The Pulfrich Effect is an optical phenomenon where objects (or images) moving in a single plane can appear to be in 3D when the light reaching one eye is dimmed, e.g. with a filter. It also has a curious history – Carl Pulfrich (biography – pdf), who discovered the phenomenon, was blind in one eye and never observed it for himself, but nonetheless made many contributions to stereoscopy (the study of 3D vision) in both theory and the construction of apparatus.
Unlike other forms of stereoscopy, this only works with moving objects or animations; it does not work with still images! But what’s really cool is that you don’t need any special equipment to view it, beyond a piece of darkened glass or plastic to act as a filter. Videos exhibiting the Pulfrich effect can be viewed on a normal monitor or TV screen.
In my day job I work with metagenomes from animals and protists that have bacterial symbionts, and I’ve blogged here before about why visualizations are so useful to metagenomics (mostly to flog my own R package). However most existing tools, including my own, require that you install additional software and all the libraries that come with them, and also be familiar with the command line. That’s pretty standard these days for anyone who wants to do serious work with such data, but it can be a big hurdle for teaching. Time in the classroom is limited, and ideally we want to spend more time teaching biology than debugging package installation in R.
Recently stumbled across a 2013 paper from Ryan and Irene Newton describing a tool, called PhyBin, for binning phylogenetic trees, i.e. clustering them by similarity into groups (“bins”). They use the Robinson Foulds metric to represent the distance between trees.
The reason for doing this is to look at the phylogenies of individual gene ortholog clusters in a set of genomes, to find those genes that have a phylogeny different from the others. This might be useful e.g. to detect genes that have undergone horizontal gene transfer. The example they used for their paper was the insect symbiont Wolbachia.
It seems like a nice way to screen a set of genomes for genes that might be interesting. I had wanted to try to do something like this, but with a concordance-factor approach instead. Some other thoughts:
- Each gene is represented by one tree – uncertainty is not taken into account, unlike with concordance factors, as implemented in BUCKy for example
- If there are horizontally-transferred genes, they would probably have patchy distribution and not be in every species. But such genes that are present in only some genomes would be pre-excluded from the analysis, also in concordance analysis. In PhyBin paper the authors mention the case of Wolbachia prophage which has precisely this limitation.
- Collapsing short branches is a good idea
We are often interested in ratios between two quantities. As an example, let’s use data from a study on the sugar content of soft drinks, where the the sugar content declared on the drink label was compared to the actual sugar content measured in the laboratory (Ventura et al. 2010, Obesity – pdf). The paper includes a nice table summarizing their measurements, which I have adapted to produce the plots shown here.
How can we present this data to get the most insight? In my opinion, presenting such data as ratios can obscure useful information; showing scatterplots of the two quantites can make it easier to spot patterns.
What I want for next Christmas is an obsolete Illumina machine: this blog from a Swarthmore professor documents how he is tearing down a used Illumina GAIIx sequencer to scavenge the parts to build an automated fluorescence microscope on the cheap. Human ingenuity (and the perfectly good things that people throw away) will never fail to amaze me….
Browsing the web for more fun cartography stuff, I found this remarkable website on map projections by a programmer called Carlos Furuti, who has been maintaining it as a hobby since the 1990s (!). He wrote his own software for drawing maps, which can do super-cool things including generate polyhedral projections which can be printed out and folded into pseudoglobes. He was kind enough to reply to my fan mail and told me that my lantern globes are actually an instance of polyconic projections (also described on his site). There’s even tips on how to do the cutting and pasting. This takes things to a whole new level….
Stereoscopy (3D vision) is fun, and maps are also fun. Therefore, stereoscopy + maps = even more awesome!
Remember Magic Eye 3D? As a kid I didn’t “get it” for a very long time, and it was frustrating to look at those crazy dots without seeing anything. But the moment your eyes click into the right place is immensely satisfying. Magic Eye is an example of autostereograms. The Wikipedia page gives a very detailed and understandable explanation of how they work and how to make them, so I won’t go over that here.
Briefly, when you view the rows of repeated images cross-eyed or wall-eyed, you are overlapping the adjacent images. The difference in the repeat period between rows gives the effect of depth. What if the adjacent images themselves were also stereoscopic? Then you would see an array of 3D images popping in and out! A 3D effect on top of a 3D effect. And what’s more – with globes. Continue reading