Plotting the geological timescale in R

225px-Calycoceras_(Newboldiceras)_asiaticum_JIMBO_spinosum_KOSSMAT_microconchI’ve been figuring out nice ways to use R to plot the entire geological timescale. This being R, there is a package (called “geoscale“) which does this already, but I want one where the age is converted linearly to greyscale, and which can fit entirely onto one page, with the short periods of the Holocene and Pleistocene crammed in somehow. I also want to be able to update it easily when new values are published. Continue reading

A pragmatic redating of our 700 million year ancestry

As part of the second edition of the Ancestor’s Tale, I have been reassessing the dates on the backwards journey from today’s humans to the origin of animals. What is written below is rather technical, and mostly for my own benefit, and also for Richard Dawkins. Nevertheless, perhaps others may be interested in my reasoning, which I hope is seen as a pragmatic assessment of our current beliefs. Continue reading

Founding a new human population

I’m very pleased have another query to answer from a listener to More or Less. And what a great question:

BlofeldI am embarking on a Career as a James Bond baddie, and I want to make sure everything is very carefully planned.  I am under no illusions that Commander Bond will thwart my first efforts to take over the world, however I am keen to become a recurring character, and that’s where you come in.

I intend to escape from Mr Bond at the last minute and I intend to populate an island or other planet, depending on budget.  However I am not clear how many men and how many women I will need to take with me to ensure we do not have issues with inbreeding in the population creating genetic disorders and the like.  How many people do you need to create a new race of people?

Continue reading

Ancestor’s Tale list of concestors, revised


Some surprises in store for Concestor 23

When I helped write the Ancestor’s Tale, one of the big tasks was to make a human-centred tree of life: to list of all the point at which, backwards in time, the human lineage joined with lineages of other extant lifeforms. In February last year I was forwarded an email from someone using these “rendezvous points” as the basis for a song and story for children. She had seen the O’Leary (2013) paper and wondered how much revision was needed to our original list.

For those who wish to skip to the chase, I’ve come up with a new list at the end of this post. Continue reading

Visualizing data on large phylogenies at the pixel-level


A phylogenetically organised display of data for all placental mammal species. Red pixels are those without a picture on EoL.

Modern technology, coupled with molecular taxonomy, means we now have very large evolutionary trees: ones with tens or hundreds of thousands of species. In fact, the Open Tree of Life project aims to create a tree of all living things, which would have millions of species. The obvious question is how to display these enormous amounts of data.

Here’s one possibility I’ve come up with: use a single pixel for each tip of the tree (each species). Then, if we could use the whole of a one megapixel canvas, we could display information about a million or so species. Continue reading

Schrëwdinger and her descendants

Mosaic of placental mammals

670 descendants of Concestor 13, appropriately arranged.

I’ve been meaning to write about this for a good while, ever since the release of a paper which hit the science headlines last year. For the first time to my knowledge, researchers have tried to do professionally what I, together with a graphic illustrator, did in an amateur fashion for The Ancestor’s Tale. I’m talking about attempting to reconstruct what our distant ancestors looked like, an intriguing task that also leads to some striking visual possibilities.

Continue reading

Human impressions of animal sounds

If a friend tries to do an impression of an animal call, how easy is it to work out the animal? Alternatively, how good are different people at making animal noises? If a computer could assess the accuracy of these impressions, it would open up some fun possibilities. Imagine searching a database of animal sounds, or a set of known animals in a nature reserve, simply by doing an appropriate impression. I haven’t been able to find many people researching this topic, but I reckon I’m halfway to solving it. I just need a little extra help with some image analysis. Continue reading

Finding public domain images of lifeforms

A PD bat, from Commons via EoL

I’ve put up a page to help get hold of pretty pictures of living organisms. I often need to do this when giving talks and trying to avoid text-heavy slides. One time I might need a rather general picture, such as a bat to discuss animal sonar. Other times I might need much a more specific image, such as a vampire bat nose (when talking about the nasal heat receptors of bats, and their evolutionary links to spicy heat).

Continue reading

Burn holes using an invisible sunlit rainbow

HoleBurn While messing around with ideas for my talk at the Cheltenham Science Festival, I hit on the idea of combining a piece of acrylic that only passes infrared light, with a cheap Fresnel magnifying lens. Completely by accident, I managed to get the rather pretty effect to the right. You can see that the paper is burning where there is no visible light, in the infrared portion of the spectrum. Even better, it’s quite a cheap effect to achieve.

Continue reading

Spotting maps, part II

Grasses drawing

Gratifyingly, my technique correctly classifies drawings like this as pictures, not maps.

How effectively can a computer distinguish pictures or drawings of organisms from maps of their distribution? Based on my previous thoughts on recognising maps, a simple statistical technique allows a computer to correctly identify 99% of maps from within a training set of 1210 images (including 272 maps). Pleasingly, this classification has only a 0.5% false positive rate.

Pretty good, but in the case of images submitted to the Encyclopaedia of Life, we can do better. If we make a guess as to the original format of the image, and include this into the model, we can correctly separate all 272 maps from the 938 pictures and drawings in my particular dataset. If you want to try it out, the dataset is here, and the R code to perform the classification is near the end of this post.
Continue reading