Raptor's Nest

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...

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 interpretable R is based on vectors R 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 program...

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...

From Wikimedia Commons (CC BY-SA 3.0) 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 ...

I thought I'd do a fun post for once. And since list based articles are the norm for fun on the internet, I thought I'd do one on dinosaurs, but given that I know most about theropods, I've decided to restrict my list to theropods (...maybe in a future post, I'll do other clades). My ranking is based mostly on scientific importance so it may not reflect awesomeness, and it is obviously subjective as to how I rank importance to science. For instance, interesting discoveries or unique palaeobiology are ranked relatively low compared to wealth of information and data or completely revolutionising our understanding of the evolution of theropods. So here are my top 10 scientifically important theropod dinosaurs of all time (off the top of my head) 10. Megalosaurus Being the first dinosaur to be named, Megalosaurus automatically deserves a spot on this list, but given the fragmentary nature of known fossil specimens, and being mostly useless as a meaningful source ...

It is probably safe to say that to many, the idea that dinosaurs were slowly in decline , or that they weren't 'evolving' as fast as they should have been, is an uncomfortable thought. I thought some context will make this idea easier to appreciate. Palaeontologists are generally happy to say that Velociraptor is a very close relative of birds. It is morphologically very similar to birds, and there is even strong evidence that it possessed secondary feathers on its forearms ( Turner et al., 2007. Science 317 : 1721 ). Velociraptor lived during the Campanian Stage of the Late Cretaceous, 83.6 - 72.1 million years ago (Ma). Velociraptor from Wikimedia Commons On the other hand, the oldest bird known to date, Archaeopteryx , is known from the Tithonian Stage of the Late Jurassic, 152.1 - 147.7 Ma. Archaropteryx as a Blue Jay Archaeopteryx with red plumage So that's on average about 72 million years (Myr) between these two dinosaurs, with a...

There is no dispute that non-avian dinosaurs went extinct at the Cretaceous-Paleogene (K-Pg) boundary, most likely owing to a large asteroid hitting the Earth, but what has been debated for decades is whether dinosaurs were reigning strong up to the end of the Cretaceous, or whether they were already in decline and were on their way out only to be killed off by the asteroid impact 66 million years ago (Ma). That is the question that Mike Benton, Chris Venditti and I hopefully helped resolve with our new paper that came out electronically Monday in PNAS. The paper is pretty straightforward, and we provided lots of details in the supplementary information, so it shouldn't be a difficult read. Please do have a read . Below I provide a brief summary. 1. Previous studies The majority of previous studies dealt with counting the number of dinosaur species in geologically defined time bins (such as geological stages), charting the resulting diversity curve through time, and making ...