Pebble

My Pebble arrived! It may be a one of the smartest watches around, but it is also shiny and curvaceous. Explore the curves and reflections in my macro photos in this flickr set....

 Software used:
ImageJ: Photograph animation
UFRaw: Raw extraction

Cilia

Each term I make a research comic for the Oxford University Biochemical Society magazine called Phenotype. This term's topic; cilia! These organelles can be found on a huge number of eukaryotic cells, ranging from nearly every cell in your body, to free living single cell microorganisms and protozoan parasites. The most famous function of cilia is swimming or moving a cell's surroundings, like the sperm flagellum (flagellum and cilium are different names for the same structure) or the cells in your lungs which help keep them clear of mucous.

Cilia are famous for their movement, but cilia are one of our the most multifunctional cell structures and have extremely important sensory and development functions. Can you guess which four if the five classic senses (touch, taste, smell, hearing, sight) need flagella to work?

This term's research comic feature in OUBS Phenotype is all about the diverse functions of cilia/flagella. Check out the comic here, or download the whole issue for free here.

Software used:
Autodesk Sketchbook Pro: Drawing the cells.
Inkscape: Page layout.

Cloud memory

We all know the feeling; you know you know the answer to something but you can't quite bring it to mind... But you remember exactly how to find it online! It's a well known problem that Google is messing with our heads, and its about time we had a name for this new kind of memory. How about:

cloud memory

"I know this great bike shop, but I can't remember what its called! I need to check my cloud memory"

"It's totally in my cloud memory, can I borrow your phone to find it?"

"Exams are so pointless these days, who needs to learn facts when we have such good cloud memory?"

Thanks to Sam Dean for the idea, and you read it here first!

Shooting Jupiter's Moons

It was a nice clear night, so I cracked the camera out to see how clear a picture I could get of the moon.

 Not bad, considering my 5 year old camera really isn't a telescope!

It really wasn't much of a challenge, though in some ways you wouldn't expect it to be. The moon is quite close to Earth in the grand scheme of things; 'only' 249,986 miles on this particular night. It is also normally the biggest and brightest object in the night sky, running at about magnitude -10 on that night.

So I set myself a more difficult challenge... How about aiming for a picture of some moons around a different planet? Jupiter is the obvious choice because it has four huge moons (the Galilean moons Ganymede, Callisto, Io and Europa) and sits relatively close to the sun. Jupiter is also nice and bright and easy to spot in the night sky, although is still about 200 times fainter than our moon.

The problem with taking a picture of Jupiter's moons lies in their sheer distance from Earth. Jupiter was 531,833,620 miles (over half a billion miles) from Earth on that night. This causes two problems: Firstly because the moons are over 2000 times further away from Earth than our moon they appear much much smaller in the sky. Secondly Jupiter's moons are also about 5 times further from the sun than ours, which means they are illuminated much more weakly by the sun than our moon... Together this means that Jupiters moons appear about 2-5 million times fainter than our moon in the night sky. A proper challenge!

So what kind of picture can you get of Jupiter and its moons? It took some tweaking to get a good picture (I had to capture 20 images, align them and average them together to remove the background noise) but here it is:

Huh, that looks plausible... A big blob (Jupiter) and four smaller blobs (its moons?). It was easy to check where Jupiter's moons are expected to be:

The positions of the Galilean moons: 16/04/2013 20:58

A perfect match! Even down to the brightnesses of individual moons with Ganymede appearing brightest and Callisto faintest. This really is quite incredible; with a standard, modern, off-the-shelf camera and lens you can get a clear picture of the Galilean moons. In comparison in 1610, when Galileo discovered these moons, he was at the cutting edge of optical technology. 403 years for technology to go from a cutting edge revolutionary idea, to a cheap consumer commodity.

At the moment astronomers are just about able to image some planets around other stars. Now imagine in 403 years time, the year 2416; will people be able to buy some consumer camera, pop out into the garden one evening and take a picture of planets around another star?

Software used:
ImageJ: Image processing
Stellarium: Simulated images

The geeky details:
Canon EOS 450D
Sigma 18-200mm f/3.5-6.3 DC OS HSM
The lens was used at 200mm, maximum aperture (f/6.3), with focus set manually to infinity. 20 images of Jupiter were captured at ISO 800 with a 2.5 exposure time. Short exposures and high ISO have to be used because through a telephoto lens the stars drift rapidly through Earth's rotation. The moons were visible in the raw images, but to get a clear and less noisy image they had to be aligned and averaged in ImageJ.

This one goes out to the immunologists...

If you are totally confused start reading here, and here. Oh, and it's not called a FACS plot by the way.
Search engine optimisation: CD25 FOXP3 CD4 Tcell T cell T rex Tyrannosaurus

Valentine's Day Electron Microscopy

Electron microscopes are pretty impressive machines. By firing electrons at a sample they can generate images thousands, or even millions, times sharper than you can make with light. With the right sample you can spot individual protein molecules in a cell, and even individual atoms within a molecule. When using these microscopes to look at the structures within biological samples like cells there are two big problems though:

1. Proteins, sugars, fats, DNA, water, plastic, etc. all block electrons by about the same amount. 
2. Electrons can only travel very short distances through materials.

These two issues make looking at a cell tricky: firstly the cell is too thick for most electrons to travel through it. You can up the power of the electron beam, but then you just vaporise the cell. To solve this the cell has to be sliced up into very thin layers called 'sections'. The next problem is therefore how to slice up a cell, which is basically a bag of proteins dissolved in water. The answer is to replace the water with plastic, making a solidified version of the cell which can be sliced up into thin sections. Finally, to actually tell the difference between protein, fat and DNA in the sample, you need to stain them to make them stand out from the plastic in the background. This is done by using heavy metals, like osmium and lead. The huge positively charged nuclei in these atoms scatter electrons away from the the detector; this makes regions where heavy metals have bound to proteins, fats, etc. look darker.

A block of plasticated cells stained with heavy metals (the black bit) in an epoxy resin plastic (the amber bit) in a metal holder (the silver bit).

So how thin does one of these sections need to be? In short, very. Even travelling through air an electron may only go a couple of centimetres before an atom captures it or deflects it from its path. In a solid material like plastic the distance is far shorter, about 1 million times shorter, with electrons travelling less than 1 millionth of a metre before being scattered or captured. The sections a sample is currently in into must be very thin, about one ten millionth of a metre (100 nanometres) is common.

Cutting a sample into slices one ten millionth of a metre thick is a challenge. It is like cutting a human hair into 1000 slices, each section is about 2000 times thinner than normal office paper. A lab machine called an ultramicrotome is designed to do this, and can cut slices as thin as 30nm. This is a tiny distance, about the width of 15 DNA double helices. The next problem is; how do you know you have cut a slice of the correct thickness? The sections are far too thin to be able to pick them up and measure them by any normal method. Luckily a physical phenomenon called thin film interference gives an easy way to do this.

When light hits a thin film, like a thin layer of oil in water or a soap bubble, some light bounces off the front of the film and some off the back. If the film is a similar thickness to the wavelength of light (around 500 nm) then interference between the two paths the light takes will occur. The interference can be constructive (boosting the light intensity) or destructive (reducing the light intensity). Because different colours of light have different wavelengths, different colours will experience constructive or destructive interference, for example if blue and green wavelengths destructively interfere, but red does not, then only red light will be reflected. The film will look red, even if the material it is made of is totally transparent.

Thin film interference in a soap bubble. CC-BY-SA by link.

Sections of cells embedded in plastic for electron microscopy act just like an oil or soap film, and have distinctive colours based on their thickness. We use these colours to check that the sections we have cut are the correct thickness, without having to directly measure them. It really is very quick and easy!

Lots of electron microscopy sections of different thickness. From bottom to top: 30nm (grey), 50nm (white), 70nm (white), 100nm (gold), 150nm (purple), 200nm (blue), 250nm (yellow), 300nm (pink/red), 400nm (green), 500nm (purple).

So what does this have to do with Valentine's day?

As far as I can work out the sectioning process you use for electron microscopy is a great way to make the smallest possible valentines heart which is still has a vivid pink/red colour. 'All' you need is:

• An ultramicrotome
• A block of plastic 
• A razor blade 
• Steady hands
• About 10 minutes

Step 1:
Trim the plastic block to a flat face, then cut a heart shape into that face. This is the bit the steady hands and razor blade are needed for, the heart needs to be about 0.3 to 0.5 mm (250 to 500 um) wide! It also needs to have tidy flat edges so sections can be cut without damaging the knife blade.

The trimmed, heart-shaped, block of plastic.

Step 2:
Use the ultramicrotome to cut a section 300 nm (3 ten millionths of a metre) thick off the block, and catch it on the surface of a pool of water next to the knife edge. From the colour scale of thin film interference we expect a 300 nm section to be a vivid red/pink colour (even though the plastic itself is a transparent amber colour).

A 300nm thick sliver of the block, the tiniest Valentine's heart ever.

Step 3:
Bask in the glory of having made the smallest, and geekiest, valentines heart ever. It is so thin that even if you scaled it up to the size of an A4/letter sheet of paper it would still be 4 times thinner than cling film/saran wrap and 40 times thinner than paper. This tiny thickness gives it a tiny volume: it has a volume of about 3×10^-14 metres cubed, and a mass of about 3×10^-11 grams. That is similar to the mass of a single, average, human cell.

Software used:
ImageJ: Focus stacking.
Photomatix: HDR image processing.

Small Polished Stones

• TL;DR Download this spreadsheet and look up your pledge date in the table. If you are really keen you can update the values in the sheet called "Production Data !UPDATE ME!" from this website to get a better estimate.

Loads of people are very excited about backing the Pebble smartwatch at Kickstarter, because if they gave a certain amount of money they would be given a Pebble once production began. The small polished stones will ship out in roughly the order that people backed the Kickstarter project. This makes it easy to guestimate when your Pebble will be made; all you need to know is the date you backed the Pebble project at Kickstarter (try searching your emails for "Backer Pebble")...


So how do you do it?

1
Pebble are giving updates on how production is going in near real time:
http://www.ispebbleshipping.com/
On the 30th Jan 2013 about 1500 Pebbles were made, taking the total to 8000 produced so far.

2
It is also easy to look up how many backers there were on each day the Kickstarter ran for:
http://www.kicktraq.com/projects/597507018/pebble-e-paper-watch-for-iphone-and-android/#chart-daily
For example by the 25th April 2012 40376 people had backed the project, most of these are in the queue to be sent a Pebble as a reward for supporting the project.

3
If you backed on the 25th April then it will take about "people in the queue in front of you (minus the pebbles already made) divided by production per day" days to get to your place in the queue. i.e. (40376-8000)/1070=30 days (I reduced the production rate to account for no production on weekends).

To make this a bit easier to calculate I made this spreadsheet. Just download it and look up the estimated production date based on your pledge date in the table. At the moment this is what it looks like as a graph:

The red cross is production as of today... There is still a long way to go!

Pebble are hoping to ramp up production to 2500 Pebbles a day. That will make a huge difference to estimated production dates, roughly halving the wait. To update the spreadsheets estimate fill in updated values from http://www.ispebbleshipping.com/ in the "Production Data !UPDATE ME!" sheet. All the estimated production dates will be recalculated automatically.

Disclaimer
This is just an estimate! And it is a pretty bad estimate based on very little data. Don't blame me if it's wrong.