Information Technology Reference
In-Depth Information
interactions between genes and gene products. Marijuán [27] describes these
activities respectively, as
self-organizing
,
self-reshaping
, and
self-modification
.
Self-organization is the ability of a distributed system to carry out a unified task.
Self-reshaping is the ability of an existing system to carry out multiple tasks to
satisfy varying needs. Self-modification is the ability of a system to change its
constitution in order to solve unforseen problems. Interactions between the three
classes of pathway unify these activities and bring out the emergent behavior
of the whole.
Metabolic Pathways
Cellular computation takes the form of the metabolism of the cell's chemi-
cal state. Metabolism of this state involves transformations, implemented by
constructive and destructive chemical reactions, between chemical species, in-
creasing the concentrations of some and reducing the concentrations of others.
Temperatures in biological systems are relatively low, and many of these reac-
tions will not occur without the help of enzymes, catalytic proteins that bind to
specific chemicals and mediate their interaction and subsequent transformation.
The chemical species to which an enzyme binds, its substrates, are determined
by a property called its specificity; a result of the spatial arrangement of amino
acids found at the enzyme's binding sites. Substrate binding occurs through
inexact matching. The closer the match is between the substrate shape and the
binding site shape, the stronger the bond between enzyme and substrate and,
consequently, the higher the likelihood of recognition.
The presence of enzymes activates transformative paths within the me-
tabolism. This forms a network, a metabolic network, where chemical species
are nodes and enzyme-mediated reactions are the connections between nodes.
Metabolic networks are composed of metabolic pathways. A metabolic pathway
is an assemblage of enzymes which, roughly speaking, carries out a unified task
involving a shared group of chemical species. This cooperation emerges from
the sharing of substrates between enzymes, where the product of one enzyme
becomes the substrate of another.
Proteins, including enzymes, have computational characteristics similar to
artificial computational elements like transistors and logic gates [8, 9, 11] (and
some that are quite unrelated [10]). The computation provided by metabolic
pathways has been modeled using Petri nets [34], which are normally used to
describe distributed computation in artificial systems. In other work, artificial
analogues of enzymes have been applied to information processing [37].
FUNDAMENTALS OF ENZYME GP
Enzyme GP [22-25] is a genetic programming system that evolves executional
structures using a genetic algorithm. The biomimetic program representations
