Questions & Answers
from Peer Reviews
These are some of the questions posed by the excellent and generous (yes, generous, because s/he even went to great lengths to correct my English) reviewer at Complex Systems, whose comments contributed to make my paper a much better one. Many thanks!
What is the rationale for describing GEP genes as having a head and a
tail? It makes intuitive sense, but is confusing in light of the genetic
terms (e.g., ORFs, genes, chromosomes, etc.) used throughout the
narrative. Would some alternative pair of terms be equally descriptive,
but more appropriate in this context?
In describing genetic operators as insertion sequences and
transposition, the use of biological terms is inaccurate. In DNA
molecules, an insertion sequence is "a transposable element that carries
no genetic information except that which is necessary for transposition"
(Li & Graur, 1991, Fundamentals of Molecular Evolution, Sinauer
and Associates, Sunderland MA, p. 240; see also Li, 1997, Molecular Evolution, Sinauer and Associates, Sunderland MA). Transposition is
"the movement of genetic material from one genomic location to another"
(ibid, p. 250), and duplication is "the presence or the creation of two
copies of a DNA segment in the genome" (ibid, p. 237).
You say that "duplication of genes plays an important role in biology
and evolution...Interestingly, in GEP, individuals with duplicated genes
are commonly found...". I have two complaints about this part of the
arguments. First, the observation that duplication occurs in living
systems does not help explain why it is important or helpful in GEP.
Second, the reason that duplications are found in GEP searches can be
simply explained by the existence of a genetic operator for duplication
(misnamed gene transposition). The argument is circular. (Gene
duplication is important in evolution. We observe duplication in GEP.
Thus, duplication is important.)
I do not understand why mean fitness should fluctuate as in
Fig. 10 and
Fig. 12. Why does mean fitness decrease from one generation to the
next? Even after a perfect solution exists in the population, mean
population fitness continues to oscillate. Does this suggest that the
evolutionary dynamics might be adjusted to search the solution space
Last update: 23/July/2013
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