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that enzyme GP uses during evolution differ considerably from the parse tree
structures used by conventional GP, yet enzyme GP still generates conventional
program expressions during its evaluation phase.
A metabolic network is a group of enzymes that interact through product-
substrate sharing to achieve some form of computation. In a sense, a metabolic
network is a program where the enzymes are the functional units, and the in-
teractions between enzymes are the flow of execution. Consequently, the set of
possible interactions between enzymes determines the possible structures of the
program. Enzyme GP represents programs as structures akin to metabolic net-
works. These structures are composed of simple computational elements mod-
eled on enzymes. The elements available to a program are recorded as analogues
of genes in an artificial genome. These genomes are then evolved with the aim
of optimizing both the function and connectivity of the elements they contain.
From a nonbiological perspective, enzyme GP represents a program as a
collection of components where each component carries out a function and in-
teracts with other components according to its own locally defined interaction
preferences. A program component is a terminal or function instance wrapped
in an interface that determines both how the component appears to other com-
ponents and, if the component requires input, which components it would like
to receive input from.
Modeling the Enzyme
Enzyme GP captures the enzyme as a computational element that transforms
the products of other enzymes and does so according to its predefined affinity
for their products. The components of the model are depicted in Figure 3.4.
Shape
f
Activity
Specificities
Substrates
Figure 3.4 Enzyme model. An enzyme consists of an activity and a set of speci-
ficities. Shape describes how the enzyme is seen by other program components.
Specificity determines, in terms of their shape, which components will be bound as
substrates to provide input.
 
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