The Origin of Life

DNA crystals

DNA computing

Interesting material relating to the hypothesis of Crystalline Ancestry has arrived from a somewhat unexpected direction: DNA computing.

The work has largely been pioneered by the members of The DNA and Natural Algorithms Group at Caltech.

DNA computing may not sound like a promising direction for work relevant to clay minerals - but the work is all about the processes of crystal formation.

The authors are fully aware of the relevance of their work to the idea of Crystalline Ancestry.

The following abstract from one of the papers provides a flavour of the material:

Is it possible to create a simple physical system that is capable of replicating itself? Can such a system evolve interesting behaviors, thus allowing it to adapt to a wide range of environments? This paper presents a design for such a replicator constructed exclusively from synthetic DNA. The basis for the replicator is crystal growth: information is stored in the spatial arrangement of monomers and copied from layer to layer by templating. Replication is achieved by fragmentation of crystals, which produces new crystals that carry the same information. Crystal replication avoids intrinsic problems associated with template directed mechanisms for replication of one-dimensional polymers. A key innovation of our work is that by using programmable DNA tiles as the crystal monomers, we can design crystal growth processes that apply interesting selective pressures to the evolving sequences. While evolution requires that copying occur with high accuracy, we show how to adapt error-correction techniques from algorithmic self-assembly to lower the replication error rate as much as is required.
- [Self-Replication and Evolution of DNA Crystals]

The sentence: "Crystal replication avoids intrinsic problems associated with template directed mechanisms for replication of one-dimensional polymers" may offer some amusement value to Crystalline Ancestry enthusiasts. The 'intrinsic problems' which prevent it from operating in the absence of complex enzymes, you mean? ;-)

Why use DNA - rather than clay minerals?

Unlike most types of clay crystal growth, DNA crystal growth is tractable in the laboratory and occurs at time scales (hours) that are suitable for experimental investigation.
-[Self-Replication and Evolution of DNA Crystals]

Clay mineral synthesis in the lab is not always easy.

Genetic Takeover puts it this way:

[...] at ordinary temperatures, clay synthesis is only successful from very dilute solutions. Furthermore, the reactions are slow, often needing periods of months or even years.

- Genetic Takeover, Chapter 6.

It is easy enough to find other reasons for playing with DNA crystals. The units are bigger - so you can see what you are doing better. You get to form your own units, rather than being stuck with the ones nature provides for you - and the results bear on the problem of how to automatically manufacture tiny machine parts out of a uniform soup.

Anyway, this work is very interesting. Erik Winfree, Paul Rothemund and the other guys at the Caltech DNA and Natural Algorithms Group are obviously smart fellows - and have done a great service by exploring this material so thoroughly.

I encourage other interested parties to check out their work using the links below:


A big list of the Caltech The DNA and Natural Algorithms Group's publications
Proofreading Tile Sets: Error Correction for Algorithmic Self-Assembly
Self-Replication and Evolution of DNA Crystals
Programmable Control of Nucleation for Algorithmic Self-Assembly
DNA Computing by Self-Assembly
Algorithmic Self-Assembly of DNA Sierpinski Triangles
One Dimensional Boundaries for DNA Tile Self-Assembly
Self-Healing Tile Sets
Complexity of Compact Proofreading for Self-Assembled Patterns
Design and Characterization of Programmable DNA Nanotubes
Complexity of Self-Assembled Shapes
Two Computational Primitives for Algorithmic Self-Assembly: Copying and Counting
Self-Correcting Self-Assembly: Growth Models and the Hammersley Process - Yuliy Baryshnikov, Ed Corman, Nadrian Seeman, and Teddy Yimwadsana
Xgrow - DNA Lab: Tile Assembly Simulator

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