COMPUTING SCIENCE
Ode to the Code
Brian Hayes
Antievolutionists
The idea that the genetic code is evolving under pressure to
ameliorate errors—or indeed that it is evolving at
all—has not won universal assent. Some cogent objections were
set forth as early as 1967 by Carl R. Woese of the University of
Illinois at Urbana-Champaign. Among other points, he noted that if a
trait is actively evolving, you would expect to see some variation.
In particular he called attention to the various
"extremophiles" that live at high temperature, high salt
concentration, and so on. These organisms tend to have unusual
proteins and unusual nucleic acids, but they all have the standard
genetic code.
The few variant codes known in protozoa and organelles are thought
to be offshoots of the standard code, but there is no evidence that
the changes to the codon table offer any adaptive advantage. In
fact, Freeland, Knight, Landweber and Hurst found that the variants
are inferior or at best equal to the standard code. It seems hard to
account for these facts without retreating at least part of the way
back to the frozen-accident theory, conceding that the code was
subject to change only in a former age of miracles, which we'll
never see again in the modern world.
Another challenge to the error-reduction hypothesis is the
difficulty of showing causation in an evolutionary context. Even if
the pattern of codon assignments is consistent with such a
mechanism, the same pattern might have arisen in some other way.
Computer experiments like Alff-Steinberger's and Freeland's reveal
nothing about pathways of evolution. A program churning out a
million random genetic codes is not what you expect to see in
nature. To simulate the step-by-step process of mutation and
selection is much more demanding; after all, the biosphere has been
working at it for a few billion years. Nevertheless, models of this
kind are being attempted. Guy Sella and David H. Ardell of Stanford
University are running a simulation that includes both a nucleic
acid genotype and a protein phenotype, linked by a mutable genetic
code. They point out that change can be introduced into the genetic
code without utterly disrupting cell metabolism if there are
multiple codons for a given amino acid, and some of them fall into
disuse; these rarely used codons are then free to take on new roles.
The mechanism is analogous to the gene duplication that often
precedes evolutionary divergence of proteins: One copy of the gene
carries on the original function, allowing the other to explore new
territory. Thus degeneracy or redundancy is not just an accidental
feature of the code but is necessary to allow scope for evolution.
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