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is made and used to direct the synthesis of the protein. Thus, in terms of
information, the RNA copy contains exactly the same information as the
original DNA.
The messenger RNA is not the only kind of RNA molecule working in a
cell. Despite its central role in information decoding, structurally, mRNAs
are very dull. The structural diversity discussed below is typical of the other
classes of RNA, namely transfer RNA (tRNA) and ribosomal RNA (rRNA).
Like DNA, RNA molecules are also long, linear strings of four nucleotides
(ribonucleotides, in this case: A, U, C, and G). In contrast to DNA, RNA mol-
ecules are single-stranded and some of them are capable of folding in a unique
three-dimensional structure. One of the reasons for the folding of RNA mol-
ecules resides in the existence of short sequences which are complementary to
other sequences within the same molecule. Obviously, if these complementary
sequences were to stumble upon each other, short double helixes would be formed.
These intramolecular double helixes are indeed fundamental for the unique three-
dimensional structure of some RNA molecules.
Thus, like proteins, some RNA molecules can have a unique three-dimen-
sional structure (tertiary structure) and therefore can exhibit some degree of
structural and functional diversity. The rules of complementarity in RNA
double helixes are much the same as in DNA, with A pairing with U, and C
with G. In RNA molecules with tertiary structure, some nucleotides are in-
volved in helix formation and therefore are not chemically available, but
other functional groups are free and exposed and thus can engage in differ-
ent kinds of interactions and even participate in biological catalysis. Indeed,
this, together with a unique three-dimensional structure, allows RNA mol-
ecules to function as real biological catalysts (ribozymes).
So, despite its reduced chemical vocabulary, RNA is the kind of molecule
that can simultaneously function as genotype and phenotype, that is, as a
simple replicator. Note, however, how in such cases the genotype and the
phenotype are tied up together: any modification on the replicator is imme-
diately reflected in its performance. That is, there is no room for subtle or
neutral changes in these systems. And subtle and neutral changes are funda-
mental to an efficient evolution (Kimura 1983; see also Ferreira 2002c for a
discussion of the role of neutrality in artificial evolutionary systems).
Another important constraint of these simple replicator systems can be
very well illustrated using the artificial system of GP, also a simple replicator
system. In GP, if one were to introduce genetic variation as freely as it is
done in nature, most modifications made on the parse trees would have
