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Monthly Archives: December 2008

Every year at UCL, the graduate school holds the Research Images as Art competition. I’m happy to announce that, out of about 250 entries, my mosaic of Charles Darwin was runner-up in this year’s competition!

My image is based on a photograph of Charles Darwin by Julia Margaret. I’ve turned it into a 1.2 gigapixel mosaic using images of protein structures from the Protein Data Bank (PDB), generated from X-ray crystallography and nuclear magnetic resonance data. The mosaic is composed of image tiles from a pool of about 19000 non-identical PDB structures and so represents the current content of the entire PDB. To produce the image I used a mosaic generator called Metapixel.

At the moment I’m struggling to embed the flash applet into (free) WordPress, so to explore the image using the flash applet click here. If you zoom in using the flash controls (the triangular slider works best), you should be able to make out one or two crystal structures. If you can’t view the flash applet, you can see the various levels of zoom here.

charles darwin pdb mosaic

As Darwin’s 200th birthday is rapidly approaching, I’ve had some very enthusiastic feedback from my department who are keen to display a large print of this image in the entrance hall as part of a celebratory Darwin exhibit.  This is pretty exciting for me – I just hope they can afford to do it justice and print it at a scale where you can make the proteins out. At 300DPI you could print it at 9×11 feet though I dread to think how much that would cost. For more large scale science images you may want to check out some of Ben Fry’s projects. His image of chromosome 13 is very big.

My other entry in the competition is an image of a potassium channel. Due to the use of detergents in protein crystallography, transmembrane proteins are rarely visualised in their natural state – embedded in a lipid bilayer. However, computational approaches now allow us to predict the position of such proteins within the membrane and reconstruct the ensemble. This image shows a bacterial inward rectifying potassium channel [pdb code 1p7b] embedded in the inner membrane, with potassium ions flowing through it into the cell. It was generated using Pymol, taking about 4 hours to render due to the huge number of atoms that make up the membrane. The potassium ions were added afterwards using Gimp.

potassium channel 1p7b

Unfortunately I didn’t win anything for this one, which actually took a lot longer to produce than the Darwin one. However, I’ve got some ideas to expand it into a more panoramic view of the plasma membrane, with a large number of membrane proteins embedded inside it. Roll on the 2009 competition..

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On sunday I went to see the BBC Wildlife Photographer of the Year exhibition at the Natural History Museum. It’s an exhibition I’ve been to for about the last four years and really showcases the best in wildlife photography. I’m particularly keen on underwater photography and again the standard here was exceptional. One of my favourite shots was a black and white image of a whale shark by Fergus Kennedy entitled ‘Little big mouth’. This is the real reason I bought my fisheye lens – to take pictures of huge critters like this. Now I’ve just got to start saving for a trip to Djibouti. Oh and a housing for my D90..

The museum is particularly famous for its dinosaur skeletons and ornate architecture, both exemplified by the large Diplodocus cast which dominates the vaulted central hall. I stopped to take a quick planet or two before diving in to the gift shop, which has always been my favourite part of visiting museums! The toys in there are pretty high tech these days – the remote control tarantulas and humming birds looked like great fun. They still do those little bugs on a ribbon with googly eyes too.

nhm planet

Speaking of bones, a quick get-well-soon to Alexandra (below, next to the diplodocus) who today had to undergo the surgeon’s knife in order to get her snowboarding career back on track. Go easy on the Oramorph…

nhm planet aleo