[ExI] auto-catalytic sets

The Avantguardian avantguardian2020 at yahoo.com
Tue May 15 14:02:17 UTC 2012

 ----- Original Message -----
> From: Anders Sandberg <anders at aleph.se>
> To: ExI chat list <extropy-chat at lists.extropy.org>
> Cc: 
> Sent: Monday, May 14, 2012 2:53 PM
> Subject: Re: [ExI] auto-catalytic sets
>T he original paper is here: http://arxiv.org/abs/1205.0584
> Nice to see that Kaufmann has not given up, but rather turned to quantitative 
> analysis. Cool that the sets are not just the giant component.
> What I wonder about this model is the waste set. Autocatalytic sets that use 
> food sets will also produce waste chemicals that are not used by it and are not 
> autocatalytic in themselves (otherwise they would be in the maxRAF). There needs 
> to be a process that turns some of the waste set into the food set, otherwise 
> the process will grind to a halt.

Thanks for the link to the actual article, Anders. You are right that the process would grind to a halt without some way of regenerating the food set. From the way he defined autocatytic sets, it seems that he was using them to model genetics instead of metabolism. Despite the fact the binary polymer model he describes allows for both cleavage and ligation, his example uses only ligation. Actual metabolism actually goes in both directions, anabolism where complex molecules are built up from simpler subunits and catabolism where complex molecules are broken down into their constituent subunits. So his algorithm seems completely biased toward anabolism.
Another shortcoming is that it seems that the autocatalytic sets/subsets require at least one element of the food set to be a catalyst. In his example, it is the {0} that is the catalytic superfood, but I think it might be a general problem with his method that one of the food elements must be a catalyst to bootstrap the rest of the autocatalytic set. The problem with this observation is that known biological catalysts are polymers. If there were a biological monomer that could catalyze the polymerization of other monomers, then the origin of life would be obvious.
Stuart LaForge
"Man is a strange animal, he doesn't like to read the handwriting on the wall until his back is up against it."  -Adlai Stevenson

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