Monday, 21 October 2013

The Shape of a Cell

Each term I make a research comic for the Oxford University Biochemical Society magazine called PhenotypeThe topic for this cartoon; the function of cell shape in bacteria. You might not know, but bacteria can have one of a huge variety of different shapes, but why cells have a particular shape is not a commonly asked question. To quote Kevin Young: "To be brutally honest, few people care that bacteria have different shapes. Which is a shame, because the bacteria seem to care very much.".

Check out the comic here, the whole issue will be available to download for free from here soon.

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

Tuesday, 15 October 2013

Building a Human

Every single cell in your body is made up of four main types of chemical compound: protein, carbohydrate, lipids/fats and nucleic acids. You are made of molecules, precisely defined and complex molecules, but still just molecules.

The difference in scale between a person and a molecule is enormous. A person is around one to two metres tall. A typical chemical bond is around one to two ångstroms. One ångstrom is tiny; one ten-billionth of a meter. If you took the entire population of the Earth, scaled each person to the size of a typical atomic bond and then stacked everyone head to toe, then the stack would be about your height. This means that, while you are made of molecules, it takes a lot of them to make a person!

The most common type of complex biological molecule in your body are proteins. These are the molecular machines that run your cells. Proteins are made up of chains of different combinations of 21 different amino acids. The amino acids themselves are quite simple molecules; typically made up of 5-10 carbon atoms, a couple of nitrogen and oxygen atoms and a sprinkling of hydrogen. We now know enough about protein amino acid sequences, the structure of cells and the structure of proteins that we could make a pretty good effort of making a scale model of a person, or at least the proteins that make them up.

This picture is a plastic scale model of 100 amino acids, representative of all the amino acids in your body, at about the ratio the different types are used to make up the proteins in your cells. They are ready to clip together to make a scale model of proteins, at a scale of about one centimetre for a bond (100 million times larger than the molecules they represent). Using enough copies of this (and lots of plastic models of water molecules) you could make an accurate scale model of 75% of your body. You would need a lot though; 1,000,000,000,000,000,000,000,000 copies of this set of 100 amino acids. The scale model of your body would also stand around 100,000 kilometres tall (1/3 of the way to the moon), and would weigh much more than the entire Earth.

Your body is an incredible molecular machine, made up of a near-unimaginable mixture of complex biological molecules, all running at a molecular scale. Next time you see someone talking about nanotechnology stop and think for a second. You are nanotechnology; a self-organising, self-repairing, reproducing, thinking piece of nanotech.

Software used:
Blender: 3D design of the plastic scale model.

Friday, 11 October 2013

Making Big Things Look Small

Any photo normally give you an immediate sense of scale, but what is it about the picture that let's you know how big something is? Take a look at these two photos:

The first photo is clearly of some tiny water droplets on a plant, while the one on the right is clearly of a train running through a city. It isn't just content (train vs. droplet) and context (city vs. leaf) that inform you about the scale; you can trick you eyes into thinking a massive building is actually a miniature. There are other properties of the image that come into play.

The key is blur. In photos of tiny objects the background and foreground of the image are normally very blurred, but with big objects the background and foreground are normally sharply in focus. I talked about this effect in my last blog post; the bigger the ratio of the size of the lens to the distance to the object, then the more blurred the background and foreground look. Microscopes take this to the extreme, when out of focus parts of the image are so blurred that you can't see what is there at all.

This effect is universal, it even happens with your eyes. You can try it out: hold your finger close to your face (about 15cm/6in away) and look at it with one eye closed. Notice how blurred things in the background look. Now hold out your hand at arms length, and look at it with one eye closed. Now the objects in the background look more sharply in focus.

So to make something big looks small you need to make the foreground and background look blurred. Simple! Before digital image processing (Photoshop) effects like this had to be done in camera. It was surprisingly easy; take a camera with a detachable lens, and detach the lens from the camera. If you now set up the lens pointing at something you want to take a photo of, but tilt the camera relative to the lens, then you get an effect which is a bit like blurring the foreground and background of the image. This happens because one side of the image sensor/film is now a bit too close to the lens. This makes that side of the camera long sighted, and that side of the image blurry. The other side of the image sensor/film is also at the wrong distance from the lens, but is a bit too far instead of a bit too close. This makes the other side of the camera a bit short sighted, and makes that side of the image blurry too. The middle of the image sensor/film is still at the correct distance from the lens though, so the middle of the image is still in focus.

In principle this is simple, but in practice detaching the lens from your camera just means lots of stray light can sneak into the photo making glare. In practice you need to use a special lens which can be tilted while still attached to the camera, called a tilt shift lens. These are very specialised and cost a huge amount; it is much cheaper to fake the effect using a computer! There are many pieces of software that let you imitate tilt shift lenses, all that is needed is a gradually increasing blur as you move away from the line across the image that you want to remain in focus. I actually wrote a filter in ImageJ which does this processing. It is amazing how much this simple effect can trick your eye; it makes big things looks small by imitating the limitations of focal depth when using lenses to make an image.

This is the same photo as above, but with a tilt shift effect applied to it. This chunk of London now looks like a miniature, with a tiny toy train running through it.

The Tower of London, looking a lot smaller than usual!

The reverse effect happens too, though is psychologically less strong. This is part of the reason scanning electron microscope images are so compelling; they don't use light or lenses (at least in a conventional sense) to generate the image. This lets everything, from background to foreground, be sharply focused. It makes the microscopic world feel free big and accessible.

This diatom shell is less than a 0.1mm wide, but the sharpness of the foreground and background make it feel larger.

Artificially blurring the foreground and background makes it seem much smaller.

When communicating science it is important to think about the scale things appear; scanning electron microscope images break your intuitive concept of scale, and it is hard to imagine just how small the sample is. The image below, by Donald Bliss and Sriram Subramaniam and awarded Honorable Mention in the National Geographic best science images of 2008, is of the structures inside a single cell, and is a perfect example of why you need to think about scale. This image is a computational reconstruction, so it could be presented with pin sharp focus, but by blurring the background it conveys the sense of scale extremely well. It feels like a single cell.

Software used:
Photomatix Pro: Generating the tonemapped HDR photos.
UFRaw: Camera raw file conversion.
ImageJ: Custom tilt shift filtering.