London water authority Thames Water has discovered what it calls the UK’s largest “fatberg;” a mushy deposit of congealed fat and sanitary wipes. Found in a sewer in Kingston, South West London, the fatberg was roughly the size of a bus, and weighed 15 tons.
Tom Phillips - A Humument (1966-73)
“In 1966 Phillips set himself a task: to find a second-hand book for threepence and alter every page by painting, collage and cut-up techniques to create an entirely new version. He found his threepenny novel in a junkshop on Peckham Rye, South London. This was an 1892 Victorian obscurity titled A Human Document by W.H Mallock and he titled his altered book A Humument.
The first version of all 367 treated pages was published in 1973 since when there have been four revised editions. A Humument is now one of the best known and loved of all 20th Century artist’s books and is regarded as a seminal classic of postmodern art.”
A slightly better stacked bar?
OTU tables contain a lot of data, but they’re also sparse - mostly zeroes. Sample numbers are going up and up and displaying the data is more of a challenge. In an exchange on twitter with Nick Loman and Rachel Poretsky a little while ago, we bitched about stacked bar plots. Here is my attempt on how to improve on one in R using the ggplot package and starting with a standard OTU table from QIIME. It’s an iterated stacked bar plot - so you’ve deconstructed your stacked bar (like a posh cheesecake) and each OTU now has the same base-line.
For me, I think it’s easier to spot differences in particular OTUs across the whole sample set. I quite like it for longitudinal data too and I add a white geom_vline between samples from each individual to delineate.
The code is a real bodge, I’m no coder, please suggest improvements on both that and the plot itself - we can definitely do better! Thanks to Saffron for her help resolving some stickier bits.
Starting off in QIIME you will have a .biom format OTU table, Mothur also supports this format. I haven’t come across an R package that can use .biom yet though (I’m sure there will be be one - perhaps via picante?), so we have to convert it back to a more straight-forward table. I use QIIME for this, making sure I keep the taxa string (why you would ever want to lose this when you’ve spent time making sure you get it in the first place, I’ve no idea).
convert_biom.py -i otu_table.biom -o otu_table.txt -b --header_key taxonomy --output_metadata_id "ConsensusLineage"
That’s it for QIIME, now we switch to R, which is much more flexible and makes nicer pics.
The taxonomy string handling needs improvement, as does the for loop and that awful bit where the data is read out to a text file then read back in again, but hey! It’s a start.
If anyone has another method for displaying this kind of data that’s better or different, please let me know!
Dark and Wobbly
An adaptation of Nigella’s Gin and Tonic jellies (delicious though they are), here we have the…
Dark and Wobbly!!!
We halved the recipe, it makes 6 jellies if you use these cheap individual moulds (100 ml each) available from just about anywhere. I’ve also upped the gelatine concentration slightly, with Nigella’s concentration it was all a bit slumpy when we turned them out and I wanted pert ones.
150 ml water (from the tap - could use sparkling for extra fizz)
150 g caster sugar (I want to try something dark like muscovado too)
Zest and juice of 1 lime (actually, a bit more juice is better)
200 ml ginger beer (we use Fever Tree as it’s tasty and has a kick)
125 ml dark rum (we used Captain Morgan’s spiced, rather than dark)
7 gelatine leaves if you’re leaving it a container (shot glass or something) I reckon 9 leaves for unmoulding and keeping shape (platinum grade - mmmm, hoooves).
We’ve got electronic scales and it saves time on measuring and washing up if you weigh the liquids. 1 ml = 1 g. Also it’s more accurate as kitchen measuring jugs are incapable of doing 125 ml. Com plettley uncappabal.
1. Put the water and sugar into a saucepan, stir, boil for 5 mins, then take off the heat
2. Zest the lime and add the zest to the hot sugar syrup to steep for 15 mins.
3. Pour the ginger beer, rum and lime juice into a measuring jug, strain the sugar syrup through a sieve to remove the lime zest and add it to the jug as well. At this stage you’re aiming to have about 300 ml in total volume. If it’s really under, add more ginger beer and lime juice to make it up. Careful adding more alcohol as you will start to affect whether the gelatine sets.
4. Soak the gelatine leaves for about 5 mins in tap water to soften. In a saucepan (I just give the sugar one a quick rinse) bring about 50 ml of water (2-3 tablespoons) to the boil, it’s just a puddle in the bottom so will boil quickly.
5. Squeeze your gelatine leaves out a bit and add them to the boiling water, off the heat. Whisk them quickly into the water and they should dissolve away completely.
6. Stir this liquid gelatine thoroughly into your tasty Dark and Stormy mix and pour into the moulds. Bung in the fridge to set.
The gelatine will set in a few hours, but will harden further over time, so make 1-2 days in advance if you want to turn them out of the moulds. The jelly also retains some fizz, but this lessens over time and by day 3 is a bit flat, I reckon the night before is fine.
We were introduced to the Dark and Stormy by Tim Scott, @picklepeppers and @mikeyj (us!) tweaked the G&T recipe and @ojatkinson came up with the name.