Animating our DNA*

By Grant Jacobs 20/01/2012

One part of biology that fascinates me is the three-dimensional structure of genomes and all that goes with them within the nucleus, the central organelle in our cells containing our genomes and the molecular machinery that organises, moves and processes our genetic information.

In the TED lecture below Drew Berry speaking in Sydney, Australia, shows off animations of molecular life.

The animations he shows are of DNA, chromosomes and the proteins that work with them.

Here, let me get out of the way so you can watch it –

Let me add a few scraps. I would add a whole lot explaining each of the different systems he shows, but they’d each be very long articles. So let’s make do with scraps.


A point about molecules being smaller than a wavelength of light is that a light microscope cannot ‘see’ things smaller than the wavelength of light.

Early-ish in the piece he shows a still illustration (below) by David Goodsell, who has an excellent book of these, The Machinery of Life.** Note the density of molecules. Life isn’t a few bits swimming around in water. There’s lots of molecules, all jostling together.


Drew mentions how molecules ‘jiggle around’. When you look at the structures of molecules shown on various websites –there are open access databases of these for scientists–usually the picture is static, with the molecule standing still in it’s ‘average’ position. In reality atoms making up the molecule each constantly move a little with the overall effect that the molecule ‘jiggles’. (In a sense. It’s hard to get the right adjective to describe this accurately.)


I would make a few remarks about those ‘legs’ walking the molecules along the microtubules (left), but that’s a post in it’s own right. (In fact probably a series of them.)

Sufficient to say here that it’s impressive what molecules can do, all evolved from the basic chemistry and physics of the molecules.

There’s a part of me that looks at this and thinks this would be truly fun. Why? Not just the ‘pretty pictures’, but because it blends a lot things I’ve enjoyed. My original high school orientation was actually strongly towards art, not science – that came later. I’ve worked on molecular simulation, if you like a more formal sort of animation used to explore how molecules behave. I’ve long been interested in how the larger complexes form together the biophysical nature of what goes on in life – it’s what got me into my field in fact. I can recall first learning about how molecules really worked and realising there was a ‘hidden’ layer of life beyond what microscopes can see – the sort of thing that these animations visualise. My earlier research was in proteins that interact with DNA. And, of course, I’ve ‘fooled around’ programming and using computers since the mid 1980s.

I guess some would have graphics work on Lord of the Rings, others visualising life on small scale.


* Scientists would more accurately say our chromosomes or chromatin – it’s also the proteins that are part of chromosomes and the proteins and RNAs that works with the DNA to process or transform it.

** I haven’t seen a copy, but I have seen many example of the illustrations and pages online.

Other articles on Code for life:

Coiling bacterial DNA

Doggie ERVs

Transcribing a gene, free poster

Deleting a gene can turn an ovary into a testis in adult mammals

Temperature-induced hearing loss