3D Genes

3D information storage

The possibility for storing replicated information in in 1D and in 2D in crystals is well established, both theoretically and experimentally.

However, - perhaps somewhat suprisingly - 3D-information storage also appears to be logically possible in a self-replicating crystal structure.

A. G. Cairns-Smith once wrote:

On the other hand the information itself must not be three-dimensional if it is to be at all easily replicated; for a simple copying process there should be at least one spare dimension for it to be replicated into.

- Seven Clues to the Origin of Life [1] p. 95.

The required patterm combines the conventional 1D and 2D growth patterns, using a screw dislocation.

3D information storage

Information can be stored in the polytype repeat pattern - and in the cross section (and fault structure).

Break-up is as for the 2D model.

A screw dislocation is used - resulting in continuous growth.

We call this a "Type-3 genetic crystal" - following the terminology used in Genetic Takeover [2], p. 155.

Type-1 and type-2 genetic crystals can both form with - or without - screw dislocations. However, type-3 genetic crystals are dependent on the presence of at least one screw dislocation for their existence.

I described the 1D model as helped by long thin repeating elemants, and the 2D model as facilitated by short, fat ones. The 3D model combines them - so we might wonder if it arises at all - since growth is more likely to occur in all directions. However, if surface nucleation is improbable there seems to be no reason why such crystals could not form.

Certainly, I do not know of any crystals that commonly employ this mode of growth.

I propose mechanisms which deal with the issue of unwanted surface nucleation in my sweet crystal hypothesis.

Catalytic activity

With a 2D information storage clay mineral, the enzymatic "clay fingers" are fundamentally two-dimensional - they are long grooves.

Modern industrial use of clay minerals as catalysts indicates that there is a great deal of interesting chemistry that can be done without any specific programming of the structures at all - however, there are likely to be limitations to what a simple groove can do in terms of its catalytic activity.

The possibility of a 3D information-storage medium opens up the possibility for three-dimensional programming of the catalytic surfaces - in effect allowing the clay to more finely adjust its hold on molecules present on its surface.

The control in the third dimension would be necessarily limited - the surfaces would still have to essentially grooves - but it would allow more in the way of adjusting the details of the "clay finger" positions.

The greatest potential is likely to occur - not in the physical shape of the groove - but rather in the charge distribution along it - which can now be periodic.

Growth rates

In practice the growing surface will look something like:

Growth on many fronts

Any particles moving across the surface are likely to find themselves in a corner faster. They are thus more likely to stay attached than to drop off again. If you are in competition with other agents for resources, the resulting increased growth rate may well be advantageous.

Layer mutations

• if surface nucleation of a single layer happened on the growing surface - and existing layers then were able to step up on top of it.

• if reduction to a single layer occurs.

Problems

• Some common polytype mechanisms might inhibit ordered vertical growth.
  • Polytype mechanisms that involve significant horizontal displacement between adjacent layers seem likely to be incompatible with retaining the strict vertical alignment necessary to grow a long, thin crystal.

• Screw dislocations with many layers can become significant faults.
  • This can cause local energetic disturbances in the crystal structure, which may act as a source of mutations.

The possibility of 3D information storage gives a glimpse of some of the activities which may be available to more advanced crystalline organisms.

References

1. Seven Clues to the Origin of Life - a scientific detective story, A. G. Cairns-Smith, Cambridge University Press, 1985;
2. Genetic takeover - and the mineral origins of life, A. G. Cairns-Smith, Cambridge University Press, 1982;