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Cross-module optimization has been used, and it shows to reduce code size by removing unused functions from the application.
The decay of unused functions during E. coli controlled evolution [ 25] decreases the consumption of nutrient for physiological adaptation purposes.
The question is whether and how the decay of unused functions produces the increase in cell volume and fitness found in evolutionary time scale [ 2].
In addition, the fact that unused functions decay during evolution reduces nutrient consumption for physiological adaptation, saving nutrient that is used for growth.
We propose that genetic diversity of the CP sequence in this strain reflects functional decay due to relaxed selection outside the nasopharynx, enabling mutations to accumulate in the portions of the genome that encode unused functions in the integumentary system.
As a consequence, one would expect that, if the model gives a good representation of the evolutionary process, the mutations causing the decay of the unused functions in the laboratory experiment also become fixed and maintained by selection.
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Unused function tends to be lost when evolutionary selection pressure is removed, as in the case of eye and pigment loss in cave-dwelling animals [ 41].
The work Aharoni et al. [ 2] suggested that if a new previously unused function is suddenly placed under the spotlight of selection, such new functions can be found (and substantially improved) in proteins that are already are doing something else.
Unused aldehyde functions were blocked with ethanolamine or with glycine, as specified.
The decay of unused catabolic functions, found experimentally, is introduced in the model using simple population genetics.
Table 3 addresses the question regarding whether it is necessary to block potentially unused benzaldehyde functions on the AFM tip.
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