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If a functional gene becomes a pseudogene, its product will no longer be available to the biochemical pathways in which it formerly participated. The transformation of a gene to a pseudogene will not have catastrophic consequences if the biochemical pathways in which its product formerly participated are redundantly complex - other products can take over the role of the missing product. Perhaps not as efficiently, but efficiency is something that can be improved by selection. In this way, redundant scaffolding can be reduced, ultimately to the point where a system or pathway is irreducibly complex.
