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Interesting I only noticed the mention of regulatory genes once in the article. It does not say whether the fast evolving new genes are coding genes or regulatory /master switch genes. The former would indeed be a challenge to dogma such as I recently read in Some Assembly Required by Niel Shubin. The latter is exactly what makes sense.

A programming analogy made most sense to me reading Niel's book. The coding genes are like the lower level functions like for loops if then else statements etc. The regulatory genes are the blocks of code or procedures that use these common functions to make lots of unique things.

Evolution by natural selection works by rapid changes to the regulatory genes or master switches while holding the coding genes basically constant at pain of death before reproduction.