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Showing posts from 2017

Spinosaurus, the gigantic pangolin of the Cretaceous?

I was made aware of this not long ago - it kind of looks creepy, but it gave me an idea:

Did Spinosaurus walk like a pangolin?

That is, with it's hands low to the ground but not touching the ground - so no knuckle walking - and maintaining balance as a biped...

This pangolin seems to maintain balance on its hind legs even though, on cursory glance, its centre of mass seems too far forward for that.

Spinosaurus is supposed to have had a dense femur, so maybe its centre of gravity was farther back than you'd think from overall proportions. Maybe the sail helped tip the scale back?

...or maybe it was a giant ant-eater? Those giant claws look particularly suited to breaking open termite mounds?

Who knows. This is me being silly, but thought it was hilarious enough to share...

Cope's Rule and rates of body size evolution

The evolution of body size has been the focus of countless studies, not only in palaeontology but also in evolutionary biology using data from extant animals (or neontology as palaeontologists would say). While some colleagues have argued recently that body size is not necessarily a good trait to study, nonetheless, it still stands that body size is an important factor of fundamental biological phenomena, including metabolism, physiology, biomechanics, and ecology. For instance, the largest source of variance in biomechanical performance measures like bite force is body size - a lion's bite force is an order or two higher in magnitude than that of a domestic cat just purely out of simple scaling. Similarly, prey size categories, such as large, medium/mixed and small, are highly affected by predator body size - obviously a tabby cannot kill an ox while a lion or a tiger can. Thus, body size is not only an important biological trait, but necessarily a fundamental physical trait.


How I would have set up Indominus rex in Jurassic World

Palaeontologists have commented a lot on the inaccuracies in Jurassic World, so I'm not gonna repeat that here. What I want to do instead is to provide my ideas on how the concept of Indominus rex could have been better, in my eyes.

I actually don't really like the idea of genetically engineering a hybrid dinosaur - that kind of goes against what made the original Jurassic Park (both novel and film) so "magical" (for want of a better word). As a kid enthusiastic about dinosaurs, the idea of bringing dinosaurs back to life from fossilised DNA was really breathtaking and exciting (yeah, yeah - they weren't real dinosaurs because their genome were augmented with amphibian DNA, blah, blah), but the core concept was that resurrecting past life may have unpredictable and undesirable consequences - like JP staff not being able to control their dinosaur population despite their genetic engineering - "life finds a way".

So in that vein, I would have made I. rex

R for beginners and intermediate users 4: object oriented programming

The topic of this post was mentioned in a tangential rant featured in my previous post, and I thought I might as well expand on this a bit. I'm not going to talk about programming language model or anything like that since I'm not a programmer - rather, I will treat this more like a tutorial or a "Pro-tip" kind of post.
I will be focusing on an aspect of R that is often taken for granted and maybe not well known by entry-level users. That is, R is an object-oriented programming language. If you already know this, then this blog post is not for you.
First, I'll list out a few interesting/useful features of R: R is interpretableR is based on vectorsR can utilise functions (e.g. functional programming)R utilises objects (object-oriented programming) Like I've already mentioned, this post will focus on point 4, that R is an object-oriented programming language (or simply that R can be object-oriented if you don't want to call R a programming language...).
We can s…

Reproducibility of science and open source

I'm all for open access.
I'm all for open source.
I'm all for reproducible science.
I'm all for replicable studies.

So I like that data are shared.
I like that protocols are shared.
I also really appreciate it when code is shared - but only when it is appropriate.

Times that I think are appropriate to share code are, for instance, when there's an entirely new method introduced - then I think it is important to release the code/script as source code, package, program etc so that it enables other scientists to reproduce your work or use it in their own analyses.

However, I've noticed that, often times, shared code/script are nothing more than just the authors' workflows - in which case I don't want to see it. Everyone has a different workflow and I don't want to have to get into the heads of other people to figure out exactly what I'm looking at and what the code is doing - because commonly associated with shared workflow are uncommented code. Thi…

‘Residual diversity estimates’ do not correct for sampling bias in palaeodiversity data

This blog post is way overdue, being mostly written months ago in late Oct. Anyway, it's a bit technical - but it relates to how palaeontologists quantify biodiversity through time (like the famous Sepkoski curve shown above).

I have a newish paper (‘Residual diversity estimates’ do not correct for sampling bias in palaeodiversity data) in Methods in Ecology and Evolution, with Chris Venditti and Mike Benton, that became available in Early View version in Oct last year (24 Oct 2016). The paper is very simple and straightforward. In it we assess a popular method that has been used numerous times to 'correct' for sampling bias in palaeobiodiversity data.

It is safe to say that most palaeontologists would agree that the fossil record is far from complete and that any kind of tallying of the numbers of species that were present in any given time period would suffer from this incompleteness - biodiversity curves (such as the famous Sepkoski curve, a variant of which shown abov…