The Surface of the Thing is the Thing?

Nearly all that we call a thing, has a surface which bounds its existence. The surface is what we see, the surface is what we touch and hold. The surface contains the essence of the thing. Beyond the surface a thing can have a certain range of action impinging on other things with defining surfaces of their own.

If there is no surface, as with an evanescent cloud or transient musical sounds, we call these not things, but phenomena.

So what are we to make of this computer graphic rendering I created six years ago?

There are three things shown at different scales, the thing in the lower right being a part of the thing in the upper left, and the thing in the middle being a part of the thing in the lower right.

The thing in the upper left is a model I made of Bacteriophage T4, a virus of E. Coli bacteria made famous for its use in many laboratories for many purposes. 

The thing in the lower right is the baseplate of Bacteriophage T4, a mechanism that grabs a bacterium cell when the long fibers seen in the upper left are triggered by touching it.

The thing in the middle, looking evil and potent, is the needle structure that penetrates the cell wall of the bacterium, injecting into the bacterium the virus DNA, thus commandeering the bacterium cell to make hundreds of new virus copies.

A portrait of a weapon of mass destruction at the nanometer scale, disassembled into components like a field artillery piece. 

The Bacteriophage T4 is about 200 nanometers long. The shortest wavelength of visible light is 400 nanometers. Therefore, this picture could not be taken with a camera. In fact, it is not a picture at all, it is a rendering of data.

You could say that X-rays were used to gather the data, but not in any photographic sense. Thousands of frozen samples of Bacteriophage T4 were exposed to X-ray bombardment, being destroyed in the process. The X-rays were deflected according to the density of electrons in the atoms of the proteins making up the virus. Sensors surrounding the sub-microscopic virus registered these deflections.

Each of the individual T4 viruses was too small to arrange with any particular orientation. But the overall symmetry was known, and the top was distinguishable from the bottom. So the deflection data was converted by computation into a density volume fitted to be congruent with the expected symmetry.

In truth, the virus in its entirety was never examined this way. Instead, each major component, with five-fold or six-fold symmetry, was turned into data using this method, Cryo Electron Microscopy. These components were fitted together by scale and structure, to make a model of the whole virus. The volumetric density data was produced by the Rossmann Lab at Purdue University. The long tail fibers were imaged by transmission electron microscopy, also using X-rays.

I took that data, all publicly available, and used various software applications to turn the volumetric densities into geometric meshes. The meshes represent values where there is a sharp drop off in density, in other words, they represent surfaces.

But a surface of what? Think of what you see in this rendering as a shrink wrap of a complex compound of protein molecules. The atoms of the molecules are only hinted at in the surface shown because the resolution afforded by X-rays does not tease out distinct atoms. Instead, the structure of a given protein is synthesized in computer graphic programs and fitted into this shrink wrap to make sure it is accurate.

The rendering does not show these molecules themselves, but it does show the structural arrangement of the molecules in the needle. The ribbons are symbols of molecules with their atoms arranged in chains. The surface portrayal of the ribbons is purely arbitrary, they could as well be shown flat rather than plump.

Mostly absent from the data are the water molecules embedded in the structure. The water molecules might play essential roles in the adhesion of component parts and the mechanics of the components when the virus is triggered to penetrate the bacterium cell wall, but this is not known and not well studied.

What we don't see at all are are the surrounding water molecules. A water molecule is not spherical but it would just fit into a sphere two tenths of a nanometer in diameter. This means that a 200 nanometer high Bacteriophage T4 is to a 0.2 nanometer wide water molecule, as a 12 foot high model of T4 is to a BB, or small shotgun pellet. A twelve foot high model would be about five million times life size.

Water molecules vibrate and move violently. The effect of this pummeling on microscopic things in the water is called Brownian Motion. A T4 virus doesn't float around serenely in a placid fluid, rather, it is whacked around vigorously and constantly. Imagine yourself in a vat of violently moving shotgun pellets.

So look at the image again and think about what it shows. The surface of the thing is not the thing at all, it is a representation of data constructed not by optical imaging but by computation. The most significant aspects of the thing, like its structure, can only be shown symbolically. The environment of the thing isn't shown at all, and yet the whole apparatus that we call a virus must function within that environment.

And for all of the exquisite detail revealed by scientific visualization, we still don't know very much about how this thing, not so much a creature as a protein robot, makes its way in the wild. 

Bacteriophages. There are more of their kind, by individual count, than any other biological entity on earth.