CHON: Experimental validation of an old idea

by Ian Page.

The CHON vat is created from a theoretical idea by Stephen Wolfram many years ago.

Imagine a system of names of various lengths made up randomly from the alphabet.

Imagine that any name can be disassembled as in scrabble tiles and any other name created out of the bits lying around, and imagine that this can be done with very little loss of energy.

Imagine that the transformation of a name to any other name is catalysed or restricted by all the other names to various extents.

Provide a flow of energy through the system.

What wolfram showed in a computer simulation is that such a system settles into a stable pattern, with only a subset of possible names.

Sounds pretty abstract!

However once you realise that letters are amino acids, and names are genes and their resulting proteins, this suggests that if you throw a stew of amino acids and protein formers into a vat and stir well, after a while it will settle into a pattern of proteins changing and processing the energy flow. This looks a lot like a cell.

The CHON Vat was based on this same idea – obviously I have no idea what the letters and the formers are going to be, but the intuition from Wolfram’s work was that it would do the job of transforming any possible CHON component or product into any other; fairly autonomously given the right conditions.

It would be nice to have some actual experimental support!

Well Hecht at Princeton (conference proceedings) thought that as life has been rather ergodic, essentially grabbing the first combination of proteins that worked to some extent and then slowly incrementing them, there must be amongst the nearly infinite number of untried proteins some that might work and even better perhaps.

So he knocked out 80 genes from e-coli, made a million random genes encoding a million random proteins, and popped them into e-coli. Four of the 80 gene deletions had their function restored by at least one and in some cases hundreds of the random proteins.

What this means is that jumping across the gene configuration space to non adjacent points can find acceptable non-related alternatives to existing biochemical pathways.

Now this experiment is actually only replacing a few bits of the aircraft in flight – the biochemical pathways and the pattern of the existing e-coli is retained.

A true experimental proof would involve throwing a soup of trillions of random genes into an ecoli with no existing DNA and seeing what happened. If Wolfram is right a minuscule proportion of the cells would survive and grow and an examination of them would show new life patterns using previously unknown proteins.

Jonathon Swift would be proud!

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