“Information” is insufficient

The codicalist (yang = languages, yin = substrate) view of the so-called information model of physics (nature is information processing) is that “information” is (philosophically) insufficient because it only involves languages and not substrate: Information processing only involves language-to-language mappings.

An example would be a domain-specific language (DSL) for chemical reactions [1, 2, 3]. There are two types of compilers: a linguistic compiler (which compiles a high-level DSL program into a lower-level language for simulation) and synthetic compiler (which compiles the same source program into an actual chemical assembly).

Linguistic compilers are substrate-independent. Synthetic compilers are substrate-dependent.

The output of a linguistic compiler (e.g., machine code running on a MacBook Pro) can only light up pixels on a screen as an animation, whereas the output of a synthetic chemical compiler could light up a brain (e.g., a synthetic alcohol).

[1] Generation of Complex Reaction Systems through a Specialized Computer Language
The Reaction Description Language, RDL, is a computer language developed to describe generic types of chemical reactions. Using the keywords of RDL, commands may be formed that locate the reaction site, manipulate the reactant to form the product, and determine whether a reaction may be applied to a specific reaction site. The syntax and the types of operators in RDL mimic the way in which a generic reaction is often described informally, Thus, the reaction descriptions are usually self-documenting. Modification or addition of reaction types is accomplished easily and transparently.

[2] A domain-specific compiler theory based framework for automated reaction network generation
Reaction Description Language (RDL) has been extended to describe the chemistry rules for catalytic systems, and the molecules are represented by Simplified Molecular Input Line Entry System (SMILES).

[3] GReg : a domain specific language for the modeling of genetic regulatory mechanisms
Molecules are only described by their names, as it is the only information relevant in our language. The DSL approach emphasizes specification of only the required information for the particular domain. No molecules other than the ones described here can be used in the mechanism. After the molecules declaration, a GReg description specifies the chemical reactions that take part in the mechanism.


Philip Thrift


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