You can find out more about this on Tom’s own blog –


In previous posts, I described the science behind the Four Mountains Test, a memory test which we developed using computer generated landscapes to assess the ability to recognize places from their layout even when the viewpoint changes. The test was designed from the outset to depend on a part of the brain, the hippocampus, which is important in forming new memories of the events we experience but also in maintaining a sense of direction and keeping track of where we are as we move about. We found that patients with damage to the hippocampus had particular difficulty with the test.

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A chemist’s view of a bruise

Bruises happen when connective tissues and muscle fibres under the skin are compressed but the skin doesn’t break. With a graze or a cut, the blood can easily escape but with a bruise, blood from your ruptured capillaries can’t. And with nowhere to go, the blood is trapped.

Bruises generally go through a whole range of colours. If you have a really nasty whack, it will start off red then within the first couple of days turn a purply-bluey colour. Within 5 to 10 days, it develops into a greeny-yellow and finally, before it fades away after about 10-14 days, it’ll go yellowy-brown. This obviously depends on the severity of a bruise, your age, if you’re on any medication or have an illness which means you’ll bruise more easily.

When the red blood cells break open after you hurt yourself, they release substances which signal the body to send white blood cells to the healing site and cause all these weird colour changes. The white blood cells consume the hemoglobin and then release chemicals which cause inflammation.

Your bruise will start off red because the tissues surrounding it fill with blood. The most significant substance of red blood cells is hemoglobin – the protein which makes blood red.  The next colour, purple, is caused by the hemoglobin being broken down and losing its oxygen. This happens immediately after the injury and persists until all of the hemoglobin is broken down. The first breakdown product of hemoglobin is called a chemical called biliverdin, which appears within a few days.  Biliverdin is green which is why after the bluey-purply phase, your bruise will go green.

The green biliverdin is then converted to a yellow molecule called bilirubin. And finally the brown colour, just as your bruise vanishes, is caused by hemosiderin – another chemical converted from bilirubin. And there we go. From red to blue to green to yellow to brown. Bruises really are fastinating.

Making sense of smell – the physicist’s way

This is a post that I wrote a while ago but never got around to publishing. It’s no longer a current news story, but still interesting!

There’s a story recently reported by the BBC and others about a theory of the sense of smell – what’s interesting about this theory is that it’s not based purely in biology, as you might think, but instead applies quantum physics to biological systems.

This is particularly interesting for me as it’s related to my own work (I study the theory of vibrations in quantum nanostructures).  Anyway, the essence of the story is this:  conventionally, biologists have always thought that our noses process smell by using the shape of molecules.  Each molecule has a specific shape that fits another “detector” molecule in the nose, like a key fitting in a lock.  This then sends a signal to the brain which it then interprets as “mmm, coffee” (or more likely, “oh dear, time for a nappy change”, in my house).

But this new theory depends not on the shape of the molecules, but on the way they vibrate.  You can imagine a molecule as little balls (the atoms) held together by springs.  If you could give one of the balls a little flick, you give it some energy that travels through the springs and makes the whole molecule vibrate.  Each molecule has its own special way of vibrating, with several “notes” at different frequencies, much as the way different musical notes make up a chord.  Physicists call these different vibrational frequencies (notes) “phonon” modes – a phonon is quantum of vibrational sound energy, and each phonon has an associated frequency, or mode.

The new study that’s been published used fruit flies (Latin name drosophila) to see if they could tell the difference between normal molecules and ones where the hydrogen atoms in the molecules were replaced with deuterium (just the same as hydrogen, but it’s heavier as it has a proton in addition to hydrogen’s neutron and electron).  Changing the hydrogen to deuterium is a good test because the extra mass changes the vibrational frequencies of the molecules, but not their shape.  In my musical analogy, this is as if a molecule that would normally “play” a chord of C major now plays a C minor chord instead.  So if the flies can tell the difference between the ordinary molecules and the heavy molecules, this would be good evidence that smell is based on the vibration of the molecule, not the shape.

And guess what?  The flies can tell the difference! Apparently they didn’t like the molecules with deuterium rather than hydrogen and flew away from them (I am no fly-behaviourist, so not sure how they did this bit of the research).

I think there’s a lot more work to be done in this area before we can know for certain what role vibration plays in the sense of smell, but this is a very interesting piece of research that couples together phenomena normally only found in quantum physics with biology.

More information:


I don’t think university is for everyone, but I do believe that in every school in the country there are young people who would enjoy university life, who would succeed academically and who would benefit enormously from doing a degree. At the moment, students from many schools are missing out.

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My Chambers dictionary (I paid for the app, so I may as well get some mileage from it) defines science as:

1. Knowledge ascertained by observation and experiment, critically tested, systematized and brought under general principles, esp in relation to the physical world.

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Scientists are involved in finding out how nature works by looking at and generating new evidence. The idea is to build up a set of well-founded, testable beliefs about the natural world. This system seems to work pretty well – our everyday existence, quality of life and indeed lifespan has benefitted hugely from scientific advances and the technologies which flow from them from: antibiotics, brain scans, the internet, television, transport, contraception. It’s easy to think of less positive examples, like nuclear weapons, but none of this stuff would work unless the underlying scientific beliefs had some truth in them.

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This is my brain.


I am excited this morning, because I have finally begun to get to grips with Freesurfer a package for processing brain imaging data created by the Martinos Center. Freesurfer is a very powerful program which allows you to extract a very precise brain surface from an anatomical image. I rendered the picture above using the surface data for my brain, and a 3D animation program called Blender. Freesurfer allows you to project your brain imaging data onto this realistic surface. This is important because a lot of the interesting processes take place on the outer surface (cortex) which, as you can see, is scrunched up.

Brain imaging experiments help us figure out what different parts of the brain do (this is called functional imaging). From these experiments and from research with patients with brain injury we know that different parts of the human brain…

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