made a few revisions to the analyses afterwards (as a response to my reviewers), but the main points are pretty much the same.

This study is pretty much a revamp of my MSc thesis where I compared biting efficiency using a novel numerical method. In my MSc thesis, I looked at how the crushing component of the bite force is affected by jaw margin morphology and how they compare across different theropod taxa. Since it was back in my early days of quantitative comparative analyses, I had no idea (or never occurred to me) how I would go about and compare them numerically (e.g. statistically). So I just basically plotted out bite force profiles and compared them qualitatively (e.g. this squiggly line looks a bit more squiggly than this other squiggly line). Furthermore, after I started my PhD studies, as I was looking back at my MSc material for possible publication, I realised that the calculations were based on an erroneous fundamental assumption; or more strictly speaking, my quantification procedure depended entirely on a subjective orientation of the skull image. Attempts at computing orientation-free force profiles were faced with complications (i.e. the computer scripts didn't work). At that time, I didn't have much computing skills (not that I am any better now) but I needed to come up with another way of quantifying the same thing. But I couldn't really think of any so I kind of gave up and focused on my PhD.

It didn't occur to me until after I defended my PhD thesis that all I needed to do was to look at the patterns of mechanical advantages along the entirety of the tooth row, and I would effectively be looking at something very similar to what I intended in my MSc thesis. Mechanical advantage is an established biomechanical metric and is much easier to compute. Most importantly, mechanical advantage is simply a ratio of the in-lever and the out-lever so it is free of jaw/skull orientations; this solves my problem of orientation. Further, since mechanical advantage is a ratio, it is size-independent as well. This makes it possible to directly compare taxa spanning several orders of magnitude in size.

But using mechanical advantage isn't free of complications. The most prominent when applying to theropods is the issue of homologous biting positions. In mammals, where use of mechanical advantage has been common practice for a very long time, mechanical advantages can be taken at homologous or functionally analogous biting positions, such as the canines, the molars or the carnassials. In theropods, tooth counts are variable, and the only homologous/analogous biting positions are the anterior-most and posterior-most biting positions (any other biting position is not directly comparable; for instance how does a 7th maxillary tooth position of Tyrannosaurus relate to in Allosaurus? Or what if the 'longest mid-maxillary tooth/teeth' aren't immediately obvious?). The only way to compare biting positions in between these two points would be to use a proportional positioning system such as percentages. One can use the position of the tooth in relation to the total length of the jaw but that would have undesirable effects of making the posterior-most biting positions incomparable across taxa with differing tooth row length relative to jaw length. So the most consistent way of standardising biting position is to fit every biting position along a percentage scale of the tooth row length with the posterior-most biting position being the 0% tooth row position and the anterior-most biting position being the 100% tooth row position.

To make it clear here (because one of my reviewers confused this) the standardised biting position is employed after mechanical advantages are computed using absolute distances. The standardisation is to make comparisons of mechanical advantages across taxa possible, not to standardise the mechanical advantages themselves.

The result is that you get a plot of mechanical advantage against standardised biting positions. And you can compare how mechanical advantages change along the tooth row (see figure to the right). To be clear again, the 0% tooth row position at the left hand side of the plot is the tooth at the back of the tooth row. As expected, that is where the biting efficiency is highest in any taxon studied. Towards the right hand side of the horizontal axis, we get further along the tooth row towards the front of the snout. As usual in lever mechanics, towards the tip of the snout, mechanical advantage gets lower, or less efficient. This is kind of like trying to cut something tough with a long pair of scissors; it is easy to cut/crush through a strong twig at the back of the scissors but really difficult at the tip of the scissors.

It may occur to some that maybe this profile would be consistent across theropod taxa; after all, they all seem to have longish tooth rows with little variation in tooth row morphology. This is true to some extent that the majority of the profile morphology is relatively similar, in that they are all simple parabolic curves. However, there are major differences in the vertical positioning of the curves, or the absolute values of the mechanical advantages (see figure to the left). This graph is from an older version so it's not exactly the same one in the final paper, but the overall pattern is the same; you see a vertical separation in biting profiles, albeit along a continuum (kind of like a smear I guess). Nonetheless, there are prominently unique profiles. For instance the ones in black, Coelophysis and Syntarsus. These profiles criss-cross the entire vertical spectrum from very high mechanical advantages at the back of the tooth row to very low mechanical advantages at the front of the tooth row. Other theropods do not have this extreme combination.

The ones in red are close but not as extreme. These are represented by the two primitive taxa, Herrerasaurus and Plateosaurus. So this is quite likely the ancestral condition in theropods. Dilophosaurus is also showing a similar profile, consistent with this profile being ancestral (although coelophysoids are an exception). Interestingly, some more derived theropods also share similar profiles with these basal taxa; most notably and surprisingly, Carcharodontosaurus. This type of biting is typified by an extremely high mechanical advantage at the back of the tooth row with relatively high to moderate mechanical advantage at the front of the tooth row. What this reflects is that these taxa have their muscle attachments relatively close to a long tooth row, so the overall mechanical advantage is high at the same time the range in mechanical advantage along the length of the tooth row is high as well. In a way the coelophysoid-type profile is an extreme form of this profile.

The rest of the theropods (the blue and pink ones) are almost indistinct from one another in terms of profile (except for a few), but are different in vertical positions, spread out along a continuum. But there is a noticeable gap, hence the different colour designation. This distinction can be a bit arbitrary so I don't make such a distinction in the paper and is discussed in terms of a gradual spectrum; the high-efficiency end of the spectrum towards the top and the low-efficiency (weak/fast biting) end towards the bottom. The high-efficiency function types (blue) have relatively high mechanical advantages along short tooth rows, while conversely the weak/fast function types (pink) have low mechanical advantages along their short tooth rows.

At this point we are still comparing squiggliness of squiggly lines, so in my next post, I shall introduce what I did in my paper in order to make a more meaningful comparison.

On biomechanics: simplicity vs complexity

2010-05-15T10:52:00.018+01:00

I've been preparing this humongous post on this but decided in the end to postpone it and just put up a short and easy one instead.

I wanted to for some time to voice my opinion regarding biomechanical modelling. And in particular the subject of complexity versus simplicity. Biological systems are frequently very complex, the details of which are often poorly understood. The musculoskeletal system is no exception. I shan't linger on how complex the musculoskeletal system is, but I will comment on the approaches in which we try and model this complexity, or approximate it.

With the advent of affordable computers, it has become expected for biomechanicists to perform high-complexity analyses with many parameters. I'm all for development of sophisticated models and analyses. It helps identify elements of the musculoskeletal system that are otherwise difficult if not impossible to determine. But herein lies the problem; a lot of the complexity, be it the actual values of the parameters or the interactions between them, are at the moment shrouded in uncertainties. This is because various properties of muscle or bone are very difficult to determine and quantify in vivo. The best we can do is to use some kind of approximation, but it is quite difficult to say if our approximations are appropriate either. So what we are left with is a complex model where we don't really know if the input parameters are realistic.

My approach has been to focus on a specific aspect of biomechanical performance, using a specifically defined biomechanical metric, like mechanical advantage. The benefit of this approach is that the functional trait is defined and is based on first principles mechanics. So it really doesn't need to be validated in vivo. The added benefit of using specific metrics is that we can accumulate a sample size large enough for statistical testing due to its simplicity. This is exactly what classical functional morphologists and biomechanicists have been doing for a very long time, and more recently functional morphologists using phylogenetic comparative methods (like Mark Westneat for example). I think that this old-school approach is still very important and we shouldn't criticise it as being overly simplistic. My opinion is that it is still better than increasing uncertainty.

*Please note that I am not 'attacking' anyone doing 3D stuff, I really think it's exciting research. I just get a lot of crap thrown at me for sticking with the old-school stuff and just need to make my position clear.

On Republic Commandos: the books not the game

2010-05-08T23:35:00.019+01:00

I'm going to comment on Star Wars again, this time on a series of books I recently read; Republic Commando and Imperial Commando by Karen Traviss. This series is supposed to be an official tie-in to the game Republic Commando, which I really liked (although I thought it could be longer; only three stages?!). I was hesitant to read this because I was scared that I would be disappointed by the novels (which I tend to more and more these days) so I had put off reading until Order 66 had just come out. Now being a fan of stormtroopers and clone troopers, I had to read Order 66; that was a requirement for me. But because it was the newest book in a series, I had to first read the other three books, Hard Contact, Triple Zero and True Colours. So I decided to buy these books and started reading.

Hard Contact I found was kind of interesting, not bad at all. Although I found it a bit boring and not at all like the game I was so used to - you know, working as a unit and blasting through enemy defences (and destroying hundreds of droids along the way, woohoo!). In all fairness, it did kind of have the "four republic commandos against impossible odds" scenario, but for the majority of the book there isn't much coordinated squad activity. But it was all right and satisfactory enough for me to keep reading on.

Now, the next book, Triple Zero, I thought was a bit odd. It's supposed to be another Republic Commando novel, and we meet the same characters introduced in Hard Contact, but now, it's set on Coruscant, the capital planet of the Galactic Republic, rather than behind enemy lines. OK, so a bit more of a digression from the game concept than in Hard Contact. Apparently, this is because there is a terrorist threat at the capital and special forces are necessary to track them and neutralise them. ...Right... Somehow, I find that hard to follow. I'm sure Coruscant has its own version of CIA or MI6, or any of those domestic security agencies like FBI or NSA, and sure enough there is something called Coruscant Security Force (CSF) but they are portrayed as kind of useless. According to the plot line of the book, a small band of special forces clone troopers led by an old Mandalorian mercenary named Kal Skirata is the perfect if not the only group of people that can expose a terrorist network on Coruscant. But you'd think clone troopers on Coruscant would be a bit conspicuous for intel work. Don't worry, Kal Skirata arranged for a whole legion of clone troopers, the Forty-first elites, to be on leave on Coruscant. I guess the best place to hide a leaf is not in a forest, but you just dump a whole load of leaves on top of it...

Aside from a few of these strange plot devices, I kept having a strange uneasiness about the whole book that I couldn't really place where it came from. One obvious detachment I felt was the rather awkward need to place a "terrorist plot" into the Star Wars franchise; quite clearly a bad juxtaposition of current topical events. I felt that a story of a terrorist plot on Coruscant does not need to be told as a Republic Commando story. It feels like an unnecessary attempt at a topical commentary or whatever the author's intentions were - or maybe it was supposed to be the 24 of Star Wars, who knows.

Another awkwardness I felt from Triple Zero (and this was further confirmed beyond doubt when I read True Colours) is the "buddy-buddy", "warmy-touchy" kind of attitudes that all the characters seems to feel towards Kal Skirata, and this includes not only most of the clone troopers mentioned by name but also the CSF officers and the two Jedi, Etain Tur-Mukan and Bardan Jusik, the latter even going as far as wearing Mandalorian armour and acting like a Mandalorian instead of a Jedi. So considering how weird the plot was, I just couldn't help but think that this whole book was just an excuse to introduce Kal Skirata, his Null-Arc troopers, and the whole Mandalorian family business. If I remember correctly, the book even had a glossary of Mando'a or the supposed language of the Mandalorians. This last bit got me a bit unnerved (and perhaps may be a future post) - why would you want to learn an incomplete fictional language when there are hundreds of real living languages out there that are much much more interesting, even only for the simple fact that there is a real live culture associated with it (in other words it's not totally made up)?

I can't even remember now what the plot of the third book True Colours was aside from a lot of Mandalorian culture (lots of dinner table scenes) and lots of Jedi bashing. That's all I got from this third book. Mandalorians = kind and loving, while Jedi = evil hypocrites. Now before I read these books, I also thought Jedi are hypocritical characters to a certain extent so I didn't have much of a problem initially (though I did feel a bit uneasy reading all the Jedi bashing). Up to that point, I've never bothered to read any of the prequel tie-in books so I didn't know much about Jedi philosophy aside from what was depicted in the six films. After I read Traviss's books, I went ahead and read the novelisation of Revenge of the Sith that I had bought a long time ago and never bothered to read (I got the hard back edition even before the paper back came out so imagine how long it's been sitting on my bookshelf). To my surprise I found a completely opposite depiction of Jedi through the narrative of both Obi-wan Kenobi and Anakin Skywalker (even Anakin!). Obi-wan is a very compassionate character and very humble as well. There is a scene in Revenge of the Sith where a Jedi council member says something along the lines of "we must send our best" clearly meaning Obi-wan who is present in the room but Obi-wan is thinking "oh, who must that be?". He has no idea how his peers (and even seniors) view him. I liked reading the novelisation of Revenge of the Sith because I got a better sense of the character's thoughts and emotions than I got from watching the film (...sadly...).

I suppose you can argue that these books are written from the point of view of Mandalorians and clone troopers trained by Mandalorians so maybe it's an alternative view of Jedi, a public opinion if you will. I suppose that would be fine and I'm sure lots of Star Wars citizens would have animosity towards Jedi in one way or another. However, I find it strange that all of Karen Traviss's Jedi characters are sympathetic towards Mandalorians (even the bureaucratic Master Arligan Zey). Jusik and Etain even leave the Jedi Order to become Mandalorians. There are no other Jedi in the series that have a narrative (that we read through their point of view) and behave like a normal Jedi. In fact, I don't think there are any normal Jedi depicted at all. So there is clearly a Mandalorian bias.

The other two books I read, Order 66 and Imperial Commando 501st were equally unmemorable in terms of plot except that lots of Jedi get killed - some young padawans were even slaughtered by the protagonists because one of them unintentionally kills Etain. However, there are a lot of Mandalorian culture, especially lots of dinner table and kitchen scenes. I really don't know why. I guess there is much to know about a culture from their food (I must admit that one of my favourite parts about travelling is the local food) but I kind of think that excessive depiction of family dinners (with lots of uncles and aunts) is really at odds with a Republic Commando setting (at least in the sense of the original game). I got so sick of it I started skipping these scenes all together.

Any part of the story that was vaguely memorable was driven mostly by Kal Skirata or his Null-ARC clones, so again, there really was no "Republic Commando" in the sense of the game. The excitement I got from the game play just wasn't recreated in these books. Instead I got a lot of Kal Skirata and his Nulls following trails in a kind of spy or detective mystery story, not really a coordinated special forces feel you get from the game.

Having said that, I was a bit overwhelmed by the military slang that was prevalent in the whole series. I know Karen Traviss was specifically brought in as a military Sci-Fi author, and Star Wars has always had some military feel to it, but having a strong military overtone just doesn't sit with me too much. The reason for it is that even if Star Wars has a certain military look, the dialogues don't show any hint of modern military culture. For instance, any commanding officer (even Moff Jerjerrod!) of any unit no matter the size (e.g. a legion, a squad, or a Death Star!) is referred to as "Commander" repeatedly throughout the films. Very rarely do we really get to hear actual military rank, like Private or Lieutenant. This suggests to me that we're not supposed to take the military organisation or structure too seriously. The whole usage of "Legion" in Star Wars to refer to a military unit, to me indicates that we are supposed to think of the Republic or Imperial armies much in the same way as the ancient Roman legions, not modern military. The "Grand Army of the Republic" says it all. Everything is grandiose and operatic in Star Wars, so modern military slang just doesn't fit in comfortably. But of course, this is just how I felt; I'm no expert on ancient or modern military topics so I may be wrong in this interpretation.

Last but not least, I felt really uneasy in one of the books where Kal Skirata enlists the help of a university professor to try and find a cure for the accelerated aging engineered into the clones. What I found disturbing was the depiction of university academics as useless snobs completely detached from reality. Now, I know many people feel this way towards academics and maybe because Skirata is a mercenary we are supposed to see the world through his "practical" eyes. But I've had enough of this "ivory tower" prejudice in real life that it's not necessary in a Star Wars novel. I mean come on, I've gone through unemployment recently, and I still have to go through extreme competition to get a job in the future. How detached from reality am I? Further, throughout the books I got the message, "if you don't put your life in the line of fire then you are a coward and not worth any respect". Perhaps this is a Mandalorian view of life but judging that Mandalorians are glorified throughout all the books I get the feeling that this really is the message of the books.

On calipers

2010-05-05T18:02:00.009+01:00

I'll ramble on about calipers today, just because I like calipers. In my line of business I use calipers very frequently. And not just a normal handy 150mm caliper, but a larger 300mm caliper or an even larger 600mm calliper. So I'll just list my callipers in size order.

150mm glass fibre dial calliper

I really like this one, despite the fact that I bought it at a local hardware shop - if it's good enough to refurbish your kitchen or build a bed, then it's good enough for me. So far I've trusted my life with the works of carpenters/engineers so I don't see why I can't trust my measurements using their tools. To begin with, craniometrics are not the most precisely defined measurements and taking these at the precision of 0.01 mm is absurd - rounding to the closest mm is fine, at least it's accurate to the mm or maybe 0.1mm.

Anyway, I digressed. I like this dial calliper because first of all it is very easy to read. Unlike vernier calipers dial callipers are very straight forward; you can just simply read off the dials and there is no need to get confused with the vernier scale. Of course you sacrifice the precision - vernier scales typically can let you read to the precision of 0.02mm whereas dials only allow to the level of 0.1mm - but like I rambled on above, I don't really need that level of precision. Secondly, my dial calliper is glass fibre so it pretty much doesn't leave any scratches. This is kind of important when you're working with fragile or old specimens in bad conditions - sharp metallic callipers can leave scratches on specimen surfaces if you're not careful.

300mm digital calliper

After visiting a couple of museums it soon became clear that a 150mm calliper wasn't going to be enough for some larger specimens, for instance crocodilian skulls or all the mid- to large-sized cat skulls. So I got myself a decent 300mm digital calliper from ebay (I was a self-funded student so I didn't have the luxury of charging it to a grant). This calliper is very nice in that it has the precision at 0.01mm but also it is digital so the measurement gets displayed on a LCD which reduces transcription error considerably. I remember being very excited by this large calliper and I happily measured larger specimens. Again, I rarely read the measurement to the 0.01mm scale.

600mm vernier scale caliper

Despite my delight at the size of the 300mm calliper and its capabilities in measuring larger specimens, it became apparent once again that some measurements for very large specimens could not be measured by even my 300mm calliper. So I got myself a decent 600mm vernier scale calliper (I think I found this on ebay as well). This was good to some extent but this calliper was difficult to use in several ways. First, I could never read the vernier scale correctly, despite having had training in University (I just vaguely remembered I had to line up the scales). Second, and more importantly, I found out that the jaws were too short for any easy use against objects that had considerable depth, like a lion or tiger skull. Frankly, I don't really know what kind of object would be 600mm in length but can be measured by callipers with jaws that are only about 50mm. Skulls are typically obscure in shape and can be very awkward to measure direct distances between two landmarks, and too frequently the 600mm calliper proved to be a very clumsy tool for this. For instance, if you wanted to measure the greatest length of the skull taken as the direct distance between the tip of the snout to the tip of the occipital crest, then quite frequently, the skull roof would get in the way of the calliper. It was clear that I needed something with longer jaws.

600mm tree caliper

Initially I couldn't find any callipers with jaws that were long enough. However, after many hours of searching online using a variety of key word combinations, I finally came across something close to ideal: tree callipers. Tree callipers are commonly used by forestry people to measure tree trunk diameter and are available in very large sizes, even up to 2m in length. But most importantly tree callipers have very long jaws, exactly the kind of thing I was looking for. It is worth noting here that there was an option to buy an anthropometer but the price of such an instrument was way beyond my then financial capabilities (maybe now I can charge my grant). But in any case, a tree calliper is sufficient for my purposes. Unfortunately, my tree calliper only has the precision to a mm, but given the specimen size of 350 or 400mm (and sometimes even bigger) a mm precision is good enough; e.g. 404mm and 405mm is nearly identical, let alone 404.3mm and 404.4mm. In other words, a precision of less than a mm is overkill in these cases.

I am very happy with this calliper. The jaws are sufficiently long enough to bracket large cat skulls with ease so it allows me to measure distances more or less parallel to the direct distance between two landmarks by taking the jaws roughly perpendicular to that imaginary straight line. One drawback is that the jaws are too long for easy transport so I always have to take it apart when I leave the museum; fortunately, the jaws can easily be detached by unscrewing a couple of screws.

Phylogenetically structured variance in felid bite force II

2010-04-11T21:06:00.003+01:00

A while back I attempted to introduce my recent publication. But of course as always I think I got carried away with the phylogenetic aspect of it. So unless I hear otherwise I shall suspend my fascination with phylogenetic signals and here discuss a bit about another interesting aspect of my paper on cat bite forces.

I've discussed bite force a lot in the past so I need not introduce it any more. One idea that is fairly widespread is that bite force is somewhat correlated with ecology and in particular prey preference. This can include dietary categories (hypercarnivorous, omnivorous, etc) or prey size categories (small prey hunter, large prey hunter). Previous studies have indicated that relative bite force (after adjusted for size) seem to have a correlation with prey size categories (Wroe et al., 2005; Christiansen & Wroe, 2007). Other craniodental morphofunctional characters also seem to have some correlation with prey size (Meachen-Samuels & van Valkenburgh, 2009). However, surprisingly, my results indicate that in felids relative bite force does not have any correlation with relative prey size. This does not mean that previous studies are in error in any way, but merely that I got a different result, probably because of the differences in data treatment and methodology. I was kind of surprised and a bit disappointed honestly with my results because it would have made an easier paper if relative bite force and relative prey size were in agreement with each other. But that was not the case; and perhaps it's more exciting that they betrayed my expectations.

So cats that bite harder than expected for their sizes do not necessarily take on prey that are relatively larger than them, and vice versa. This indicates to some extent that biting ability does not govern prey killing ability. A cat with an average bite force can kill prey that is up to 10 times its own body weight. This includes the Lynx and the Clouded Leopard, both having average bite forces but able to kill very large prey. There is still a lot that we don't know about the hunting behaviours of the Clouded Leopard so I shan't mention any more about this cat, but the observation that relative bite force and relative prey size don't match up for most of the cats is saying something. I think that relative prey size is not a controlling factor of relative bite force and that relative bite force does not necessarily represent a biomechanical adaptation for killing ability (but only with respect to relative prey size of course).

OK - I lied, I shall mention phylogeny here again. What I find more interesting however is that the relationship between relative bite force and phylogeny is, while statistically significant, actually not so strong. This means that closely related taxa don't necessarily have close values in relative bite force. In other words, relative bite force doesn't show a particularly strong phylogenetic signal (although statistically significant). The most interesting thing about this is that this is consistent to some extent with the idea that functional (biomechanical) adaptations are free of phylogenetic constraint and conform more to an adaptive form of evolution. So although relative bite force may not be explained by relative prey size, there is still the possibility that it is correlated with some other form of predatory behaviour, for instance mode of prey killing or average biting time, etc.

"Is there a palaeobiologist on board?"

2010-02-15T20:52:00.002Z

"Is there a doctor on board?"

This is one of those lines you hear in movies, dramas, cartoons, etc. but you never expect to hear in real life. But recently I actually heard this announcement on an airplane, though unfortunately I don’t know what the situation was, nor did I have the chance to find out if there really was a doctor on board, if he/she came forwards, and what happened afterwards. So no story there…

But I did have a thought:

“What if they wanted a PhD instead of an MD? And what kind of emergency situation would require the services of a PhD in palaeobiology?”

Perhaps the following:

Announcement: Is there a doctor in palaeobiology on board?

Palaeobiologist (PB): Why yes, I happen to have a PhD in palaeobiology.

Flight attendant: Thank goodness. Please follow me to the cockpit.

PB: Certainly.

- IN THE COCKPIT

PB: What seems to be the problem?

Pilot: We have a terrorist situation here and we need your expertise.

PB: Umm…I don’t think I’m qualified to deal with terrorists…

Coilot: Oh, you’re more than qualified.

Pilot: You see, there are explosives on this plane and the only way we can prevent them from being detonated is for us to comply to a series of commands. The terrorists sent us a data matrix and a phylogeny, and we have to analyze the data following their protocol and get the correct results within the remaining flight time. That would defuse the bomb.

Copilot: But we keep getting an error. We simply followed what they did but it just doesn’t seem to work.

Pilot: I’m afraid this is beyond us.

PB: I see…may I?

Pilot: Of course.

PB: Ah, the reason for the error is because you’re using the whole dataset; you have more rows in your matrix than there are tips on your phylogeny.

Pilot: …meaning?

PB: meaning, there is a discrepancy between the numbers of entries in the data and the phylogeny.

Copilot: Right, but a lot of the data entries seem to be duplicates.

PB: Actually, they’re not duplicates because the data is on the specimen level. So each species can be represented by more than one row.

Pilot: So how do we deal with this?

PB: Not to worry, I know a sorting code that will sort out the data so that we have one datum per taxon. According to their protocol they took mean values, so we just compute the mean for each species. But you’d also have to realign the data so that it is in the same order as the tips of the tree. I have a code for that too.

Pilot: Why didn’t they write all this in their protocol to begin with?

PB: Well, it never really occurs to many people that what they think is common sense may not necessarily be for others.

Copilot: Damn, terrorists!

PB: There you go. Now if you rerun the analysis, it should give you the correct results. But since the tree is huge, it may take a couple of hours to run.

Pilot: Thanks very much; I don’t know what we would have done without you.

PB: No worries, just glad to be of service. By the way, how did you know to ask for a palaeobiologist instead of a computer scientist or a statistician?

Copilot: I noticed that the list comprised of Linnean binomials, and I noticed further that they represent fossil species

PB: I'm impressed; how do you come to know fossil taxonomy?

Copilot: I took a basic palaeo course as an undergrad.

PB: Good man!

……but of course the crew could have asked for an evolutionary biologist instead because those guys tend to be more numerical than us!

Phylogenetically structured variance in felid bite force: the role of phylogeny in the evolution of biting performance

2010-01-28T22:14:00.007Z

I have been too busy lately.

Firstly because I started a postdoc and settling down etc takes up some time. But also, I've been revising a manuscript on dinosaur jaw biomechanics that came back from review; I am currently struggling with a method new to me that one of the reviewers suggested I use.

But before all this happened, I was pretty much occupied by this single paper that finally came out online:

Phylogenetically structured variance in felid bite force: the role of phylogeny in the evolution of biting performance.

I checked the dates on this submission and it was received by the Journal of Evolutionary Biology on 22 January 2009, and accepted 30 November 2009, but didn't become available on EarlyView until 14 January 2010. The actual print date is March 2010. So a year since submission. And three rounds of review in between.

Phew.

This was based on a chapter from my thesis that I thought was fairly robust and well-written that it would be the easiest chapter to convert to a manuscript for publication. Boy, was I wrong. Through the course of the review process, I had introduced so many new analyses that except for the basic premise, the final paper is nothing like my original thesis chapter.

Thanks to that, it is a much better paper; or so I think.

Anyway, I suppose I shall provide a brief overview of the paper here.

The main idea is to investigate just how much, if any, of the variability inherent in cat biting performance measures can be explained by phylogeny. In other words, do cat biting performance measures exhibit a strong phylogenetic signal. A strong phylogenetic signal would imply that the evolution of biting performance (and thus its underlying morphofunctional character complex) exhibits some phylogenetic conservatism. I discussed phylogenetic conservatism in an earlier post so I shan't repeat myself here. But determining whether a morphofunctional character complex is showing phylogenetic conservatism/signal or not is quite important to our understanding of the evolutionary processes in functional morphology.

For instance, if a functional character shows phylogenetic conservatism it could very well be that the associated morphological changes could be: a, somehow constrained (genetically, developmentally, structurally, geometrically, etc) and character change is limited; or b, conforming to a Brownian motion model of evolution and character change accumulation is proportional to branch length (or in other words, the differences between two taxa would be proportional to their phylogenetic distances). If in the case of the former, your functional character of choice may actually be something that is very difficult to modify because of constraints put upon it (perhaps because it requires modifications to vital organs or whatever). On the other hand, if in the latter case, your functional character may not be exhibiting much directional evolution or responding to external selective pressures and thus the function may not be something that is under selection (like its relationship with ecology/environment is very stable).

However, on the other hand, functional characters could also exhibit a strong phylogenetic signal and still show directional evolution (i.e.neither constrained nor with inertia [in the sense used here]); for instance, if there were trends across phylogeny. So perhaps there would be a functional change that is consistent with phylogeny but with directionality. For instance, maybe panthera lineage cats persistently evolve higher bite forces throughout their lineage.

This is all very interesting to speculate about, but we'd need to know if our functional characters of interest exert phylogenetic signal or are independent of phylogeny, in order to actually discuss anything in detail. It would be pretty difficult to determine exactly what the underlying mechanism would be (i.e. constraint, inertia, or perhaps directional) but its effect can be observed as phylogenetic signal.

There are several methods to do that, but I can't be bothered to provide a review here (maybe that's a future post, if I can ever get around to it...). Anyway, I tested for phylogenetic signal in biting performance measures (absolute and relative bite force) in 36 extant and 3 extinct felids but also the proportion of variance in bite force that can be attributed to phylogeny. In other words, I quantified how much of the disparity in bite force values is due to phylogenetic distances. I chose cats, initially because I supervised a Masters student who worked on the biting performance of the sabre-tooth cat Smilodon fatalis (we have a nice skull specimen in our Department), but also because I can get a large enough taxonomic sample from the very plentiful British collections of extant cat skulls, thanks to all the fine Victorian gents (Sirs, Colonels, Lt. Generals, etc.) who just shot the heck out of these poor animals, and to their widowed wives who after the deaths of their esteemed husbands donated the cat skulls to local museums (like the Bristol City Museum and Arts Gallery).

I kind of ran out of steam here, so I think I'll save my findings or interpretations for a later date.

On stormtrooper pauldrons from Star Wars

2009-10-18T17:23:00.013+01:00

I am going to veer off from my usual (but infrequent) blog posts on palaeontology and blog about another geeky subject.

Star Wars.

I've been a big fan of Star Wars ever since I was a little boy - Return of the Jedi must be the first film I remember seeing at the cinema; my dad took me to see it when I was three but all I remember was being freaked out by Jabba the Hutt and I went through the rest of the film asleep as a sort of a defensive mechanism.

When I was a teenager, I read Kevin J. Anderson's "Jedi Academy Trilogy" then went on to read Timothy Zhan's "Thrawn Trilogy", and from there, I pretty much read every single Star Wars related novel - until I got bored after the story arc reached a time period around 20-25 years since the events of Return of the Jedi (by this point I thought it became pointless to continue reading...).

Anyway, there is one thing that has been bugging me since I was a teenager: when reading through Star Wars materials, I frequently came across passages about stormtrooper commanders being distinguished from normal troopers by wearing shoulder pauldrons (see photo of sandtrooper with orange pauldron), but you never ever saw stormtrooper commanders wearing pauldrons in any of the original three films. Granted, the commanding officer of the sandtrooper unit in Star Wars: A New Hope was wearing a pauldron (see above photo), but all sandtroopers in that sequence were wearing pauldrons, every single one of them. The only distinguishing thing about the commander was that he was wearing an orange pauldron while most troopers were wearing black, but then again, you can see at least one more stormtrooper wearing orange as well. And then there's the one wearing white, which apparently is supposed to be a sergent...

So where did this come from? What is the original source? - I have no idea...

In Revenge of the Sith some clone commanders do wear what look like pauldrons, but a lot of other Clone Wars materials seem to indicate that a pauldron is more of a garment of a distinguished clone officer rather than that of rank (e.g. ARC troopers, or Captain Rex who wears a pauldron as opposed to the more senior Commander Cody who does not). So clearly, pauldrons only have a loose relationship with rank. Of course, one can argue that sandtroopers have clear rank designations by the colour of their pauldron but as I've mentioned above, there are more than one trooper with an orange pauldron and at least two with white; it's not like the colours reflect frequencies that you'd expect from rank, so I think the colouring variation is more to do with cinematography than anything.

The reason why this issue has bugged me is because there are widely held interpretations of on-screen material (such as the role of a pauldron) that was only subsequently given by someone (mostly sci-fi authors) and somehow became "canon". My issue with this is that despite these novels, comics, games, whatever, being licensed by LucasFilm or LucasArts (or by whomever the rights are held), they are only glorified fan-fiction, as far as I can see. So I don't see any difference from these widely accepted interpretations from my never-ending imaginations. I don't especially see why I have to believe something that is not even reflected on-screen; such as the pauldron as a designation of rank in non-sandtrooper stormtroopers (we don't see any evidence for this in the films). Of course, it's fun to imagine specialised stormtrooper armour, equipment, etc, but we should bare in mind that even published materials are just fan-fiction in the end.

SVP 2009 Bristol, and the Romer Prize Session

2009-09-27T20:55:00.004+01:00

Despite the complaints that I've heard about the hills and distances from one session to another (come on, it was only a few minutes by foot!), SVP this year was pretty good, in my opinion anyway. I noticed some really good talks with some impressive analytical methods, some really interesting posters, and I also chatted with some intelligent and enthusiastic people.

Of particular interest for me was the Romer Prize Session - not only because I was presenting, but more because Romer Session talks were almost always of high quality research, self-contained and conclusive (unlike some "on-going research", a new locality, or some more scrappy fossils...). Romer talks tend to be more analytically/numerically oriented so there are some stats and numbers to support certain ideas and claims.

There were two talks in particular that I liked, one by my very good friend Tai Kubo (Evolution of limb posture in terrestrial tetrapods inferred from Permian and Triassic trackways), and the other by the Romer Prize winner, Christian Kammerer (Effects of the Permio-Triassic mass extinction on synapsids).

Kubo's talk was on his study using trace fossils to infer limb posture in tetrapods, which on its own is quite unique already because there has been really limited efforts on using trace fossils as a potential source of data. But what makes his research truly unique was his validation of his metrics using observations of limb posture in extant reptiles and their relationship with trackways. His results are already published so I shan't go into the details but his conclusion is that the shift to an erect limb posture occurred rapidly in the Early Triassic much earlier than predicted previously by body fossils.

And on to Krammerer. I really liked his talk. The methodology was robust, statistics were sound, and above all, the sample size was just pure astonishing. One of the things I found rather exciting about his talk was that his results showed that geologically deformed skulls fall within the range of morphospace occupation (albeit perhaps at the extreme margins) expected for that species. This, I think is a significant discovery; although you'd still need a sufficient enough sample size to say that this is true for your own pet group of fossils as well... In any case, I really admire his work and his talk and I think he rightfully won the Romer Prize. So a very big congratulations to Christian Krammerer, and it is a shame I had not had the opportunity to do this in person at the conference (yes, I couldn't find half the people I wanted to meet because of the disparate locations).

All in all, a successful conference (for me): I met half the people I was meant to meet; I met some new people; I learned some new things; I caught up with a bunch of friends and colleagues that I had not seen in months, some I had not seen since our last meeting at Cleveland; and perhaps the most important aspect of the meeting for me, I disseminated my work in front of a large audience. I didn't get much feed back on my talk but I assume either no one really liked it or that no one really understood what I do...

Updates ... and SVP Romer Prize

2009-09-07T18:04:00.002+01:00

I've just noticed that it's been about four months since I posted my last blog entry...It is rather scary how time seems to fly even when you are not necessarily having fun...

Anyway, I thought I might as well advertise this. In the upcoming SVP at Bristol, I shall be giving a talk in the Romer Session:

Myology and functional morphology of biting in avian and non-avian dinosaurs.

It's mostly about non-avian theropods now but I have a couple of birds in there for comparison; I don't know now why I emphasised birds in the title, I could have just said dinosaurs... Perhaps it's because I made much of my myological observations in birds (but also a few crocs).

I shan't write too much about it here, but the work is basically a suped-up version of my Masters thesis from way back, almost six years now... I had to come up with a way to rescue the concept if not the work, after I'd realised I had some fatal flaws in the basic assumptions of the calculations in my Masters work, and it took nearly six years to perfect.

Phylogenetic constraint

2009-09-02T10:01:00.008+01:00

My coauthors and myself recently submitted a manuscript in which we deal a little with phylogenetic constraint. In the process, I came across something interesting and I thought it would be worthwhile to share it here.

Phylogenetic constraint is a concept of evolutionary biology that has had quite a lot of discussion. Mary McKitrick (1993) has a great way of introducing the concept of phylogenetic constraint:

"in some sense, all evolutionary studies implicate phylogenetic constraint, and reviewing the topic is like trying to catch a greased pig."

How eloquently put.

It means everyone loves talking about phylogenetic constraint but it just goes all over the place and there is no real consensus on what phylogenetic constraint is. So despite all this widely held discussion, phylogenetic constraint remains one of the most difficult and least understood subjects, and possibly one that is actually ill defined as well. The problem is, when we talk about phylogenetic constraint, we are actually talking about some causal factor for a way in which some trait evolves. For instance, we may see some evolutionary changes in skull morphology that is relatively consistent in closely related taxa, thus we may conclude that some phylogenetic constraint is working on this trait preventing it from evolving more disparately from one taxon to another, e.g. in a classic adaptive radiation model. But causation is always difficult to determine if not impossible to confidently assign.

We may not be able to satisfactorily determine if phylogenetic constraint actually is a plausible mechanism in some trait evolution, but we can observe its presumed effects, as phylogenetic conservatism or phylogenetic signal in your phenotypic data. Thus, when many of us say "phylogenetic constraint" we may actually just be talking about an observed phylogenetic conservatism, i.e. some trait that is showing a pattern of evolution consistent with phylogeny. In other words, some trait evolution that shows up as phenotypic difference in two or more taxa that is consistent with the amount of time (or phylogenetic distance) separating these taxa. Phylogenetic conservatism is thus shared characteristics amongst taxa that can predominantly be explained by phylogenetic distance.

The underlying mechanism of phylogenetic conservatism may be due to several causal factors, phylogenetic constraint being one of them (constraint due to developmental, structural, etc. that is shared amongst closely related taxa). But there is another possible mechanism for phylogenetic conservatism in a character, and that would be phylogenetic inertia (as defined by McKitrick (1993)). Characters evolving under phylogenetic inertia would not particularly be under strong selection, and change would be minimal, or in other words, "if it ain't broke, why fix it?". This is a slightly different case from constraint because there isn't really an active constraint working against evolutionary change; there just ain't any selection for that character to change faster than expected. But if there were any evolutionary changes then they would be due to inertia, so more consistent with a random walk model of evolution (i.e. Brownian motion). Under such circumstances, character change is directly proportional to time and thus proportional to branch length (thus differences between phenotypic traits in two or more taxa would be consistent with phylogenetic distance); or the rate of evolutionary change per unit branch length (or time) is constant.

Funnily enough, some widely used methods (maximum likelihood and independent contrasts analysis) actually assume this a priori (i.e. that character evolution conforms to Brownian motion), so before you go on and use these methods in your characters to say something about how characters changed through phylogeny, you really ought to test to see if your character actually does show a strong phylogenetic signal. Because if it doesn't then you may be violating the assumptions of the methods, or these methods aren't suitable for your character. But that's another matter all together.

Anyway, that aside, the terms I used here are probably all used in different contexts elsewhere (e.g. phylogenetic conservatism = phylogenetic inertia) but the point is, these concepts need to be defined well and used to mean specific things.

Principal coordinate analysis and the quest for a solution to a non-existent problem

2009-05-12T09:43:00.004+01:00

I had an interesting experience yesterday - spent a good few hours on a silly problem. You don't need to know the technicality of the analyses at all, but I'm sure you'll appreciate the humour in this.

I am frequently running principal coordinate (PCo) analyses recently. This is because I am using an interesting application of multiple regressions and PCoA on phylogeny vs phenotypic variables called the phylogenetic eigenvector regression (PVR; Diniz-Filho et al., 1998; Desdevises et al., 2003). In short, you take a phylogenetic tree of a given group of animals (or plants, or whatever your favourite group of organism), reduce the complex topology into manageable columns of numbers (by PCoA), and test these columns with some phenotypic/ecological variable of your choice for any correlations using multiple regression. Sounds pretty easy, and it is, in practice at least. You can code R to do this very efficiently, if you know the R language already.

Anyway, yesterday, I reread the protocol that I had been following for the last few weeks and realised that, PCoA on phylogenetic trees could sometimes result in negative eigenvalues - which is kind of annoying if you think of eigenvalues as representing the "amount of variation in the data explained by that axis" (Hammer and Harper 2006); a negative value indicates a negative contribution???. Supposedly, this is because of the nature of the phylogenetic distance matrix not necessarily being Euclidean distances. So I had a look at my PCoA results and realised to my horror that a lot of my values were negative. Holy shit! Do I have to go back and reanalyse?

But first, I did the sensible thing and checked if my distances were Euclidean or not (using the is.euclid() in R). Surprisingly, or unsurprisingly, my distances were Euclidean. Strange. But the values are negative...

I sat there scratching my head for a while.

I read further and noted that in cases where you get negative eigenvalues, you may need to transform your original distance matrix following some standard procedures.

I searched for the relevant references and there were several suggested transformation procedures. All of them seemed pretty straight forward. So I tried all of them in turn.

None of them worked. The negative values are still there....

I'm really stuck now. I don't know what the cause of this problem is. Is there something inherently wrong with my data? Is there some other transformation that I could still use? Is there another command in R that could potentially solve this problem - it's really common in R for you to miss a basic command - ? or, is there something fundamentally screwed up with the PCoA command in R, and I've discovered some serious programming failure?

But at this point, it's time for my coffee break. I went out for coffee with my girlfriend, complained to her about it, of course with no solution other than stress relief (which of course I am extremely grateful for her to provide me). I went back to my office, sat down in front of my computer again for more head scratching - by this time, it's more like head-banging-on-desk.

But then, as I was reviewing the R commands for PCoA, it all hit me. How could I be so stupid?

There's this thing in R that returns what's called "points" and "eig", the former being the coordinate points of each specimen along each PCo axis within the multidimensional space, and the latter being the eigenvalues associated with each axis. And "points" are returned by default. I had been looking at the "points" all this time. Of course, the points are going to include negative values because the whole ordination is done so that the points are scattered around the origin.

I turned the "eig" feature on, and R returned the eigenvalues; all positive.

I never thought I could be extremely happy with myself at the same time as being incredibly furious for making such a stupid mistake.

The moral of this story is: you learn from your mistakes.

Chimpanzee plans stone attack

2009-03-10T09:27:00.007Z

I just read an interesting BBC News article. Apparently, a chimpanzee at the Furuvik Zoo in Sweden had been storing hundreds of stones in anticipation of throwing them later at the zoo visitors. Planning ahead is a cognitive behaviour that has not been traditionally associated with nonhuman animals. This behaviour was observed over the last decade and reported in the journal Current Biology.

Previous reports of planning for future states in animals were all experimentally induced and as such one can be skeptic about these behaviours as being potential lab artefacts. However, this zoo chimpanzee showed spontaneous planning that provides support that previous observations made in the lab may not necessarily be artefacts of experiments; at least in great apes. Primary evidence for this is: that the chimpanzee had collected stones or made concrete discs (see below) early in the morning before the zoo was opened to the public but never when the zoo visitors were present; that the chimpanzee was in a calm state of mind during caching of stones and not at all agitated as he is during his dominance displays towards zoo visitors; that there is a delay between the collecting and throwing of the stones of a few hours; that the chimpanzee does not collect stones for subsequent throwing during the zoo's off-season; and that 'the caches were always located at the shoreline facing the visitors’ area' (Osvath 2009, p. R191).

So this chimpanzee was clearly preparing to throw projectiles at zoo visitors later during the day.

Another striking behaviour is the preparation of concrete discs or missiles from the concrete structures at the centre of the enclosure. Because the zoo is in the subarctic, concrete structures undergo extreme conditions, and are vulnerable to freeze-thaw fracturing (from expansion of freezing water in microcracks and the gap left behind in subsequent thawing) and the surface layer gets partially detached. This is visibly unrecognisable but can be detected by the hollow sound it makes when the damaged area is knocked on. The chimpanzee knows this and has been seen knocking on concrete surfaces from time to time and occasionally hitting harder to knock off concrete fragments. This process of making and using concrete discs is suspected of being a discovery or an invention by the chimpanzee as no one showed him this behaviour. Further, the regcognition that a hollow sound is indicative of damaged concrete and the subsequent link to making projectile weapons out of this, shows just how chimpanzees are actually capable of 'sequentially ordered advanced cognitive operations'.

On a side note, considering the amount of rude mannerisms I've observed and heard in zoo visiters, it's no surprise the chimpanzee did this. If I were in a zoo being stared at by noisy visitors all day long, I'd soon start throwing stuff at them too. My mother told me about a bunch of noisy 7-8 year-olds from a local football club shouting and screaming at all the monkeys at the Ueno Zoo (and believe it or not, this behaviour was led by the team coach!). But because they were so loud (and systematically shouting at all the monkey enclosures), by the time they arrived at the Japanese Macaque enclosure, the alpha male had already rounded up all the troops and retreated them into their den, and the kids (and the coach) were left to wonder where they'd gone...I sometimes wonder who is the smarter...

Reference:
Osvath, M. 2009. Spontaneous planning for future stone throwing by a male chimpanzee. Current Biology, 19: R190-R191. doi.org/10.1016/j.cub.2009.01.010

more on Styracosaurus

2009-03-09T21:36:00.003Z

Further to my previous post, I've added on some background to my Styracosaurus sketch.

I drew in lots of generic plantlife. I've previously done some research into the Hell Creek flora as a consultant job for Be the Dinosaur. As it turned out, the Hell Creek flora was dominated by angiosperms (about 90%). A lot of that was lobe-leafed plants, and lots of modern families, including the Arecaceae (palm), Zingiberaceae (ginger family), Nelumbonaceae (family including lotus), Rosaceae (rose family), Fagaceae (beech), Urticaceae (nettle family), and Cannabaceae (the family including hops and canabis!). So I drew some random lobe-leaf plants and somethings that look like roses and marijuana...

Of couse, Styracosaurus ain't from the Hell Creek Formation, but who cares.

Styracosaurus albertensis

2009-03-04T11:40:00.004Z

I sent this in over to the Ceratopsian Gallery at ART Evolved: Life's Time Capsule but I thought I'd repost it here with a bit of my commentary...

I'm sure everyone's seen an image of Styracosaurus albertensis before. It is readily distinguishable from other ceratopsians by the presence of elongated horns on the back of the frill...I don't have much to comment on the dinosaur itself so I will comment on my drawing.

With this one, I didn't bother with skeletal reconstructions. Instead, I reverted to my good ol' habit of drawing from the outline in; I imagine what a live Styracosaurus would look like and draw out the outlines and fill in the details. I guess it's more intuitive and I draw something that I think looks right to me; a very unscientific methodology, I must admit. But this way of drawing is more comfortable for me; it reminds me of when I used to doodle on the back of ads that came with our newspaper.

Anyway, the original is a small sketch on an A5 size sketchbook

ART EVOLVED: Life's Time Capsule - The Ceratopsian Gallery

2009-03-02T09:26:00.004Z

I have been invited to take part in this cooperative blog on palaeoart, ART EVOLVED: Life's Time Capsule. The current feature is the Ceratopsian Gallery (icon below).

~~I was late in sending in a piece so I don't have my drawing there yet...~~[Edit: it's up now]

Olfactory bulb in theropods

2009-01-21T11:39:00.006Z

Ever since I started having suspicions of the role of olfaction in scavenging behaviours of Tyrannosaurus rex, I have been interested in the olfactory capabilities in predators and how they correlate with their behaviours. So much that I bought a nice book called Predator-prey dynamics: the role of olfaction. However, I shan't write about that book today, even though I quite like it. Instead I shall comment on a paper that became available in Proceedings of the Royal Society B.

I refer to the new study by Darla Zelenitsky and colleagues on the olfactory bulbs in theropod dinosaurs and alligator. Zelenitsky et al. (2009) provide the "first quantitative evaluation of the olfactory acuity in extinct theropod dinosaurs". They calculate relative olfactory bulb sizes (olfactory ratio: the size of the olfactory bulb relative to the size of the cerebral hemisphere) in 21 species of theropods (including Archaeopteryx) and 1 species of crocodilian (Alligator mississippiensis) using the greatest linear dimensions measured from endocasts, CT-scan slices, or from the impressions left on the ventral surfaces of the frontals and parietals. This last bit of information, I thought is very interesting. Although the authors themselves state that there are uncertainties associated with olfactory ratios calculated from the fronto-parietal measurements and thus exclude them from independent contrasts analysis, it demonstrates that we don't necessarily need complete endocasts to extract information regarding that dinosaur's brain, however partial the information may be; it still provides some information regardless. In calculating the olfactory ratios, Zelenitsky et al. (2009) use the greatest dimensions, meaning that their ratios are not restricted to homologous measurements, i.e. depth/depth or height/height, but attempt to capture a purely geometric ratio between maximum measurements; height/depth or depth/height ratios, whichever ones happened to represent the greatest diameter - so that's kind of neat.

Their total data of 29 points are replotted here (see above) as log olfactory ratios against log body mass. A least squares regression (LSR) line is fitted onto 19 of these data points. LSR is conducted on all theropod taxa, so excluding Alligator but also Gorgosaurus and Albertosaurus because the data for these two taxa are derived from the less reliable fronto-parietal measurements. Each species is represented by a single datum, i.e. redundant points are excluded. The LSR line with 95% confidence intervals on this reduced data set is shown superimposed onto a bivariate plot of the total 29 data points.

As you can see, I followed Zelenitsky et al.'s (2009) procedure in data reduction but conducted LSR directly on log transformed data while they performed a LSR on independent contrasts. In other words, their regression analysis is based on data with any phylogenetic signals inherent in the dataset removed. However, my plot and LSR best-fit line above looks identical to their Figure 2, which is labeled "independent contrast least-squares regression", but their actual independent contrasts LSR presented in their supplementary materials show a line forced through the origin so is clearly not the same line as presented in Fig. 2. But the stats presented (slope and r value) in the same fig are for the independent contrast LSR. A minor point, I know...

So regardless of what LSR best-fit line is presented, it is quite clear that the relationship between olfatory ratios and body mass for theropod dinosaurs is probably different from that of Alligator; although as crocodilians are only represented by three members of a single species A. mississippiensis there is no knowing what the crocodilian relationship truly is. However, it is obvious that Alligator has a much higher olfactory ratio compared to those in theropods of similar sizes. Perhaps, the role of olfaction is different in alligators from those in theropods.

Another thing to note is that all theropods including Archaeopteryx seem to fall along the tragectory of the best-fit line. The notable exceptions are tyrannosaurids (excluding Dilong), dromaeosaurids, ornithomimosaurs and Citipati, the former two groups above and the latter two below the line. Zelenitsky et al. (2009) determine if these groups are higher or lower than expected based on the 95% confidence intervals, but I'm not entirely sure if that is a good criterion as these confidence intervals are surely for the slope and intercept and nothing to do with the quantile of data distribution...? Analyses on residuals and other regression diagnostics are used to identify outliers so why not use that? - well, I don't know, who cares...

Anyway, the point of this paper was that, it was the first attempt at quantifying olfaction in extinct theropods, and it shows that aside from Tyrannosaurus rex, which always gets the spotlight for having high olfactory ratios, other large tyrannosaurids but also dromaeosaurs also have relatively high olfactory ratios, and that this is not unique to T. rex. On the other hand, ornithomimosaurs and an oviraptorosaur seem to possess relatively low olfactory ratios. Now, the physiological or ecological interpretations from these results are still unknown, but we could infer that there was something different in the physiology/ecology of these groups of theropods from an "average" or primitive theropod condition.

Reference:
Zelenitsky, D. K., Therrien, F., and Kobayashi, Y. 2009. Olfactory acuity in theropods: palaeobiological and evolutionary implications. Proc. R. Soc. B. 276: 667-673.

Muscle reconstructions: doing the homework

2009-01-19T08:28:00.006Z

I know I have been lazy with the postings here, and I really need to finish my Pachyrhinosaurus reconstruction. But I have been faced with a bit of a problem since I've decided to reconstruct this dinosaur one layer at a time, i.e. I wanted to be as accurate in the muscle reconstructions as possible so that the fleshed out version would look realistically three-dimensional even over the skin. Basically, I don't know enough about the postcranial musculature. Previously, I would have just roughly fleshed the whole creature out, from the outside in - basically imagining what a dinosaur would have looked like in life and just sketching it. This way, I didn't really need to be accurate in the myology just as long as the animal looked good enough. However, reconstruction from the skeleton up requires a bit more accuracy on the muscle reconstruction, or at least I would want to be as accurate.

If you have been following my blog for any period of time, you would know by now that I am quite obsessed with jaw muscles. I've dissected numerous specimens of birds (and a couple of crocs) and thus am quite familiar with the attachment sites, general architecture, and relative sizes of the jaw muscles. But dinosaurs (or indeed any animal) is not just the jaws or the head. There is something annoying (ha!) called the postcrania. While the spatial organization cranial/mandibular muscles can be three-dimensionally complex, they are fairly simple, as far as identification goes, in that there are only about a dozen well-defined muscle groups, about half of which are the large adductor (jaw closing) muscles. And when drawing dinosaur jaws, even at a wide open gape, only a couple of these muscles are visible, because most of them are tucked away inside the cranial adductor cavity! So thats all the contribution I get from my thesis when doing full-body reconstructions. But the rest of the body is covered in powerful postcranial musculature, most prominent of which are the appendicular (or arms/wings and legs) musculature. And I don't have much knowledge on the detailed myology of these systems - of course, I've glanced over some papers on reconstructing these muscles in dinosaurs but I don't know exactly which muscle originates where and inserts where...

Unfortunately, as I don't have time or any plans in the immediate future of actually dissecting and documenting first hand the postcranial musculature in birds or crocs (unless of course I suddenly switch to locomotor biomechanics for my postdoc), I have to resort to the next best option: read the existing literature on postcranial musculature, or doing the homework. There are plenty of literature out there on postcranial musculature, primarily appendicular musculature. And there are also an increasing number of papers dealing with the cervical (neck) musculature, most notably by Tsuihiji but also by Snively and Russell. The ribcage and tail musculature is something that is a bit more rare, I think, as I can't think of any publications off the top of my head - I'll have to go through my references to make sure. But I do know that one of my colleagues has been working on dinosaur ribcage reconstructions based on a myological/biomechanical model.

Anyway, some good places to start in reading on archosaur appendicular myology are:

Vanden Berge, J. C. & Zweers, G. A. 1993. Myologia, in Baumel, J. J. (ed.) Handbook of avian anatomy: nomina anatomica avium, pp. 189-247, Nuttall Ornithological Club.

McGowan, C. 1979. Hind-limb musculature of the Brown Kiwi, Apteryx australis mantelli. Journal of Morphology, 160: 33-73.

McGowan, C. 1982. The wing musculature of the Brown Kiwi Apteryx australis mantelli and its bearing on ratite affinities. Journal of Zoology, 197: 173-219

(these are one of the first studies to attempt to identify and correlate bone surface features with specific muscles)

and of course, some good papers on reconstructing appendicular musculature in dinosaurs, for instance:

Jasinoski, S. C.; Russell, A. P. & Currie, P. J. 2006. An integrative phylogenetic and extrapolatory approach to the reconstruction of dromaeosaur (Theropoda: Eumaniraptora) shoulder musculature. Zoological Journal of the Linnean Society, 146: 301-344.

(Sandra Jasinoski is a good friend of mine and so I know that the work that went into this paper is extremely thorough and of very high quality)

Is there a doctor in the house?

2008-12-08T11:47:00.004Z

Well, yes, I just happen to be a doctor...

I passed my viva last Wednesday (it's been a whole week already). Despite my fears that my examiners were going to shred up my thesis, my examination went extremely pleasantly. It was almost like an extended discussion than what I'd imagined a thesis defense would be like. Both my examiners were very pleased and I passed with minor corrections, mostly typos, and clarification.

I was gonna post a bit on the content, but one chapter is almost ready to submit so I think I'll hold on to that until things are a bit more definite...

Updates and Pachyrhinosaurus

2008-10-28T17:33:00.006Z

Having submitted my thesis on the 29th of September, a day before the absolute deadline (the University of Bristol permits exactly 48 months to submit a PhD thesis), I thought I could kick back and relax...maybe spend more time on drawing or blogging - but I was wrong.

Not having secured a postdoc position, I spend most days stressing, searching, working closely with academic staff on postdoc proposals, and working on converting my thesis chapters into manuscripts. At the same time, I'm trying to catch up on the reading that I'd put on hold while I was manically typing away on my thesis. I have quite a large 'to read' pile. There are some rather interesting papers out there that I only recently stumbled across and so I must blog about them sometime, when I get my head arround all the head-ouch evolutionary theories and models.

...I have this thing about not posting anything until I have something either interesting or useful to post, so not having devoted much time or effort to blogging, I'd kind of put off on the posting - until I realised that it's been more than a month since my last post...

So anyway, on popular demand, I'd started drawing a Pachyrhinosaurus. I still have to flesh it out, literally, but I just present here the framework on which I will be basing my live-restoration of this animal. As I intend to flesh this out, I didn't really bother with the anatomical details of each and every bone of the postcranial skeleton. I am happy just as long as I can make it look 'real' enough.

I usually want to follow original descriptions wherever possible, but not much has been written on this dinosaur. This was quite surprising to me as I had heard that there are bonebeds of this animal and thus there are plenty of materials to work on. There is that new monograph but I don't have a copy of it yet. So instead, I relied on images from the web supplimented by various photos supplied to my by Traumador Tyrannosaur (cheers!). I have ordered a copy of the new monograph last week, so hopefully I'll be able to start on a MK II Pachyrhinosaurus or more specifically P. lakusti. For this one, I guess it's the type species P. canadensis but I don't think it really matters that much.

Perhaps one of the enigmatic things about this animal is the presence of a bony boss where a nasal horn core should be in most derived ceratopsians. Nobody really knows what covered this nasal boss, such that there are many different reconstructions, some more fantastic than others. I haven't yet decided what I want to do with this but being a sceptic of many things I may go for a conservative reconstruction this time...

My PhD thesis

2008-08-19T21:04:00.004+01:00

With 42 days to go until I have to submit my PhD thesis, I haven't really had much time to blog...let alone draw dinosaurs! All I have time for is to get stressed out.

Anyway, in the midst of all this, I've finally decided on a thesis title:

Bite force, and the evolution of feeding function in birds, dinosaurs and cats.

The perfect title to show just how much unfocused my thesis is when it comes to a taxonomic group of interest, but extremely obsessed with bite force...ha! Of course it may be subject to change.

The actual thesis consists of five chapters:

Chapter 1: Introduction
Chapter 2: Myology and functional morphology of extant archosaurs
Chapter 3: Reconstruction of the jaw adductor muscles and jaw biomechanics in dinosaurs
Chapter 4: Dry skull bite force estimation in felids
Chapter 5: Tracing the evolution of bite force in Darwin’s finches and felids

Chapter 1 introduces biomechanical concepts regarding bite force and also introduces bite force as a useful single-value indicator of feeding function. So Chapter 1 is theory-heavy.

Chapter 2 is pretty much a preparation chapter for Chapter 3 and is dominated by straightforward muscle descriptions in extant archosaurs but primarily birds. Special focus is given to the Herring Gull/Lesser Black-backed Gull complex (Larus argentatus/L. fuscus), Common Buzzard (Buteo buteo) and Domestic Chicken (Gallus domesticus) but also feature the Ostrich (Struthio camelus) and other assorted birds. But perhaps the most important thing about this chapter is the data collection of cross-sectional areas of muscles for muscle force estimation.

Chapter 3 deals with jaw muscle reconstructions and bite force estimations in dinosaurs, in particular theropods. A simple method of bite force estimation is discussed and bite force is then predicted in a wide range of theropod taxa which is then used to test evolutionary hypotheses regarding feeding adaptations...

Chapter 4 is a critical reinvestigation into the Dry Skull method using extant and extinct cats. Bite force is estimated in 38 extant species of felids plus 3 extinct cats (Miracinonyx trumani, Panthera atrox, and Smilodon fatalis).

Chapter 5 takes the bite forces estimated for cats in Chapter 4 and uses a phylogenetic comparative method to test evolutionary hypotheses. Data in Darwin's finches are also analysed in the same way, mostly for the historical significance of finches in the development of evolutionary theories but also because there are plenty of data available for Darwin't finches in the literature. I gave a talk at PalAss last December on a priliminary version of this chapter.

There is also a summary and conclusions section at the end to wrap it all up.

So in summary, my thesis is really about bite force estimation methods and practical uses of bite force in evolutionary analyses...the evolution of functional adaptations intrigues me to no end and I believe that bite force is a strong tool in analysing functional adaptations regarding feeding.

The difference between Lion and Tiger skulls

2008-07-07T16:37:00.014+01:00

A quick divergence from my usual dinosaurs, and I shall talk about big cats today. This is because to my greatest delight, I had discovered today a wonderful book. It is called The Felidæ of Rancho La Brea (Merriam and Stock 1932, Carnegie Institution of Washington publication, no. 422). As the title suggests it goes into details of felids from the Rancho La Brea, in particular Smilodon californicus (probably synonymous with S. fatalis), but also the American Cave Lion, Panthera atrox. The book is full of detailed descriptions, numerous measurements and beautiful figures. However, what really got me excited was, in their description and comparative anatomy of P. atrox, Merriam and Stock (1932) provide identification criteria for the Lion and Tiger, a translation of the one devised by the French palaeontologist Marcelin Boule in 1906. I have forever been looking for a set of rules for identifying lions and tigers and ultimately had to come up with a set of my own with a lot of help from cat experts. So that is why I was so excited to find this unexpected treat in this book. What's even better is that a glance through Boule's criteria (Merriam and Stock 1932) showed that I'd derived at about 80% of it already. Not bad, not bad at all.

So here are the criteria of Boule (1906) as translated and presented by Merriam and Stock (1932). I shall only list the cranial characters. Alongside are my identification criteria as shown in a series of diagrams I'd prepared for the Departmental collections, for potential use in undergraduate practicals - I used subadults for this, as the unfused sutures come up more visibly in photos.

LION
1. The frontal process of the superior maxillary reaches the level of the fronto-nasal suture, or extends back of this suture.
2. The summit of this process is more or less acute.
3. The nasal bones are flat or slightly convex, especially toward their frontal extremities.
4. The external opening of the nasal fossae is relatively wider; it widens regularly beginning at the lower part.
5. The interorbital space formed by the frontals is wider, flatter and even commonly excavated; the Lion has a forehead which is wide and flat, transversely as well as longitudinally.
6. The temporal part of the frontals is relatively less developed; the fronto-parietal sutures are placed further forward.
7. The posterior palatine foramen is closer to the orbital border.
8. The inferior border of the mandible has a rather convex form; below the carnassial, this border presents a sort of tuberosity which is more or less pronounced (ramal process of English authors). This shape is such that a mandible of a Lion lying on a table on this inferior border can not touch the table at the symphysis and the angular process at the same time.
9. The coronoid process does not project behind the condyle.

TIGER
1. The frontal process of the superior maxillary does not reach the fronto-nasal suture.
2. The summit of this process is truncated.
3. the nasal bones are very convex throughout their length.
4. The external opening of the nasal fossae is relatively narrower; it widens regularly, only up to a certain height, beginning at the lower part.
5. The interorbital space is narrower and always convex: the Tiger has a forehead which is narrower and more arched.
6. The temporal part of the frontals is relatively more developed; the fronto-parietal sutures are placed further back.
7. The posterior palatine foramen is further removed from the orbital border.
8. The inferior border of the mandible has a rather straight and even concave form; there is no tuberosity below the carnassial. The mandible placed on a table rests on the symphysis and on the angular process at the same time.
9. The coronoid process projects behind the condyle.

(Merriam and Stock 1932, pp. 181-182)

With regards to my diagrams featuring my identification criteria, most of Boule's (1906) criteria are actually featured here, albeit in simpler language. The most immediately notable difference between a Lion and a Tiger skull is shown best in the lateral view photo. The Lion skull (top) is generally flatter and the face is upturned. On the other hand, the Tiger skull (bottom) has a rounded look to it with the face tilted sharply downwards. When the skull + mandible is placed squarely on a flat surface, the Lion skull will rock forwards and backwards, primarily due to the rounded ventral margin of the mandible, the tuberosity below the carnassial (m1) as described by Boule (1906). The Tiger skull on the other hand will just sit there firmly.

The most noticeable difference between the two taxa in dorsal view is the relative positions of the maxillo-frontal and naso-frontal sutures. In the Lion, the apex of the nasals are either in line with the apices of the frontal processes of the maxillae or more anterior to these, while the same nasal projection extends farther posteriorly in the Tiger. The shape of the frontal process of the maxilla also differ in the two species as described by Boule (1906). After the gross differences identifiable from lateral view, which is basically the same as first impressions, the relative positions of these sutures is the most reliable and concrete distinguishing character.

In frontal view (below), the Lion has a relatively wider external opening for the nares, flatter dorsal surface of the nasals, less steeply inclined lateral surfaces of the maxilla, and broader forehead. The Tiger on the other hand has a narrower external nasal opening constricted ventrally, strongly convex dorsal surface of the nasals such that it forms a prominent bridge along the lateral margin of the nasals with a concave valley along the midline, steeply inclined lateral surfacese of the maxillae and relatively narrower forehead. Overall, a Lion is broader and flatter along the bridge of the nose, while the Tiger is narrower and sharper along the bridge of the nose.

In any case, I am quite happy that my identification is corroborated by earlier work.

Albertaceratops nesmoi MK II

2008-06-18T00:33:00.005+01:00

Albertaceratops nesmoi MK II! It looks a lot better than my previous one, which is way too embarassing to link to now... You may have noticed but I am having fun with all these ceratopsians. It seems like I'm stuck in a ceratopsian phase right now...

I can't really comment much on Albertaceratops other than what's already been covered elsewhere. I don't think there's really anything done with this dinosaur other than the original description. But then again, what is there to do with a dinosaur known from a single skull and some fragments? Ah - someone should do functional morphology, like FEA - provided they have access to a huge scanner, that is... Not just in Albertaceratops but someone should look into stress distribution patterns in ceratopsian crania using FEA. Better yet, someone should look at pachycephalosaurs...

Anyway, I think it's the new paper but the pencil just came out too dark...and it started getting smudged so I couldn't really add any more to this. I am not liking this new paper at all...

Triceratops vs tyrannosaur

2008-06-15T23:56:00.004+01:00

This is my newest addition to the practice series. This time, it's not just a single dinosaur, but two dinosaurs interacting! Wow! It's incomplete as you can tell immediately...I might flesh them out and make them look nicer if I get around to it...

Anyway, its supposed to be a Triceratops flicking away a young tyrannosaur. In doing so, the Triceratops is almost rearing up...I initially wanted to draw the Triceratops standing firmly with both its forelimbs contacting the ground but ended up with this construct. So I guess the Triceratops locked its horns onto the tyrannosaur then reared upwards and flicked its head sideways, essentially pushing the tyrannosaur up off its feet then tossing it aside.

I doubt this would have happened between adult individuals. This tyrannosaur is probably inexperienced and got too close the Triceratops. Or perhaps it was starving and was willing to take the risk...who knows, perhaps we'll never know....

Centrosaurus apertus - initially Monoclonius crassus

2008-06-15T13:42:00.006+01:00

My attempt at another ceratopsian; this time, Monoclonius crassus - but I realised after reading up on this genus that my drawing is probably more like Centrosaurus. Damn! I really wanted to draw Monoclonius but I guess the picture I found on the Wikipedia that was labeled "Monoclonius" is probably a Centrosaurus...

According to Sampson et al. (1997), "Monoclonius specimens are generally defined on the presence of a thin, scalloped parietal and on the absence of hooks, spikes and horns seen on the posterior transverse ramus of other genera". The only complete skull specimen of Monoclonius, a specimen previously attributed to M. lowei, has a short nasal horn core and a pair of low rounded supraorbital horns (Sampson et al. 1997).

The absence of elaborate cranial ornamentations in Monoclonius and its occurrences in slightly older strata can be indicative of a primitive condition in Monoclonius. On the other hand, these features are also commonly associated with juvenile and subadult centrosaurine specimens, indicating a possible paedomorphosis in Monoclonius. However, it seems more likely that Monoclonius is based on subadult specimens rather than being adults with primitive/juvenile characteristics. Sampson et al. (1997) regard Monoclonius as a numen dubium because 1, diagnostic characters of Monoclonius are present in subadults of other centrosaurines; 2, suture closure and bone surface texture supports subadult status of Monoclonius specimens; and 3, Monoclonius-type cranial elements have been found in bonebeds of other centrosaurines spanning a large time period.

The third point is the most convincing argument against the validity of Monoclonius. Monoclonius-type parietals have been found in association with Centrosaurus, Einiosaurus, and Pachyrhinosaurus bonebeds in Montana and Alberta. These are indistinguishable to isolated parietals usually assigned to Monoclonius. Perhaps, Monoclonius lived alongside other centrosaurines in several different locations over a large time period. Sampson et al. (1997) however think this unlikely and proposes that Monoclonius is likely made up of subadult specimens of Styracosaurus, Centrosaurus, Einiosaurus, and/or Achelousaurus and that all centrosaurines go through a 'Monoclonius stage' through ontogeny (Sampson et al. 1997).

On the other hand, Dodson (1990) argued that the type specimen of Monoclonius is diagnostic and that this genus is valid based on biometric results. Dodson et al. (2004 in The Dinosauria, 2nd edition) also seem to follow this argument as they treat Monoclonius as a valid monotypic genus with the complete skull, M. lowei, included in the type species. Though not discussed in detail, Dodson et al. (2004) citing Tumarkin and Dodson (1998) mention the possibility of paedomorphosis in Monoclonius based on the large adult-sized 'M. lowei' - i.e. retaining juvenile characteristics while attaining adult size.

As much as I love the name Monoclonius, it seems more study is in need in order to either invalidate or validate the genus. As Dodson et al. (2004) mention, aging techniques may perhaps provide more evidences. Bone histology comes to mind...

References:

Dodson, P. 1990. On the status of the ceratopsids Monoclonius and Centrosaurus. In: Carpenter, K. and Currie, P. J. (eds.). Dinosaur Systematics: Approaches and Perspectives. Cambridge University Press, Cambridge. Pp. 231-243.

Dodson, P., Forster, C. A., and Sampson, S. D. 2004. Ceratopsidae. In: Weishampel, D. B., Dodson, P., and Osmóslka, H. (eds.). The Dinosauria (Second Edition). California University Press, London. Pp. 494-513.

Sampson, S. D., Ryan, M. J., and Tanke, D. H. 1997. Craniofacial ontogeny in centrosaurine dinosaurs (Ornithischia: Ceratopsidae): taxonomic and behavioral implications. Zoological Journal of the Linnean Society, 121: 293–337.

Tumarkin, A. R. and Dodson, P. 1998. A heterochronic analysis of enigmatic ceratopsids. Journal of Vertebrate Paleontology, 18(suppl.): 83A.

Monolophosaurus jiangi

2008-06-15T00:40:00.002+01:00

Monolophosaurus jiangi is a theropod from the Middle Jurassic of Xinjiang, China. It's phylogenetic position is rather uncertain - though there will be a monograph coming out soon but I can't remember if there was a phylogenetic analysis associated with this redescription.

Of course the most distinctive feature of Monolophosaurus is the large sagittal crest on the skull. The crest is quite thin and has several openings so is probably not a functional structure.

There was some speculation that the basal tyrannosauroid Guanlong wucaii, also from Xinjiang, represents a juvenile morphology of Monolophosaurus. However intriguing this claim may seem, at least one Guanlong specimen shows signs of arrested growth histologically so is quite likely to be an adult.

Here, you see a fine specimen of Monolophosaurus scoping out a carcass.

Thecodontosaurus antiquus

2008-06-10T23:02:00.004+01:00

This is my attempt at a reconstruction of Thecodontosaurus antiquus. No one really knows what the skull looked like except for a juvenile of a closely-related southern Welsh species Pantydraco caducus (formerly known as Thecodontosaurus caducus) so I pretty much made it up - loosely basing it on Benton et al. (2000). The interesting thing about Theco is that there are so many postcranial jumbled together that no one has any idea what the forelimb to hindlimb ratio is. I attempted a lower fore-hind limb ratio - so as to make it look like Theco is actually not obligatory bipedally nor quadrupedally, basically facultative.

Thecodontosaurus was discovered in 1834 at the Durdham Down in Clifton, Bristol, UK and is the fourth dinosaur to be named. It is also the oldest dinosaur from Britain at 203-215 million years old. The original Clifton materials were destroyed in the second world war when a bomb hit the Bristol City Museum. However, some elements, including a braincase, had fortunately escaped destruction as they had been taken back to the United States by Othniel Marsh as part of a collections exchange with the Yale University Museum in the late 19th century.

Most of the more recent studies on Theco have been conducted on materials collected from a cave deposit in a quarry in Tytherington, just north of Bristol, in the 1970s. Over the course of the next few decades, numerous specimens (at least from 30 or so individuals) were prepared out, but the University of Bristol has just under 6 tons of bone-bearing rocks still awaiting preparation.

Recent work suggests that Bristol and its surrounding areas, including south Wales where Pantydraco lived, were a series of tropical islands - in which case, Pantydraco may just be another island species of Thecodontosaurus.

Allosaurus fragilis 3

2008-06-10T21:57:00.003+01:00

So it has been a while...and for my rehabilitation, I give you, tah-dah... Allosaurus again! Well, it could be any non-descript tetanuran theropod...from this angle anyway. Again, this is one of my series(?) of practice drawings, and for that, who else but Allosaurus? I have attempted this angle before but never as "good" as this one turned out to be - at least I think it looks good enough.

Anyway, I had a bit of a problem with my scanner when trying to upload this - it always came up with some weird faint line across the middle. I tested all sorts of different papers and book covers to see what the cause was. It came out fine on really strong colours and backgrounds with multiple colours so I determined it was something to do with white so I thought it might need some adjustments or something. And I found the callibration button! Woohoo! Such a simple thing and it takes a postgrad student nearly half an hour to figure out...

Pelvic muscles for aquatic locomotion in crocs

2008-05-07T18:40:00.004+01:00

It is widely known that crocodilians use a unique form of diaphragmatic breathing (Gans and Clark 1976; Farmer and Carrier 2000). Diaphragmatic breathing in crocodilians employs a hepatic piston or the movement of the liver driven by the diaphragmatic muscle. The diaphragmatic muscle attaches to the pelvis and to the liver. Contraction of the diaphragmatic muscle pulls the liver caudally increasing the volume of the pleural cavity. Farmer and Carrier (2000) further showed that the kinetic pelvis also contributes to breathing in crocodilians. Pelvic muscle activities were correlated with both inspiration (with M. ischiopubis and M. ischiotruncus rotating the pubes ventrally increasing abdominal volume) and expiration (with the M. rectus abdominis and M. transversus abdominis rotating the pubes dorsally). Activation of these four pelvic muscles are independent of locomotion and were presumed to be primarily for breathing function. This allows for a strong breathing capability independent of locomotion, i.e. breath heavily while running, and is in stark contrast to the low metabolic sit-and-wait lifestyles of modern crocodilians. Thus, Farmer and Carrier (2000) suggest that these functional adaptations were strongly selected for early in the evolutionary history of the crocodilian lineage when high metabolic lifestyles were more common amongst the members of the group. This idea that pelvic ventilation is plesiomorphic to archosaurs is consistent with some previous studies such as Ruben et al. (1997), who determined that theropods also used a hepatic piston diaphragm for ventilation, based on similarity of pelvic morphology between theropods and crocodilians – though Codd et al. (2008) argued for an avian-style ventilation in non-avian maniraptoran theropods, based on the presence of uncinate processes in these taxa.

I came across a very intriguing study today, which got me started on this divergence into crocodilian respiration. It is a study on the activities of the respiratory muscles in the American Alligator (Alligator mississippiensis) during aquatic locomotion. Uriona and Farmer (2008) tested the hypothesis that the pelvic muscles involved in pelvic ventilation also functions in aquatic locomotion, primarily in controlling pitch and roll. Electromyography actually showed that except for M. transversus abdominis the pelvic muscles were active during a head dive. Putting weights on their tails to counter head dive resulted in greater activities of these muscles than when weights were attached to the head reinforcing the possible roles of these muscles in this activity. Presumably, when these muscles are active, it displaces the centre of buoyancy enough so that the caudal portion of the body is relatively less buoyant than the cranial portion allowing for a head-dive (Uriona and Farmer 2008). During rolling, the diaphragmatic muscle and rectus abdominis were active unilaterally. Because unilateral muscle activation requires a high amount of neural control, pelvic muscle activity is shown to be important in aquatic locomotion.

Uriona and Farmer’s (2008) inference into the evolution of respiration in crocodilians is very interesting. But I can’t explain it very well so I will cheat and quote them directly.

“We observed that alligators activate the rectus abdominis and the diaphragmaticus in synchrony when diving in water, despite the fact that the rectus abdominis is used for exhalation and the diaphragmaticus for inhalation during ventilation. Both the rectus abdominis and the diaphragmaticus were probably originally derived from the same muscle-group in alligators and the primitive function of the rectus muscle was almost certainly locomotion rather than ventilation. To have a favorable function in aquatic locomotion just one innovation would have been required, a change of the site of insertion of a portion of the rectus from the sternum to the liver. By contrast, to evolve this muscle for the purpose of respiration requires two evolutionary innovations to occur, a deviation of the site of insertion of part of the rectus from the sternum to the liver and the development of new motor recruitment patterns. Thus, the most parsimonius explanation for the origin of the diaphragmaticus is that it arose first for controlling movement in the water and was later recruited for ventilation”.

I find this notion very intriguing; that pelvic muscles involved in the pelvic breathing of crocs initially evolved as a response to aquatic lifestyles and were later recruited for ventilation. However, I’m finding it difficult to follow their logic. Surely, the development of new motor recruitment patterns would have to have occurred even if these muscles were initially adapted for aquatic locomotion? Unless, these motor recruitment patterns are plesiomorphic as well – but then that would mean that evolutionary steps for pelvic ventilation wouldn’t have to deal with developing new motor recruitment patterns and it would cost as much as adaptations for aquatic locomotion...

Unless I am an idiot and missing something obvious, I don’t really see why it is most parsimonious to think functions for aquatic locomotion are primitive. In any case, I’d be curious to see what kind of new research can test this further.

References:
Codd, J. R., P. L. Manning, M. A. Norell, and S. F. Perry. 2008. Avian-like breathing mechanics in maniraptoran dinosaurs. Proceedings of the Royal Society B-Biological Sciences 275:157-161.
Farmer, C. G., and D. R. Carrier. 2000. Pelvic aspiration in the American alligator (Alligator mississippiensis). Journal of Experimental Biology 203(11):1679-1687.
Gans, C., and B. Clark. 1976. Studies on Ventilation of Caiman crocodilus (Crocodilia-Reptilia). Respiration Physiology 26(3):285-301.
Ruben, J. A., T. D. Jones, N. R. Geist, and W. J. Hillenius. 1997. Lung structure and ventilation in theropod dinosaurs and early birds. Science 278(5341):1267-1270.
Uriona, T. J., and C. G. Farmer. 2008. Recruitment of the diaphragmaticus, ischiopubis and other respiratory muscles to control pitch and roll in the American alligator (Alligator mississippiensis). Journal of Experimental Biology 211(7):1141-1147.

Carnotaurus sastrei

2008-05-07T01:30:00.006+01:00

I got a request from Zach to draw Carnotaurus so here is my attempted reconstruction of C. sastrei. Funnily enough I have never drawn or even attempted to draw Carnotaurus previous to this - that is except for the unsatisfactory precursor to this picture...It took me forever to finish but for a first attempt I kinda think it turned out pretty good.

There are some really strange things with Carnotaurus, the first obvious being the skull. Staring at Bonaparte et al.'s (1990) skull reconstruction and photos for a prolonged time and reading their description, I noticed that the postorbital region of the skull in Carnotaurus is really strongly deflected ventrally while the sagittal crest is extremely high. This results in the supratemporal fenestrae having their lateral borders ventrally displaced compared to the medial borders. The sagittal crest in reptiles generally serves as the attachment sites for jaw adductor muscles, namely the M. pseudotemporalis superficialis (MPsTs), M. adductor mandibulae externus medialis (MAMEM), and MAME profundus (MAMEP) (Holliday and Witmer 2007), so an enlargement of the sagittal crest can allow for increased attachment area for these muscles. On the other hand, the posterior face of the transverse projection of the dorsal crest of the parietals serve as the attachment sites for the neck muscles namely the M. transversospinalis capitis (Snively and Russell 2007). The high position of the attachment site allows for a higher leverage for dorsiflexion of the skull by this muscle.

But then, perhaps the most striking feature of Carnotaurus is the frontal horns. For some reason I've always thought the horns were flatter and bladelike but on closer inspection, I was surprised to find how thick they actually are, though the dorsal surface is flat - hmm...I guess my reconstruction kind of looks like they're conical than flat on top...The horns have "a system of shallow grooves" making the surface quite different from that of the rest of the skull (Bonaparte et al. 1990). Apparently, the structure of the horns is not so different from that of horn cores in modern bovid so it is likely that horns in Carnotaurus also had some corneous covering making them longer in life.

Lastly, I was rather intrigued by the strange forelimbs. The ulna and radius are extremely short (1/4 the length of the humerus) and features on the articulation with the humerus indicate that the bones did not rotate significantly. This ristricted movement in the anteroposterior direction. Further, the parallel positions of the ulna and radius forced the palmer side of the manus to face dorsally/anteriorly (and laterally?) as opposed to ventrally/medially as in other theropods (Bonaparte et al. 1990). So apparently, the palms of Carnotaurus face outwards as opposed to inwards. Now this came as a complete surprise for me. The bones of the manus themselves are preserved but not in articulation and the distribution of the bones were interpretted tentatively (Bonaparte et al. 1990). Coria et al. (2002) report of an articulated manus in Aucasaurus providing a better understanding of abelisaurid manual morphology. In Aucasaurus, as in Carnotaurus, there are four metacarpals (mc I ~ IV). It seems unlikely that mc I and IV carried any phalanges, while mc II and III are joined to one and two phalanges respectively, but with no clear indications whether claws were present or not (Coria et al. 2002). Unlike Aucasaurus mc IV in Carnotaurus is more elongate and has a large articulation for the ulna.

So all in all, strange beast...

Allosaurus fragilis 3: Allosaurus yet again...

2008-04-28T23:26:00.003+01:00

Yes it is, it's Allosaurus fragilis yet again! The point is, Allosaurus is by far the easiest theropod to draw...I don't know why, but perhaps it's because you see images of Allosaurus skulls everywhere, being depicted as the "generic" theropod. Of course it is one of the most abundant theropods ever so we do have a good idea of its morphology and to a certain extent its ontogeny - the vast majority of fossils are of adults or subadults while juveniles and hatchlings are very rare.

I use Allosaurus when I am testing out new ideas, whether it be biomechanics or just new angles to draw...certainly this is the case of the latter. It's not entirely a ground-breakingly new angle at all but one that I have attempted in numerous previous accounts and have never really gotten right. Though, I think I've got it almost right this time. I find angled shots really difficult - as you may have noticed, most of my drawings have got the skulls captured in a lateral aspect or just slightly angled. Depth perseption in dinosaur drawings are quite hard - I find, at least...

Ceratosaurus nasicornis

2008-04-26T19:22:00.003+01:00

One of my all-time favourite theropod is for some reason Ceratosaurus nasicornis. You might think its the horns but I'm actually more drawn to the overall skull morphology. I can't remember now why but Ceratosaurus was one of the first theropods that I attempted to draw the skull of. So I guess it was the first theropod that I actually paid attention to the skull morphology in some detail...

In any case, Ceratosaurus is still a taxon of significance. It represents the diverse group of basal theropods otherwise known as Ceratosauria, though what constitutes the group has never been stable. Aside from Ceratosaurus, Ceratosauria has traditionally included such taxa as Elaphrosaurus, Dilophosaurus, Coelophysis, Syntarsus, abelisaurids and other "ceratosaurs". Recent work however seem to show Ceratosauria in this traditional sense to be unsupported. Most recent phylogenies would separate coelophysoids (Coelophysis, Syntarsus, possibly Dilophosaurus, etc.) from Ceratosauria but the exact taxonomic make up of Ceratosauria is still controversial. Thus a more inclusive definition is preferred - that is, Ceratosauria is all dinosaurs sharing a more recent common ancestry with Ceratosaurus than with birds.

Even then, the vast majority of ceratosaurs are abelisaurs anyway so I can't see why they can't just be called basal abelisaurs or something...Ceratosaurus itself seems to be very closely related to abelisaurs, an enigma as all abelisaurs (with the exception of Tarascosaurus) are known from the Cretaceous of Gondwana. But then again, Ceratosaurus is basal to abelisaurs and its earlier presence may just be that basal abelisaurs weren't necessarily restricted to Gondwana...but who knows, maybe we'll never know.

More on jaw muscle reconstructions

2008-04-20T16:39:00.004+01:00

I have some more old images of mine, this one is of the jaw muscle reconstructions in Deinonychus. The skull is reconstructed from Ostrom's (1969) original figures. And jaw muscles are based on personal observations in numerous modern bird species. Off the bat it's obvious I've only referred to birds and not crocodilians or other diapsids because of the way I've reconstructed the MAMES attaching with a tendonous attachment onto the coronoid process. The muscle attached to the dorsal and medial surfaces of the surangular just medial and posterior to the MAMES is the MAMEM. In contrast, the MAMES in crocodilians attach along the dorsal surface of the surangular with the MAMEM attaching just medial to that. I suspect given the arrangement of cranial bones that the muscles arrangements in theropods would be more similar to crocs (and other diapsids) than to birds. The MPT is reconstructed as wrapping around the ventral side to attach to the lateral surface of the angular as in crocs.

Another picture I drew of muscle reconstructions in theropods, or rather another one of them hypothetical dissections, is one in Allosaurus. Again it is evident the muscles are based on birds from the MAMES attachment. Like in a previous post, the skin is peeled off halfway and the tongue and hyobranchial apparatus have been removed to reveal just the jaw adductor muscles. I just think this is a rather comical drawing, more so than the last one.

You might think that all this is pointless and we will never know what the muscles in theropods were like, but a large part of biomechanics actually rely on muscle data and the more we know about them the better it is.

Centrosaurus

2008-04-19T23:45:00.007+01:00

I've broken my routine and drew a Centrosaurus instead of a theropod. I couldn't decide what theropod I wanted to draw but I was getting a bit bored of theropods.

Anyway, I guess this would be Centrosaurus apertus Lambe, 1904 because of the cranial ornamentation. C. apertus and C. brinkmani Ryan et Russell, 2005 differ in their cranial ornamentations with C. apertus having larger parietal ornamentations. C. brinkmani is also restricted to the Oldman Formation of southern Alberta.

I don't really know enough about ceratopsians to write anything interesting (I just think they look great!) but I might as well comment on the forelimb posture...for the longest time, there has been a debate regarding the forelimb posture of ceratopsians. Some argued for an erect parasaggital posture while others argued for a sprawling posture with the humerus averted laterally. Anatomically, the sprawling posture seems to make sense. However, this left a discrepancy with ceratopsian trace fossils that had shoulder-width manual trackways. The manual impressions are also directed laterally unlike sprawling reptile manual impressions that are directed medially.

As Paul and Christiansen (2000, Paleobiology 26: 450-465) pointed out, this bipolar reconstruction of erect versus sprawling posture is misleading, as "fully erect" is suggestive of columnar elephantine limbs, while most large mammals don't even have this posture. "The issue of forelimb posture in ceratopsians is primarily a question of whether the humerus operated in a largely parasagittal fashion or employed significant mediolateral rotation during locomotion" (Paul and Christiansen 2000, p.451). Manual trackways would enforce the hands to be directly beneath the shoulder - the humerus likely operated in a largely parasagittal fashion but with the elbows slightly averted, instead of a "sprawling" manner. The elbows were probably flexed, so that takes care of the anatomy.

The problem, as I've heard from a friend who's worked on ceratopsian forelimb posture, is as mentioned above that the manual impressions are directed outward but most reconstructions force the hands to face forwards. Now, anatomically, that would rotate the whole forelimb laterally hence the sideways averted humerus and sprawling posture. But if the hands were to face sideways, as the trackways suggest, then the whole forelimb rotates so that it is pretty much underneath the body in an "erect" posture but with the elbows flexed, not the elephantine columnar fully erect posture.

So to summarise, I believe ceratopsians held their forelimbs pretty much underneath their shoulders with their elbows flexed and hands facing slightly outwards.

Dromaeosaur head dissection

2008-04-19T15:34:00.003+01:00

I was going through my older drawings and came across this. It's quite comical but its a dromaeosaur head midway through dissection. The skin has been peeled off to reveal the jaw adductor muscles, jaw depressor muscle, parts of the neck muscles, and trachea. I got this idea from my own numerous dissections of bird heads. Minus the fact that this looks like a dinosaur, the initial phases of dissections in bird heads also look something like this...

Even in birds there really isn't much of a subdermal layer of muscles, except some really thin sheets that presumably control the feathers. But other than that, archosaurs don't have facial muscles seen in mammals and the skin is pretty much attached directly to the skull and mandibles in most parts, especially the rostrum.

The jaw adductors visible in this phase are the M. adductor mandibulae externus (MAME) superficialis (MAMES) filling the lateral temporal fenestra, MAME medialis (MAMEM) occupying the supratemporal fenestra, and M. pterygoideus (MPT) attaching on the ventral/medial side of the mandible and inserting/originating at the pterygoideus/palatine/quadrate on the upper jaw. The M. depressor mandibulae (MDM) is the slim body of muscle attaching on the back of the skull down to the retroarticular process if there is one or the posterior edge of the mandible.

Be the Dinosaur: a travelling museum exhibit

2008-04-19T14:39:00.001+01:00

For some time now, I have been working as a scientific consultant on a travelling museum exhibit called Be the Dinosaur. The main attraction to this exhibit is the virtual simulation of the Late Cretaceous Hell Creek Formation. Visitors can navigate through the environment as a Tyrannosaurus rex or a Triceratops and try and complete some tasks, such as gathering food, or crossing a river, etc. However, in order to survive these simulations, the visitor must be very keenly aware of what they need to do and where to look for necessary stuff such as energy-rich food - the dinosaurs have a virtual digestive system and need to stock up energy for severe tasks like fording rivers. These information are provided in the panel-based education kiosks located throughout the exhibit so you can't skip the kiosks and go straight into the simulator pods - because you won't be prepared to survive. I think this is a clever way to educate visitors in various fields of science associated with dinosaur palaeobiology, including hunting behaviours, social behaviours, nutrition, energetics, biomechanics, etc.

Currently, the simulation features Tyrannosaurus rex, Triceratops, some insects for the background and lots of plants but will in the future include other animals such as fishes, turtles, lizards, crocs, and other species of Hell Creek dinosaurs possibly including birds.

You can view a few sample movies on Youtube
Wildlife Documentary
It's good to be King
Visitor response

60mb version of Wildlife documentary:
Wildlife documentary large

"this is the test article and as such is a work of progress, improvements, refinements are constantly being added in both graphics and technology - and will constantly be added during the lifespan of the exhibit" - from the developers.

The "Wildlife documentary" and "It's good to be King" are both basically a nature documentary in that the camera is just placed strategically to capture the actual behaviours of the animals. In that, I mean that their behaviours are not preprogrammed or part of a scenario, but are completely governed by their AIs. The interractions between the rexes and coordinated hunting you see in "Wildlife Documentary" are completely spontaneous. The AIs only have a few simple and basic drives and needs and "some universal information that any animal that would know about its environs". So the rexes are responding to each other the way they are through whatever the AIs decided was desirable under those circumstances.

The background movements like leaves swaying in the wind or water currents plus all physical interactions are generated by a physics engine and all animals have separate AIs governing their behaviour. All of these simulations are occurring real time and thus it is virtually a new experience every single simulation. Because all events are unfolding real time, the above videos are in essence a documentary and the cameras have to be placed in a good position to actually capture anything interesting.

In the actual simulator pods though, it is not just watching a nature documentary but actually getting involved as a T. rex or a Triceratops. You can be part of a hunting party or a member of a large herd in search of fresh vegetation...

The exhibit will premiere at the Louisville Science Center in mid May and then go on tour.

Suchomimus tenerensis: colour

2008-04-15T00:25:00.002+01:00

Phew...so this is an Adobe Illustrator version of the Suchomimus drawing from a few days ago. As always, I used Illustrator to trace out the outline and then use different layers to colour, shade, and add a bit of effect. The stripes took me forever to do...

DinoBase, 1 year anniversary coming up!

2008-04-13T15:17:00.007+01:00

Well, it's almost a whole year since the launch of the new DinoBase. The actual one-year anniversary for the relaunch is the 17th of April (see here for my post on the launch day last year). I'm sure most of my readers are already aware, DinoBase is an online resource hosted by the Department of Earth Sciences, University of Bristol which I just happen to be the administrator of. The main feature of DinoBase is as the name suggests, its online database of dinosaurs. Visitors can search for dinosaurs using a number of search criteria such as genera, species, author, or year of description. I'll just go through the basic search function here.

Let's say we want to search for Tyrannosaurus rex but can't be bothered to spell out the whole name so we type in "tyranno".

Now we click on "search" and DinoBase will return the following list:

Note that DinoBase returns all records alphabetically, so the first few are the ones of interest, in this case, Tyrannosaurus bataar and Tyrannosaurus rex. Now to view the record we don't want to click on the dinosaur names because that will research the database under a new search criterion, i.e. the name you just clicked as the new keyword, so we want to click on the magnifying glass icon to the right of the names. When you place your cursor over it, a little pop-up comes up with "View Record".

Now we can view the information as a new window. Incidentally, Tyrannosaurus bataar is listed twice once as Tyrannosaurus and again as Tarbosaurus. This is due to a glitch in the system that doesn't let me delete entries so it stays for the moment. The only solution around this problem is to state its synonymous situation and redirect the user to the correct name, i.e. Tarbosaurus bataar, though I'm sure some people would prefer Tyrannosaurus bataar...

We do try to keep the information up to date as possible but currently there are only two of us doing data entry and management on the side (as we are both students) so there is a bit of a limit. New entries are stored on the waitlist until approved by myself - which is quite harsh as we need size data for taxa that is known from a single vertebra...so you can imagine why I'm reluctant to just approve every single new entry - I want to get as much as an accurate size estimate as possible, motly because information on DinoBase is supposed to be "academically approved".

Some of the entries will have pretty pictures like this one for T. rex. But a lot of them don't so if you're reading this and you're an active palaeoartist and want to use this chance to promote your dinosaur reconstructions, then please do contribute. We are always looking for good images of minor or rare dinosaurs!

Sinraptor dongi

2008-04-13T00:13:00.003+01:00

Second drawing of the day...though the date has changed already. This is Sinraptor dongi an allosauroid from the Jurassic of Xinjiang, China. There are two recognised species of Sinraptor, S. dongi and S. hepingensis. S. hepingensis was initially described as the third species of Yangchuanosaurus after Y. shangyouensis and Y. magnus (Gao 1992 Vertebrata PalAsiatica 30: 313-324) but was subsequently assigned to the genus Sinraptor (Currie and Zhao 1993 Canadian Journal of Earth Sciences 30: 2037-2081). Compared to Yangchuanosaurus, Sinraptor has a relatively longer and lower skull. The two genera are united as Sinraptoridae. One of the distinchuishing features of sinraptorids is the high number (more than two) of accessory openings in the antorbital fossa. Another interesting feature of Sinraptor is the tall plate-like neural spines of the dorsal vertebrae. This is quite similar to Metriacanthosaurus such that Paul (1988 Predatory Dinosaurs of the World) synonymised Yangchuanosaurus with Metriacanthosaurus - he used M. shangyouensis instead of Y. shangyouensis.

I had two opportunities of studying the specimen of S. dongi at the IVPP. S. dongi is stored in an offsite warehouse about an hour's drive out from the IVPP. It is really a warehouse and mounted specimens of Sinraptor, Monolophosaurus, and a prosauropod (I forgot what it was) are just standing there amongst wooden crates and discarded packing materials, literally collecting dust. And it was damn cold...

Suchomimus tenerensis

2008-04-12T21:59:00.005+01:00

Ok. Back to my usual passion - drawing theropods. This time, it's Suchomimus tenerensis. As always, I ran out of paper but this time, I scotch-tapee another piece of paper to fit the tail...however, the extra length made it too big for my scanner so I had to scan it in twice and stitch them together using Photoshop...

Anyway, a bit about Suchomimus - though this dinosaur is really famous that I probably won't have anything unique to comment on. Suchomimus is a spinosaurid dinosaur from the Lower Cretaceous (Aptian) of Niger (Sereno et al. 1998). It is quite distinctly different from the other famous African spinosaur Spinosaurus in snout morphology and in the lack of the giant sail - although Suchomimus also has elongated neural spines along the posterior dorsal, sacral, and anterior caudal vertebrae. The elongation is most pronounced in the sacral vertebrae but it is nowhere as long as those seen in Spinosaurus.

Along with the slightly older Baryonyx from the UK and contemporary Cristatusaurus of Niger, Suchomimus is phylogenetically distinct from Spinosaurus and Irritator of Brazil - the former three forming the subfamily Baryonychinae and the latter forming the subfamily Spinosaurinae. However, it has been suggested that Suchomimus is congeneric with Cristatusaurus as well as with Baryonyx. In which case, both Cristatusaurus and Suchomimus should be sunk into Baryonyx because of senior priority...whatever - I don't really know much about taxonomy but personal observations of the skull elements of Baryonyx and a cast replica of the same elements in Suchomimus lead me to believe that this may be the case - at least with Suchomimus and Baryonyx. Suchomimus is just slightly bigger than Baryonyx. Then again it is believed that Baryonyx is a sub-adult anyway, so if they were the same genus then we could just be observing an ontogenetic sequence...

Evolutionary theories...hurt my head

2008-04-10T16:12:00.007+01:00

It's been some time since my last post...

Anyway, I've been busy trying to write a manuscript on the evolution of bite forces using finches and cats as case studies. One thing I've found out through this process is that, it doesn't matter how sophisticated a method you use, nor does it matter how great you think your results look, what matters is your ability to tie that into a broader perspective of evolutionary theory. And I've sadly realised, that either I don't have the brains, or the imagination, or the creativity, to write anything remotely interesting in the grand scheme of evolutionary theory. Evolutionary theory's the interesting end-product of all this functional morphology and phylogenetic comparative methods anyway, and if you can't do that, then you're screwed...

But I don't intend to be lazy and give up. At the same time I've been trying to be greedy. So I've been trying to read as much evolutionary theories as I can...

....and my head hurts...

The taxonomic status of Megalosaurus bucklandii

2008-03-19T03:05:00.004Z

A new paper by Roger Benson of Cambridge University and colleagues discuss the taxonomic status of Megalosaurus bucklandii.

Every dinosaur fan knows of Megalosaurus, the first dinosaur to be named by William Buckland in 1824. Megalosaurus is also historically significant as being one of the taxa that Richard Owen based his Dinosauria in 1842, the other taxon obviously being Iguanodon. The type species M. bucklandii was erected by Gideon Mantell in 1827. Buckland's original description of Megalosaurus in 1824 is based on a series of syntypes, one of which is the famous dentary (fig). Over the years, many other large theropod specimens from the Middle Jurassic were "unjustifiably (Benson et al. 2008)" attributed to M. bucklandii. Over the years, many authors noted the possibility that the syntype series and all subsequent referred specimens may belong to different taxa all together. Thus M. bucklandii is suggested to only refer to the lectotype dentary.

According to Benson et al. (2008) the lectotype dentary allows for a diagnosis of M. bucklandii thus making it a valid taxon. Although the systematic position of M. bucklandii is unresolved, Benson et al. (2008) regard it as a possible member of the clade comprising of Ceratosauria and Tetanurae but not an abelisaurid or coelophysoid. Further, the characteristic dentary morphology present in all known spinosauroids is absent in the lectotype dentary. Thus, Benson et al. (2008) recommend the discontinuation of allying Megalosaurus with Spinosauroidea and also the practice of referring any other taxa as "megalosaurid".

So I guess we should stop using Megalosauridae and "megalosaurids" and start referring to these taxa (with the exclusion of Megalosaurus) as spinosauroids...

In my opinion, just because of its historical importance to dinosaur research, the most significant discovery in the future would be the discovery of a more complete specimen indisputably assignable to Megalosaurus bucklandii - that is, the associated specimen of a M. bucklandii dentary with other cranial and postcranial materials. The discovery of such a specimen is probably the only way to resolve the systematic position of M. bucklandii and the taxonomy of all other unassociated materials previously referred to M. bucklandii.

Reference:
Benson, R. B. J., P. M. Barrett, P. Powell, and D. B. Norman. 2008. The taxonomic status of Megalosaurus bucklandii
(Dinosauria, Theropoda) from the Middle Jurassic of Oxfordshire, UK. Paleontology 51: 419-424

Abstract: The lectotype of the Middle Jurassic theropod dinosaur Megalosaurus bucklandii, a right dentary, can be diagnosed on the basis of two unique characters: a longitudinal groove on the ventral part of the lateral surface of the dentary and a slit-like anterior Meckelian foramen. This taxon, the first dinosaur to be scientifically described, is therefore valid. Currently, however, no further material can be referred to this species with any certainty. Megalosaurus bucklandii occupies an uncertain systematic position but is not an abelisaurid or coelophysoid. Additionally, it does not possess the diagnostic dentary characters that are present in all known spinosauroids. Owing to this uncertainty, use of the family Megalosauridae should be discontinued until such time as its systematic position becomes clearer.

Happy birthday, Raptor's Nest!

2008-03-19T02:39:00.007Z

March seems to be a popular month to be born...both my parents are born in March, my friends' birthdays are in March, Ask a Biologist just recently had its first year anniversary, and now, today (19 March) is a whole year from my first blog post on Raptor's Nest - Woohoo!

And coincidentally, it's actually my real birthday today as well - and I had only realised this coincidence last week! I've survived 28 years and been in school in one way or another for 25 of those years...As my name wich means "to learn" in Japanese suggests, I have so far led most of my life as a student (of science) and will probably do so for the rest of my life

Deinosuchus

2008-03-16T15:19:00.013Z

I was recently asked a question about the possibility of Deinosuchus being in the Hell Creek and interacting with Tyrannosaurus rex. Since the Hell Creek is well-sampled and there are no Deinosuchus fossils it is safe to assume that it was absent from the Hell Creek. However, the person asking the question was fully aware of that so the question actually was, "if Deinosuchus were to be known from surrounding areas of the same age, would it be scientifically plausible to infer its presence in the Hell Creek?" To be perfectly honest, I had no idea of the temporal and geographic range of Deinosuchus and so it turned out to be an interesting afternoon of researching this.

As far as I can gather from the literature and also from colleagues that work on fossil crocs, there are no peer-reviewed scientific articles that ever state the presence of Deinosuchus in strata younger than the late Campanian. Lucas et al. (2006) include a review of Deinosuchus occurrences in one of their papers and they conclude the temporal range of Deinosuchus as being ~73-80 Ma, the younger of the range being about 12 Ma prior to the Hell Creek environment. David Schwimmer (not Ross from friends) states in his book that the supposed Maastrichtian (70.6 - 65.5 Ma) Deinosuchus remains (unpublished accounts) may be a misidentification of large (marine?) crocs. As I only had access to an on-line preview of the book, I couldn't track down the exact identity of this mystery croc...These are also supposed to be from the Atlantic Coastal Plain.

There was one thing that baffled me though, the exact age of the Black Creek Group, where the holotype material of Deinosuchus rugosus is from, and this took a bit of digging around the interweb and stratigraphy literature. Although according to Lucas et al. (2006) citing Schwimmer (2002), the Deinosuchus-bearing horizon of the Black Creek is supposed to be ~73-74 Ma, I couldn't find support for this figure mostly because there is no mention of exactly which formation of the Black Creek Group the holotype is from. This presents a bit of a problem, as according to this website, the Black Creek Group of North Carolina has three formations spanning from Early Campanian (Tar Heel Formation), Upper Campanian (Bladen Formation), and to the Early Maastrichtian (Donoho Creek Formation). So depending on which formation of the Black Creek Group the holotype material is from, the upper range of Deinosuchus can be as young as the Early Maastrichtian. The overlying marine strata, the Peedee Formation, is regarded as being Late Maastrichtian and dated at 66.7 Ma (Schwimmer 2002). D. rugosus is supposed to be from the upper part of the Black Creek thus placing it relatively younger than other Deinosuchus-bearing strata with an absolute younger bound at >66.7 Ma.

Fortunately, I stumbled across a PhD thesis that pretty much resolved this issue. According to Mitra (2002), Elizabethtown, the locality of the type specimen of D. rugosus, belongs to the Tar Heel Formation and Early Campanian in age. Further, the Phoebus Landing locality, where some referred D. rugosus specimens are known from, is supposed to be Campanian. So I've finally managed to find support for the ~73-74 Ma age of the Deinosuchus-bearing horizon of the Black Creek (Lucas et al. 2006, citing Schwimmer (2002)). Perhaps if I actually had read Schwimmer (2002) and not just the on-line previews, I wouldn't have had to go through all this effort but I wouldn't know if it's discussed in the book because our library doesn't have a copy....In any case, N Carolina would have been on the eastern side of the Western Interior Seaway anyway and all Deinosuchus specimens from Montana are definitively Campanian in age.

So in summary, all known Deinosuchus materials are from the Campanian, temporally ranging between ~73 and 80 Ma, thus making its presence in the Late Maastrichtian and in particular in the Hell Creek unlikely.

One thing that I thought was quite interesting is that Deinosuchus seems to be abundant in places and times where large theropods are absent or rare.

References:
Lucas, S. G., R. M. Sullivan, and J. A. Spielman. 2006. The giant crocodylian Deinosuchus from the Upper Cretaceous of the San Juan Basin, New Mexico. New Mexico Museum of Natural History and Science Bulletin 35:245-248.

Mitra, M. 2002. Paleopalynology of the Tar Heel Formation of Atlantic Coastal Plain of North Carolina, United States. North Carolina State University.

Schwimmer, D. R. 2002. King of the crocodylians: the paleobiology of Deinosuchus. Indiana University Press. 220 pages.

Velociraptor mongoliensis

2008-03-15T18:06:00.004Z

I've been fooling around again toying with the idea of a Velociraptor mongoliensis perching atop a recently deceased carcass and intimidating its competitors, presumably other Velociraptor individuals. As a few of us have discussed here, according to Roach and Brinkman (2007), the evidence for pack-hunting behaviour in dromaeosaurs is pretty slim. The authors are casting doubt over Deinonychus regularly hunting large prey in a highly coordinated pack-hunting style, mainly based on the loose cooperative hunting styles seen in extant archosaurs (a couple of species of crocodiles and plenty of examples of predatory birds) and the komodo dragon.

Komodo dragons are known to solitarily take down prey as much as 10 times its own size. On this basis, the authors mention that it would be possible for a 70 - 100 kg Deinonychus to solitarily take down a Tenontosaurus anywhere between 700 - 1000 kg.

The fossil sites are reexamined as well. The Deinonychus skeleton(s) found with the Tenontosaurus may have been victim to intraspecific fighting and were killed and eaten by larger adult Deinonychus as frequently observed in komodo dragons and some predatory birds. The large degree of disarticulation of the Deinonychus skeleton as opposed to the more articulated Tenontosaurus seem to indicate that the freshly killed Deinonychus may have been more apetising for the aggregated Deinonychus individuals. The other individuals probably aggressively tore apart and consumed the dead Deinonychus, leaving only the bony bits with not much meat like the manus, pes and tail.

That was pretty much recycling my DinoBase post but I thought it was a pretty cool study. Here, I envisage Velociraptor in a similar fashion - Velociraptor and Deinonychus are pretty closely related even within dromaeosaurs so we could infer something similar. I just like the idea of dromaeosaurs having something like a furry crest so I overdid it and gave this guy a lot of hair - or perhaps its ruffling its "feathers". Anyway, note that this raptor's got its sickle claw dug into the carcass to firmly hang on.

Reference:
Brian T. Roach and Daniel L. Brinkman 2007. A Reevaluation of Cooperative Pack Hunting and Gregariousness in Deinonychus antirrhopus and Other Nonavian Theropod Dinosaurs. Bulletin of the Peabody Museum of Natural History 48: 103–138

Happy birthday, Ask a Biologist!

2008-03-10T06:40:00.008Z

Well, it's actually this coming Friday (the 14th) but since this is a good chance to promote the site, why not start early?

Ask a Biologist is a Q&A website started up by University of Bristol graduate, Dr. Dave Hone. The unique thing about AAB is that unlike many Q&A forums around the internet, AAB's answerers are all either qualified PhDs, PhDs in training, or have a similar level of experience or qualifications. So there is a certain level of quality and authenticity to the answers provided. The questions are either answered by someone in the field or someone decently knowledgeable in the field with proper scientific research and citations to back it all up.

As with many forums, absolutely anyone can ask questions on AAB, sometimes even the contributors ask the other experts for opinions. But it is primarily aimed towards children and young persons still in school. So if you know of any kids aching to get some of their burning questions regarding biology, then please use this chance to direct them to http://www.askabiologist.org.uk.

I am a regular contributor to AAB as well and if you are aware of the DinoBase Forum then you will find the layout almost identical - in fact they were both designed by the same web-designer and software engineer.

Torvosaurus 3

2008-02-19T02:08:00.003Z

Following yesterday's pencil sketch and digital line tracings, I've digitally colored in my Torvosaurus using Illustrator. I like Illustrator as it allows me to store the image in vector format thus I can scale it to any size without losing any resolution. Plus, more importantly, I can use layers to add different tones and texture. I guess you can do the same in Photoshop but I'm more used to Illustrator.

This one turned out to be a lot better than my Allosaurus as I've been spending the last two weeks preparing figures for my manuscript in preparation basically using pretty much the same technique but on photographs of skulls and reconstructing jaw muscles on them.

Torvosaurus 2

2008-02-18T03:21:00.004Z

Line tracing with shadows of the same Torvosaurus drawing from the previous post, using Adobe Illustrator.

Torvosaurus

2008-02-17T22:22:00.008Z

I initially named this sketch Megalosaurus but then remembered that I've been relying on the proportions of Torvosaurus for the reconstruction, so it's been renamed to Torvosaurus. Torvosaurus is a North American "megalosaur" popularly used to aid in the reconstructions of the English Megalosaurus mostly because the long-held assumption that these two taxa are closely related. However, more recent phylogenetic analyses show that the traditional monophyletic Megalosauridae does not seem to exist anymore but rather a paraphyletic "Megalosauridae" with a paraphyletic grade of "megalosaurs" leading up to the Spinosauridae. Or something like that...there seems to be quite a lot of confusion in this area of the theropod phylogeny probably because of the lack of good specimens. Although, in a consensus tree of published trees, a fair chunk of the traditional "megalosaurs" still seem to come together in a smaller but yet monophyletic Megalosauridae.

Anyway, I quite like these basal tetanurans as they are so enigmatic. Megalosaurus has historically been used as a "waste-basket" taxon, i.e. if the affinities of a new taxon is indeterminable, then it is attributed to the genus "Megalosaurus". Some very famous taxa such as Dilophosaurus or Eustreptospondylus were initially attributed to Megalosaurus. In the 1960's to the 1970's many new Chinese theropods were also given the name Megalosaurus, which were subsequently reassigned to new genera. Because of this, Megalosaurus had the longest temporal range of all theropod genera starting at the Rhaetian in the Triassic ("M". cambrensis = Zanclodon cambrensis) all the way up to the Cretaceous ("M". crenatissimus = Majungasaurus crenatissimus). Of course Megalosaurus proper is fairly restricted to the Middle Jurassic.

Torvosaurus on the other hand is from the Late Jurassic of western North America and Portugal. In both settings, Torvosaurus was contemporaneous with other theropods: Allosaurus, A. fragilis in N. America and A. europaeus in Portugal; and Ceratosaurus in N. America. As with Ceratosaurus, Torvosaurus is relatively rare compared to Allosaurus.

Olfactory capabilities in T. rex and birds

2008-02-13T16:20:00.005Z

I’ve recently had the chance to review the literature regarding olfaction in birds and to my surprise found that there is little research done on the olfactory functions (e.g. olfaction threshold) and their relations to the olfactory bulbs. The main reason I got into this was primarily for the claim that T. rex had an acute sense of smell because of its enlarged olfactory bulbs. Now the latter part of this statement is obviously true. According to Brochu (2000), the olfactory bulb is 1.5 times as wide as the cerebral region of the endocast in T. rex. Following Bang and Cobb’s (1968) simple method, the greatest diameter of the olfactory bulb is about 41% of the greatest diameter (in this case the longest length) of the total brain. That’s higher than the largest proportion of olfactory bulb in modern birds according to Bang and Cobb (1968), which is as follows:

37.0% - Snow Petrel
33.0% - Wilson’s petrel
30.0% - Wedge-tailed Shearwater
30.0% - Greater Shearwater
29.5% - Dove Prion
29.0% - Black-footed Albatross
29.0% - California Shearwater
28.7% - Turkey Vulture
27.5% - Cape Pigeon
27.0% - Fulmar

Notice that the Turkey Vulture is seventh place within the seabirds. The Turkey Vulture has repeatedly been brought up (especially by Jack Horner) to suggest a similar mode of life (i.e. scavenging) for T. rex because of the enlarged olfactory bulbs in both taxa. Well, it seems that seabirds generally have enlarged olfactory bulbs as well, a higher proportion at that, and that the odd one here is the Turkey Vulture. Surely, you cannot speculate a mode of life of an extinct animal based on one modern example that doesn’t follow the general pattern – that is, that in general, seabirds have the highest proportion of olfactory bulb to the whole brain and not scavenging vultures where Turkey Vulture is the exception – the only other vulture in Bang and Cobb’s (1968) dataset is the Black Vulture with 17%; within the range of raptors and comparable to Woodcock, Belted Kingfisher, and Adélie Penguin.

So we know that T. rex had enlarged olfactory bulbs unheard of in modern birds, but that still does not answer the fundamental question of “what does that tell us about function”.

As far as I’ve read so far, there doesn’t seem to be any studies actually conducted to test for any correlations between olfactory sensitivity and relative size of olfactory bulbs. As Bang and Cobb (1968) nicely put it, “the significance of such measurements […i.e. olfactory bulb] rests on the general assumption that increase in size of a part of the brain indicates increase in function”. More recent work (Smith and Paselk 1986, McKeegan et al. 2002, 2005) that test the olfaction threshold, i.e. the olfactory sensitivity, in birds only cite Bang and Cobb’s (1968) work for the relative sizes of the olfactory bulbs but never test if there is a relationship between the two – function and size. This “general assumption” mentioned in Bang and Cobb back in 1968 still seems to hold true today as well and has remained untested for the last 40 years. That is, of course, if I’m missing some key reference.

In any case, olfaction threshold in birds are shown to be much higher than those of mammals, i.e. birds have a worse sense of smell than mammals do. Clark (1991) cite Wenzel and Sieck (1972) to suggest that birds have an olfaction threshold range of 0.01 to 0.5 ppm, while McKeegan et al. (2002) report thresholds of 1 and 2.5 ppm for ammonia and hydrogen sulphide respectively in hens, Gallus domesticus. Contrast to these results, human detection threshold for ammonia ranges from 0.0005 to 0.37 ppm and much lower threshold for hydrogen sulphide at 1×10E-7 to 0.0002 ppm (McKeegan et al. 2002).

In the Turkey Vulture, Smith and Paselk (1986) report an olfaction threshold of 1×10E-6 M (or molar, mol/L) for butanoic acid and ethanethiol, and 1×10E-5 M for trimethylalanine; three odorants generally associated with animal decomposition. Now, if my calculations are correct, then Turkey Vulture has olfaction thresholds of about 0.09, 0.06, and 0.6 ppm for the above odorants respectively, or more simply 0.06 to 0.6 ppm depending on the substance. In their odour dispersion model, Smith and Paselk (1986) predict that in order for a Turkey Vulture to detect these odorants at approximately 61 m altitude and 183 m downwind - an observed distance for carrion detection in wild Turkey Vultures - it would have to have olfaction thresholds of roughly 1×10E-12 to 1×10E-13 M for ethanethiol. If you were to trust their results, then clearly, the Turkey Vulture does not have a high enough olfactory sensitivity to detect carrion on smell alone – perhaps they also rely on other senses such as sight (watching out for activities of other scavengers), or hearing (sounds of scavenging insects). Further, since the absolute quantity and rate of odorant emission depends on the mass of the carcass, and since Turkey Vultures prefer to feed on small-bodied carrion that would be expected to emit relatively low levels of odorant, detection of odorants from these carrions cannot be expected unless their thresholds were lower. On the other hand, it could be that their experiments did not detect to the full extent the Turkey Vulture’s olfaction threshold. Or perhaps their dispersion model is wrong and odorants can disperse farther without being diluted as much.

This seems rather odd, that the Turkey Vulture with one of the highest proportions of olfactory bulbs don’t seem to have as keen a sense of smell than one would expect. Perhaps the olfactory bulbs process some other information associated with smell such as filtering out background smell. So they’d be sensitive to smell but in a way to sniff something out from other smells.

In any case, olfaction thresholds are probably more directly associated with the surface area of the olfactory epithelium, and at this point, we don’t seem to have the necessary information to relate it to the relative sizes of the olfactory bulbs.

References:
Bang, B. G., and S. Cobb. 1968. Size of Olfactory Bulb in 108 Species of Birds. Auk 85(1):55-61.
Brochu, C. A. 2000. A digitally-rendered endocast for Tyrannosaurus rex. Journal of Vertebrate Paleontology 20(1):1-6.
Clark, L. 1991. Odor Detection Thresholds in Tree Swallows and Cedar Waxwings. Auk 108(1):177-180.
McKeegan, D. E. F., T. G. M. Demmers, C. M. Wathes, R. B. Jones, and M. J. Gentle. 2002. Stimulus-response functions of single avian olfactory bulb neurones. Brain Research 953(1-2):101-111.
McKeegan, D. E. F., F. S. Smith, T. G. M. Demmers, C. M. Wathes, and R. B. Jones. 2005. Behavioral correlates of olfactory and trigeminal gaseous stimulation in chickens, Gallus domesticus. Physiology & Behavior 84(5):761-768.
Smith, S. A., and R. A. Paselk. 1986. Olfactory Sensitivity of the Turkey Vulture (Cathartes aura) to Three Carrion-Associated Odorants. Auk 103(3):586-592

Functional adaptations: ontogeny and evolution

2008-01-25T11:46:00.000Z

As I study functional morphology for my thesis, I think about this subject an unusual (or unhealthy) amount. And there's one thing that's been hurting my head for the last few days.

That is: how does physical stress as a response to function, e.g. biting reaction force and its skeletal response, work as selective pressure on morphology? In other words, what are the mechanisms behind functional adaptation as seen by morphological change through time?

Skeletal response to mechanical stresses occur during the lifetime of an individual. These are ontogenetic developments that are not the same as primary ontogenetic development, as shared by all members of the species (predestined by the genome), but secondary responses brought about by extrinsic factors. So surely, any changes acquired as a direct response to extrinsic mechanical stresses, must be acquired traits, thus aren't passed down to the next generation.

My question therefore is, how do these acquired traits get passed down to the descendants? We could trace functional adaptations through the evolutionary history of certain animals, e.g. the increasing robusticity in tyrannosaur skulls. Thus, it is quite possible that skeletal response to extrinsic forces, whether it be to withstand higher biting stresses or increased muscle forces, are effectively being passed down. Otherwise, taking structural stresses and strains of an animal and linking it in with evolution is completely pointless - we can see how extrinsic stresses affect ontogeny but not evolution.

Or is it that, every single member of derived tyrannosaurids go through this ontogenetic change independently within their individual lifetimes as a response to certain extrinsic pressures and consequently ending up with the same adult morphology? So in other words, is it that Tyrannosaurus wasn't genetically predestined to have more robust skull morphology than Daspletosaurus but rather led significantly more rough lifestyles? This basically means that responses to extrinsic factors are not passed down but acquired separately in every generation, and independently in every single individual within their respective lifetimes.

Or perhaps, the more responsive individuals fare better and naturally get selected for, thus increasing the mean response level in the population, eventually producing a descendant population with significantly higher responses to the same extrinsic stresses than the ancestral population. So, perhaps it is this responsiveness that are hereditary? In the case with tyrannosaurs, Tyrannosaurus possibly may have had higher response levels to extrinsic forces than Daspletosaurus which led to increased skull robusticity during ontogeny.

Or, from basic theory of evolution, is there a background variation in predestined skull robustness that some just so happens to perform better under extrinsic forces than others in a typical tyrannosaur lifestyle and that they are naturally selected for, and given enough time the population mean skull robustness shifts towards increased robustness in derived tyrannosaurs, most notably in Tyrannosaurus? In this case, skeletal response to extrinsic factors are not passed down but those that perform better to those factors are selected for from a population with varied degrees of responses.

I don't know the answer. I wonder if anyone has an answer...

When pigs ruled the Earth

2008-01-24T17:33:00.000Z

My good friend and colleague at the University of Bristol, Sarda Sahney and our supervisor Mike Benton recently published a paper on the extinction and recovery of terrestrial ecosystems at the Permo-Triass boundary.

Here's her blog about it:
Fish Feet

Here's the University of Bristol news on it:
http://www.bristol.ac.uk/news/2008/5785.html

And here's the actual paper at the Royal Society:
http://journals.royalsociety.org/content/qq5un1810k7605h5/

The PT extinction is often called the 'mother of all extinctions' and wiped out some 90% of life on Earth. The junior author of this paper (though hardly the junior) Mike Benton wrote a book about the whole thing a few years back titled 'When Life Nearly Died'. About a third of his book's about the history of the PT extinction studies, another third about his excursions in Russia and the rest is the extinction event itself - well, maybe this is a bit overexaggerated and maybe had a bit more on the extinction event than I give credit - but in any case, an interesting read.

As Sarda mentions on her blog, after the extinction, there were very low diversities and terrestrial communities were long dominated by disaster taxa such as the so called 'pigs of the Triassic', Lystrosaurus. Because Mike used this term to describe what Lystrosaurus was like to a TV crew, they named their program, 'When pigs ruled the Earth'.

I just love that name that I have to repeatedly post it all over the place...

Allosaurus fragilis 2

2007-12-26T08:52:00.000Z

Continuing on from where I left off last time, I've been painstakingly coloring in my Allosaurus line drawing using Adobe Illustrator. This is my first attempt at a dinosaur drawing with Illustrator. First of all, I just colored in the basic colors and added 'scutes' (?) and scales and what not.

Then, I started adding in shades using black and light areas using white. I used black and white hoping that by making them transparent would have the effects of shading and hi-lighting. And it seemed to work. The beauty of this is that I now have a generic shade/lighting pattern that is consistent regardless of the undertone colors. But getting it right took a lot of time and loads of trial and errors...

But then, I realised my Allosaurus looks too glossy and looks more like an amphibian or one of those old 1950's- 1960's reconstructions. So I added in a whole load of scaley patterns again with black and made them transparent. For simplicity, I just made a handful of little hexagons of assorted sizes with the polygon tool and copied and pasted the whole lot all over the animal. It kind of looks a bit grittier now, I hope...

Lastly, I resized the outline to a thinner line and got rid of excess lines. And this is how it looks. I'm quite surprised at how good it looks despite my total lack of experience in this whole thing...

Allosaurus fragilis

2007-12-12T01:21:00.001Z

Okee dokey - continuing on with the theme, I've started tracing out this hand-drawn Allosaurus. The original was drawn ages ago - I can't really remember when. But it's up on my website (http://www.geocities.jp/raptors_nest_theropoda/).

Anyway, since I already have a digital version, all I need to do now is to import it into Illustrator and trace it out.

The next step is to use the Pen Tool and just manually trace out the outline of the drawing. This is actually quite time consuming and it's taking as long or longer than it'd take me to draw a dinosaur from scratch...

Now this is what it looks like with the tracing and the coloured-in eyeball superimposed (right).

And without the original (left). Unfortunately, this is as far as I got today, and my neck and back is starting to hurt since I've been crouching in front of my laptop for over 2 hours now....I'll resume some time later and start on colouring - I am not looking forward to that process. Actually, the teeth are already coloured in, though you can't really see it.

Fighter jet

2007-12-11T22:47:00.000Z

Umm....so, this has nothing, absolutely nothing to do with dinosaurs, palaeontology or science at all, but I just drew an imaginary fighter jet. Here's the rough sketch to the left.

I scanned this into my computer and used Illustrator to trace half the outline and coloured it all in and flipped a duplicate to make it all symmetrical. Then exported it as a gif and used Photoshop to add in the details like shades, scorches, and oil stains.

The result is below.

It's still rough but I was just having a bit of fun. I guess I could brush up on this technique and apply it to dinosaur drawings...that'd be pretty cool.

Cranial skeleton vs postcranial skeleton

2007-11-21T22:17:00.000Z

Having said what I said in my last post (about a few minutes ago...) I find it rather annoying that there is a huge abundance of literature on the detailed anatomy of the cranial skeleton but less so on the postcranial skeleton. If the dinosaur is known only from postcranial materials then there is a relatively good account of it - of course what else can you write about? Howver, if there is a perfect skeleton preserved, chances are, the description would be skull-heavy. The authors may even state that "the postcranial skeleton would be described elsewhere" but it probably won't be for another decade or so until this publication actually comes out.

I mean, I like cranial skeletons. Skulls are cool! That's what I work on.

But having collected measurements of postcrania from the literature, this popularity of cranial skeleton is really inconvenient...and I don't have the money or time (well for now) to go all over the world and measure these myself. And a lot of the times, it may be "politically" difficult to get access to these specimens...

Spinosaurus aegyptiacus

2007-11-21T21:59:00.000Z

This is an old picture of Spinosaurus aegyptiacus. I drew this about four years ago using Windows Paint. These were the days before I discovered PhotoShop or Illustrator.

The anatomy may not be exactly correct as I'd only started palaeontology back then - I didn't do any anatomy for my undergrad...

Anyway, this was also about the time I started to get obsessed with spinosaurs. There was something about the skull morphology that really hooked me into them. In more poetic terms, you could say that I fell in love with the beauty of the slender and curvy silhouette of the snout. This was just purely an obsession of mine with no scientific context whatsoever.

Still, I find it quite intriguing that we find rather derived or highly specialised forms such as spinosaurs but no transitional forms. We don't have good fossils that show the evolution of such unique skull morphology...then again, basal tetanuran fossil record is pretty scrappy anyway - for instance Chilantaisaurus tashuikouensis is a giant theropod from China that is supposedly closely related to spinosaurs or maybe even belong to the Spinosauridae but it is only known from partial hindlimbs and a humerus (and maybe a few bits and bobs - I can't remember off the top of my head). So not much of the skull I'm afraid...

Albertaceratops nesmoi

2007-11-13T23:42:00.000Z

This is my attempt at Albertaceratops nesmoi. This is pretty my first attempt at a ceratopsian as well...

The plate-like epidermal structure on the face is purely speculation on my part.

Albertaceratops is yet another one of those interesting centrosaurine with a blade-like nasal 'horn' or ridge, but with postorbital horns that are very large for a centrosaurine.

If ceratopsians locked their horns in intraspecific combat, then Albertaceratops must have had a fairly similar style of combat with Triceratops and other long-horned chasmosaurines - perhaps???

Ontogeny and taxonomy of pachycephalosaurs

2007-10-26T17:47:00.000+01:00

There were two interesting talks on pachycephalosaurs at the SVP annual meeting in Austin, Texas. I don’t know if they were coincidental but both talks dealt with the possible synonymy of Dracorex, Stygimoloch and Pachycephalosaurus.

The first talk was by John Horner. Horner (2007) used comparative cranial morphology, computer tomography and osteohistology to hypothesize that Dracorex, Stygimoloch and Pachycephalosaurus all represent different stages in an ontogenetic series of a single taxon Pachycephalosaurus.

Aside from having a flat head, Dracorex differs from Stygimoloch and Pachycephalosaurus in having large supratemporal fenestrae. Dracorex also has extensive ornamentation along the squamosals. Stygimoloch has closed off its supratemporal fenestrae and have a well-developed frontoparietal dome incorporating the rostral part of the frontal and postorbital but not the lateral and caudal elements of the skull. Stygimoloch also has extensive cranial ornamentations along the squamosal. Pachycephalosaurus has an extreme doming of the frontoparietal with the incorporation of the prefrontal, squamosal, and postorbital into the dome. The squamosal ornamentations are not extensive as in Dracorex or Stygimoloch. However, all three taxa show very similar or near identical ornamentation patterns on the snout.

Bone histology and CT scans reveal the internal architecture of the domes in these pachycephalosaurs. The bones comprising the dome are highly spongy in both Dracorex and Stygimoloch but are completely solid in Pachycephalosaurus. Horner suggests that the bone was still growing in Dracorex and Stygimoloch while it had already stopped growing completely in Pachycephalosaurus.

Horner’s talk was followed by Robert Sullivan’s. Sullivan (2007) points out that while flat-headedness have been inferred to be the ancestral condition in pachycephalosaurs, small fully domed pachycephalosaurs occur much earlier in the fossil record with the flat-headed morphology occurring more frequently in younger strata. Because of this stratigraphic incongruence, Sullivan proposes the possibility that flat-headed morphology is an early ontogenetic stage that is delayed in the later larger mature individuals. If we are to accept this hypothesis and if doming and closing of the supratemporal fenestrae occurred later in ontogeny, then the taxonomic validity of many of the flat-headed pachycephalosaurs would be in doubt. This is particularly true for Dracorex and Stygimoloch as they are from the same formation as Pachycephalosaurus.

Sullivan also suggested that the squamosal ornamentations may have been rubbed off in the extremely old Pachycephalosaurus.

However, Robert Bakker, who was out in the hall at SVP with cast replicas of the skull or skull elements of Dracorex (whole skull), Stygimoloch (partial skull) and Pachycephalosaurus (can’t remember what parts of the skull he had), argued that there are substantial differences in the three skulls to distinguish them as separate genera. Dracorex in particular apparently has unique and diagnostic features in the snout. Bakker presented an analogy from the modern Serengeti where extremely similar but distinct species of antelope (? …or something) coexist. Good point. I wouldn’t be surprised if there were several species of pachycephalosaur living at the same place considering how relatively abundant pachycephalosaurs are at the Hell Creek Formation.

So who knows. I’ll just wait till these works get peer-reviewed and published before I make my mind up…

References:
Horner, J. 2007. Synonomy consequences of dinosaur cranial ontology. J. Vert. Paleontol. 27: 92A.

Sullivan, R. 2007. Doming, heterochrony, and paedomorphosis in the Pachycephalosauridae (Ornithischia: Dinosauria): taxonomic and phylogenetic implications. J. Vert. Paleontol. 27: 154A.

Deinonychus antirrhopus

2007-10-24T22:25:00.001+01:00

I painted an older sketch of Deinonychus antirrhopus using Photoshop. I must admit, I'm no where near a computer artist but I had quite a bit of fun with Photoshop. I didn't know you can do so much with it...

Anyway, the all-too-famous Deinonychus antirrhopus. One of my favourite dinosaurs thus far. I didn't draw flight feathers on this guy mostly because of the simpler integuments of Sinornithosaurus but its quite obviously outdated now that we know one of its closest relative Velociraptor was found to have quill knobs on its ulna. These are little bumps on the surface of the bone and are typically associated with flight feathers in modern birds.

Wood-eating behaviour in hadrosaurs

2007-10-11T13:43:00.000+01:00

I came across a really interesting article yesterday about some hadrosaur coprolites from the Upper Cretaceous Two Medicine Formation that contained woody materials (Chin 2007). This is direct evidence that at least some hadrosaurs ate wood. Coprolites at this locality regularly contain wood indicating that conifer wood was regularly ingested. Wood contains lignin which cannot be digested by vertebrate herbivores so there is no nutritional value on its own. Thus, in order for any animal to intentionally ingest wood it must have a very good reason of doing so as processing wood is such an effort, both in mechanical digestion (chewing) and chemical digestion. The absence of little twigs from the coprolites pretty much rules out accidental ingestion while foraging leaves.

On the other hand, the author found signs of fungal decomposition in the wood material. So apparently, the hadrosaur was eating fungus-infected, or in other words, rotting wood. Fungus de-lignifies wood and makes cellulose available for other organisms to consume. 'From an energetic standpoint, it is evident that partially degraded wood would provide a nourishing resource augmented by fungal tissues, associated microbial symbionts, and invertebrates. Decaying wood would require less energy to process and could be easily comminuted' (Chin 2007).

Modern megaherbivores consume fugus-decayed wood when high-quality browse is sparse. However, these Two Medicine coprolites were preserved during the rainy season. The author suggests that the high proportion of fungal degraded wood in the hadrosaur diet may have been because of a lack of vast grasslands. Modern large herds are largely supported by the fast regeneration of grass after consumption by a herd of herbivores. In a grass-poor Cretaceous world, large herbivorous dinosaurs obviously had to eat other sources of food, e.g. ferns, angiosperms, conifers AND decaying wood.

Reference:
Chin, K. 2007. The paleobiological implications of herbivorous dinosaur coprolites from the upper cretaceous Two Medicine formation of Montana: Why eat wood? Palaios 22(5):554-566.

Eustreptospondylus oxoniensis

2007-09-23T14:17:00.001+01:00

This is one of my favorite dinosaurs - Eustreptospondylus oxoniensis. It's also perhaps one of the most complete theropod fossils from Britain. Eustreptospondylus is a Middle Jurassic 'megalosaur' from the Oxford Clay of Oxfordshire. Now, I'm not much of a historian so I won't claim to know all the details, but it was known for a long time as 'Streptospondylus' but was subsequently renamed by Walker in 1964 in his paper 'Triassic reptiles from the Elgin area: Ornithosuchus and the origin of carnosaurs'.

Ornithosuchus is nowadays regarded as an archosaur so for some time, I was baffled as to why Walker addressed the question of carnosaur origins by redescribing a Triassic archosaur. However, it appeared I was just being lazy (as usual) as I had not even read the abstract. It is made quite clear that Walker considered Ornithosuchus to be a theropod dinosaur, a primitive carnosaur close to the ancestry of Megalosauridae and Tyrannosauridae. Thus, Walker proposed a modified classification of the Infra-order Carnosauria* within Sub-order Theropoda; comprised of the Superfamily Megalosauroidea and Superfamily Tyrannosauroidea which includes the Families Ornithosuchidae, Spinosauridae, and Tyrannosauridae.

In the process of establishing this classification, Walker naturally compared Ornithosuchus with other supposed 'Triassic carnosaurs' but also with Jurassic and Cretaceous 'carnosaurs'. Thus, much of the British 'carnosaur' materials were re-examined and several new names emerged including Eustreptospondylus oxoniensis, E. divesensis, and Metriacanthosaurus.

*Carnosauria used to include all the large theropods but has diminished substantially in taxonomic range in the last few years - I think it only includes the Allosauroidea and Spinosauroidea if these two form a monophyletic Carnosauria to begin with.

Reference:
Walker, A. D. 1964. Triassic reptiles from the Elgin area: Ornithosuchus and the origin of carnosaurs. Phil. Trans. R. Soc. Lond. 248: 53-134.

Jaw biomechanics of Smilodon fatalis 2

2007-07-25T14:28:00.000+01:00

I attended the 8th International Congress of Vertebrate Morphology (ICVM8) in Paris last week. There were a lot of interesting talks and I personally felt like I had information over-load!

One talk in particular that I found extremely interesting was that by Adam Hartstone-Rose, a PhD student at Duke University, who had painstakingly collected data of the physiological cross-sectional areas (PCSA) of extant felids, something I've always thought was in dire need. I'm particularly interested in this because this allows us to estimate bite forces in felids to a fair amount of accuracy. The most common source for bite force estimates in mammalian carnivores come from dry skulls which have been shown to underestimate (Thomason 1991). Bite forces estimated from calculations based on PCSA on the other hand seem to be in more congruence with actual in vivo bite forces (Thomason 1991). As there are currently no studies except for Binder and van Valkenburgh (2000) on in vivo bite forces in large carnivores, Adam's study on PCSA in large cats will most definitely be a valuable resource for functional morphologists.

Another cool talk was one by Blair van Valkenburg and Graham Slater (delivered by van Valkenburgh) on the cranial morphology of sabre-tooths. Results from a geometric morphometrics analysis was presented on the cranial morphology of extant cats and different sabre-tooths. Interestingly, sabre-toothed felids (macairodonts) are extreme morphotypes of modern cats diverging from extant feline morphology in which the rostrum becomes more upturned. If I remember correctly, similar trends can be seen in sabre-toothed nimravids as well. So this morphological trait of an upturned rostrum is pretty much associated with hypertrophied canines. It does make sense to have a more upturned snout if you've got massive canines.

Van Valkenburgh also briefly mentioned something interesting which made me think a bit. She suggested that perhaps sabre-tooths were extremely fast killers. At the time it didn't make much sense to me as I'd thought that sabre-tooths probably bit off chunks of flesh from the prey and waited for it to die of shock and loss of blood (Akersten 1985). However, I eventually grasped the potential that sabre-tooths may have bit into the throat much like some large cats do today but completely severed the trachea and any large arteries thus killing the prey almost instantaneously. When modern cats go for the throat or muzzle it tends to be a rather lengthy process as the canines sometimes don't even break the skin and they have to wait for the prey to suffocate (if I'm not mistaken - at least that's what it sounded like from the talk).

So the bottom line is: any kind of hunting strategy could have been possible for Smilodon as long as they kept their canines away from forceful contact with bones...

Reference:
Akersten, W. A. 1985. Canine function in Smilodon (Mammalia; Felidae; Machairodontinae). Contributions in Science 356:1-22.

Binder, W. J., and B. Van Valkenburgh. 2000. Development of bite strength and feeding behaviour in juvenile spotted hyenas (Crocuta crocuta). Journal of Zoology 252:273-283.

Thomason, J. J. 1991. Cranial Strength in Relation to Estimated Biting Forces in Some Mammals. Canadian Journal of Zoology-Revue Canadienne De Zoologie 69(9):2326-2333.

Felid skulls

2007-07-11T18:15:00.000+01:00

I've been looking at and taking measurements from felid skulls now for a few weeks. I've been up in Edinburgh at the National Museum of Scotland for three days and I've also been at the osteological collections at the Bristol City Museum and Art Galleries for the last week now. I've covered 30 species of the 41 recognised extant felid species.

The funny thing is that some of the older specimens in the Bristol Museum are either mislabeled or not labeled at all and we sat there for some time comparing specimens trying to ID the damned things. I'm starting to pick up some subtle morphological distinctions but it's all kind of useless unless I can link them to the right species. All I need is a list of diagnostic characters...