Sunday, 13 July 2008

An update on 'The Inner Life Of The Cell'

This is not what I set out to write the other day, but there were things I wanted to say.

Great animations like 'Inner Life' are exceptional. Though I do have some issues with this way of depicting molecular scale events. Over the years I have been fascinated by animations and visualizations; it was in my mind long ago.

In the early 80's I was modeling the 3D structure of heam on our BBC-B computer at work, and soon after on an Apricot Portable
It was mathematically fun, especially as processors got faster and you could do free rotations. Things like this are space filling models where the Van der Waals radius defines the size of each atom and X-ray diffraction locates their positions.

At a similar time I heard Max Perutz talk and was issued with 3D spex to look at some of his slides. It was amazing to see molecules floating in space in front of you, showing the conformational change when oxygen binds to haemoglobin. It was much better than the image here.

When I got a 486 I went through a Pov Ray period (and a mate was running early versions of Bryce). Pov is a programming language for placing objects in a space, saying where the light comes from, pointing a camera and saying 'render'. I saw the potential for scientific modeling in astronomy and biochemistry. Of course I was years behind the times by then, computing and innovation had moved faster than I did.

So what is my problem with animations like 'Inner Life'? It's simple, where is everything else? At that resolution the view should be awash (pun intended) with a blur of H2O, dissolved ions and small inorganic molecules not to mention the peptides, polypeptides and proteins, sugars and carbohydrates, fats (OMG), nucleotides and RNA's all going about their own business. Relentless kinetic and electrostatic interaction are the driving forces but it's two steps forward, one step back in a kind of chemically coordinated dance which drives to temporary equilibria. However if all this other stuff was included you would never see the points of interest. It's a compromise and we need to keep that in mind while we are watching.

In the previous comments, Mark said:

Forget the space stuff for now, more of this please.
I'll see what I can do.

Watch these movies at full screen for the best effect:

Cell Signals (Part 1 of 2)

Cell Signals (Part 2 of 2)

And talking of cell signaling... What about Calcium - or the calciun ion, Ca2+?

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