Friday, 5 September 2014

Dissection of the hindlimb of monitor lizards: V. varius and V. komodoensis, Part 1 of 4, Superficial Dorsal aspect.


One of the major questions I am trying to determine in my research is how muscle and bone strains change with body size and habitat among Australia’s giant lizards the Varanids (aka monitor lizards aka goannas aka large uncooperative lizards).

When I first attempted to dissect the hindlimb muscle of monitor lizards I was amazed about how little information there was on the topic. In the end the two most helpful bits of literature was the Snyder paper from 1954, and the book chapter, The Appendicular locomotor apparatus of Lepidosaurs, by Russell and Bauer, (2008), in Biology of the Reptilia, Vol 21. 
Luckily I had a visit from muscle expert Taylor Dick, from Simon Fraser University Canada, and we were able to dissect some big lizards. 
As a guide to help anyone else who might also be silly enough to want to follow along this line of inquiry we have made a guide below to help you identify some of the major muscles in the lizard hindlimb. 

There will be 4 posts in total, this post will focus on the dorsal superficial aspect of the upper and lower hindlimb. 


Varanus varius: This specimen was freshly sacrificed, and the muscles are very clear and easily defined. Click on the video below for a walk through.  


                      







Varanus komodoensis:  Dissection of the Komodo dragon. This specimen had been frozen for 7 years, so the separation of the muscles is a little bit more difficult. Click on the video below for a walk through.







Monday, 4 August 2014

Evolution of bipedal running



Awesome lizard shot by
Simon Pynt which
sadly the journal did not
want on its cover 
This week my paper on the evolution of bipedalism came out in the journal Evolution. This work is part of a long ongoing project understanding why these lizards sometimes run on two legs and sometimes run on four, and why Australian agamid lizards in particular seem to be so very good at the former. But to understand this we need a little bit of background into Bipedalism and why lizards are so weird.
Awesome picture of a dinosaur
I stole from the web. To make this blog
post look cooler.  

 Bipedalism (running on two legs) evolved independently many times, for example in hopping marsupials (like kangaroos), hopping placentals (like kangaroo rats), primates (like us), birds, dinosaurs, lizards, insects, and this awesome octopus! In birds, primates and dinosaurs the forelimbs appear to be used for something else so bipedalism makes sense, and hopping on two legs can save energy, but neither of these reasons seem to apply to lizards. Further I showed in an earlier paper that bipedal lizards are not faster, nor can they run for longer. So why are they doing it?

Well a dutch researcher called Peter Aerts actually suggested a different reason. Perhaps, he suggested, lizards were not trying to run bipedally on purpose, but rather they were trying to do something else, maybe they were trying to become more manoeuvrable. One way to become more manoeuvrable, is to shift all your mass backwards (which makes it easier to turn corners), and then accelerate quickly. Unfortunately for the lizards these things have a side effect, just like when a motorcycle accelerates too quickly, when a lizard shifts its mass backwards and accelerates too quickly, it can cause the front of the body to pop up, like its popping a wheelie. Seen in this light, bipedalism in some lizards might have been an accident, just a consequence of accelerating too hard, and this seems to match some of the data I have collected before on lizards. There is certainly an acceleration threshold where a lizard will pop on its two back legs, and a model produced by Peter Aerts even predicts when this should happen. And this model matches the data, for most lizards.

Another awesome dinosaur photo i stole from the web. Geez
these dinosaurs would have been so bad ass! 
The trouble is that some lizards seem to beat the model. Some lizards seem to be able to run for much longer and at lower accelerations than is predicted from this accidental model. Are these lizards exploiting bipedalism? taking advantage of the accident? This is actually not so unheard of in nature, infact it’s common enough that scientists gave it a name, they called it an Exaptation (to differentiate it from the perhaps more familiar adaptation). Exaptations are exciting since they show us another way traits can evolve. Infact one of the most common examples of exaptation is the evolution of feathers in birds. Feathers, which we now commonly associate with flight in birds, did not originally evolve for this purpose. Lots of recent reports have shown us that the origin of feathers predates that of birds and are present in dinosaurs, meaning feathers probably evolved for another reason, like keeping dinosaurs warm. It was only later that birds exploited these feathers to make their remarkable flying wings. So could bipedalism, like the feathers of birds, be an exaptation? This is what I set out to find.
Figure showing the evolution of the mass distribution
among lizards. Red means a backwards shift, blue forwards.
The bipedal lizards are marked with a red box.  

First I had to know, do lizards (and their ancestors) which run bipedally have their body mass pushed backwards, perhaps to try and become more manoeuvrable? I looked at this across 124 species of lizards, basically any lizard I could get my hands on from the Queensland museum, with the help of my student at the time Nicolas Wu, and I found yes indeed, the lineages leading to bipedalism had shifted their body centre of mass backwards.

Next I tested the model, I calculated (based on Aerts’ model) when lizards should go bipedal, and then ran these lizards a bunch of times to calculate the exact acceleration where they switched from four legs to two legs. As predicted some lizards matched the model quite well, but others were able to beat it, running bipedally sooner than expected.


This is one of the rare videos i got of a lizard transitioning from 4 legs to 2! 

Finally we looked at where these differences are greatest in the family tree of Australian agamids. We found the ones that matched the model best occurred very early on in the evolutionary tree, but as the tree branched out the differences became greater. New species were beating the model more and more. All this adds up to one thing, an exaptation. Bipedalism first appeared on the scene a long time ago, and those that ran bipedally did so only by accident. But at some point some lizards started exploiting this, running bipedally further and more often than expected, taking advantage of the consequence. This is exciting since not only are we seeing an exaptation happen, but it means that running on two lizards actually conveys an advantage to these lizards. Just what this advantage is thought, I have no idea…yet. 

Tuesday, 10 June 2014

Notes on running large lizards over forceplates

Taylor Dick, SFU (probably didn't expect
to be holding a lizard that big anytime
 during her stay).
Anyone who has had the misfortune of stumbling upon this blog, and particularly those who have suffered through many of its posts might have noticed that one of the main themes is determining how muscle and bone strains change with body size and habitat among Australia’s giant lizards the Varanids (aka monitor lizards aka goannas aka large uncooperative lizards). Recently I had convinced Muscle expert Taylor Dick from SFU to come to Australia to study these questions with the eventual goal of building a musculoskeletal model of these lizards in the open-source biomechanics software OpenSim. She had already endured one trip out to the Australian desert in order to catch these beasts, but more was yet to come.
 
Example output of the force plate
from a dragon lizard, A. gilberti
Force plate design, shown here without
a plate on the top. Photo probably taken
during one of its many repair attempts
The second part of this project was to simultaneously measure forces and kinematics of these lizards which would act as valuable input parameter for this model. To do this I had constructed a 15 meter long racetrack at the university, along with a custom made force plate which would be buried in the ground, for the lizards to run over. I will add more details on the forceplate later, but basically it consists of 4 octagon rings arranged at each corner of a metal plate. Each is capable of measuring forces in two directions vertical and horizontal, and by positioning octagons in adjacent corners at 90 deg angles to one another I was capable of measuring fore-aft, lateral and vertical forces. An added bonus of having 4 vertical force sensors in each corner is that I could accurately estimate the centre of pressure of the foot during the stride.
Taylor with probably not enough laptops

One of our uncooperative
subjects
My thoughts were that building the force plate would be the most difficult part of this project, and having already done so, I was under the ill-begotten conclusion that the hardest part was over. But yet, as always I had forgotten the type of lizards I was dealing with, and the kind of misfortune which befalls a scientist. We lost several days battling noisy electrical systems in the animal yards, and were forced to take several trips to and from the lab to repair the force plate which I had so loving crafted for lab work, but for which the real world with its various sharp protruding objects, it was no match. When we finally had a working system, two high speed cameras on a custom built scaffold, combined with the force plate, it seemed again the worst was over. 

trying to lead via example. 
We began running the lizards – and it was time for the lizards to shine. Yet by the end of several hours of work we had only a handful of useful trial. It seems the lizards, for reasons I can only assume are nefariously motivated, refused to step wholly on the platform. Instead preferring the mind-blowingly frustrating alternative of stepping neatly to one side of the force plate, or on the edge of the platform, such that while data temptingly appeared upon the screen it was utterly useless, since the proportion of the force directed onto the force plate could not be known.  

We attempted everything under the sun to encourage lizards stepping onto the forceplate, including doubling the size of the plate, halving the width of the racetrack, and painting it wholly black, such that it matched the surrounding carpet, and could not be mistaken for the presumably treacherous hazard it appeared, to be avoided at all costs. Yet none of these appeared to increase our success rate, which was as low as 1 in 30 runs. As can be seen in the video below



However, perseverance paid off, and by the end of the week we had collected over 60 successful trials, from these giant, largely uncooperative beasts. Below is a video of the rare and elusive, "successful trial"     




Sunday, 11 May 2014

How to catch a giant varanid lizard


Recently at the SEB conference in Spain I convinced a muscle expert, Taylor Dick from Simon Fraser University in Canada, to come out to Australia to study muscle variation in Australian varanids. The purpose of this study was based upon a previous paper I had written “Lizard Tricks” of which I wrote a blog about here. But incase you missed it, basically I had found that differences in the Kinematics of the lizards hindlimb were not based upon changes in lizard size (as I had expected) but rather were related to changes in the lizards habitat. The Arboreal lizards (both big and small) had a crouched, sprawling posture, as if they were in a perpetual pushup, the terrestrial lizards (again both big and small) had a more upright posture. The reason for this difference was probably since arboreal lizards wanted to be close to the surface they were climbing on to avoid toppling over (and so had the crouched posture), while the terrestrial lizards wanted to improve stride length, and so had longer more upright limbs.

But the problem with this is that these changes in posture are going to cause big changes in limb bone and muscle stresses, especially in the bigger guys. And so that’s where Taylor came in. She was to come over and study the differences in the forces produced while running and look for any differences in muscle architecture between climbing and terrestrial lizards, and in doing so hopefully solve the problems I had created.

But I wasn’t going to make it easy for her. No sooner had she got off her Trans Canadian flight (or whatever passes for airlines in Canada) than we were off to the bush to catch some giant varanids. And so the rest of this blog serves as a first persons perspective to the type of skills required to catch these big lizards. The first day turned out rainy and miserable, and the only reptiles we ended up seeing were a couple of turtles which were trying to cross the road. And soon Taylor learnt a valuable lesson in using the dunny block in the outback when she ran out of the toilet screaming cause a (in my opinion) particularly friendly looking green tree frog happened to be occupying the toilet seat she was hoping to utilise.

But soon the sun did eventually shine, and by the third day we spotted our first lizard. It was a medium sized Varanus varius. Being members of the most uncooperative group of reptiles typically they will choose the tallest and most unclimbable (well for humans) tree as an avenue of escape, but this lizard made the poor decision of escaping up a perfectly good climbing pine tree. The secret to catching a lizard up a tree is that it is generally better to be stupider than the lizard. And so I found myself most of the way up a tiny swaying pine tree chasing a lizard which, unsurprisingly had climbed to the very meagrely supported top. However I was successful in getting the noose over its head and coercing it back down. We had caught our first lizard.

The second lizard proved to be smarter than the first. It chose a very thin, but extremely tall gum tree as its method of escape. My first attempt to get it down involved taping three lengths of beach fishing rods, with a long noose, together. I had tried this technique before, and previously it had failed spectacularly, but I was sure the theory was sound. Sometime later I had added another failed attempt to my list, yet I still feel deep inside, one day, my patented super long lizard noose technique might just work. In the end, it was the less eloquent but ultimately more successful technique of shaking the bejesus out of the tree enticed the lizard down to a lower and more manageable height in the tree.


The next two lizards we caught were two very large Varius which were in comparison much easier to catch. We found them wondering around the local garbage tip, which might explain their smell, and their indifference to my presence. They barely climbed to head height up the nearest tree and thus were relatively easier to coerce down. And so we returned to Brisbane, maybe not somewhat wiser but certainly four big lizards the richer. The next part of our plan was to run them over the force platform.      

Tuesday, 18 February 2014

Making nice figures

Figures are Important
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12871.html
Everyone seems to know that figures are the most important part of the paper, so why not do a little research into not only what makes a great figure, but also what makes a unique memorable figure. 

Before you write a paper, or even start a project, its a good idea to know what figures you want to make. There are many different ways to display data, so have a look through them and decide which ones might be suitable for you. 

These are some websites I like to take inspiration from 

https://github.com/mbostock/d3/wiki/Gallery

http://nicefigure.tumblr.com/


http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007783
One important part of making figures is the use of color. Most journals will let you publish online color figures, but these must also be view-able in black and white (greyscale) format. It is therefore important to vary shading in your figure between subjects or variables. I found the following websites very helpful in choosing colors regimes for figures.   

http://colorbrewer2.org/

Change the number of classes you need for you data, then use the 'eyedropper' tool from your graphics program. 



Also here is a paper from nature methods, showing the best color and shading techniques for figures. 

http://www.nature.com/nmeth/journal/v7/n8/full/nmeth0810-573.html

Finally, most people know this, but for most figures (that aren't photos) you will need to build your figure in a program which can produce a scalable vector graphic. 

Corel and Adobe illustrator are the most popular but also cost money

Inkscape is a good free alternative. 

Learn how to use one program well, its worth the time. 

Let me know if you have any other helpful suggestions i can add.