Quote:
Originally Posted by HydrogenBond
Evolution skips from the CEO to plotting sales. This is all true but it does not tell about all the proteins in the trenches who make it all happen.
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I'm no expert (but I did study at a Holiday Inn

), but I think evolution theory incorporates all of that middle ground of proteins, regulation, timing, etc.
Notice that this leads to a lot more complexity and potential for variation than the normal view of CEO jumping straight to sales.
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Your characterization of the process by which a gene finds its proper expression, "This [gene] is new and neither the cell or the DNA have any history with it. Somehow it has to fit in, not only in terms of placement, but it also might need logistical support from transport proteins that may not even exist," reveals a normal misunderstanding of evolution; but there is no unknown "middle ground."
Today's transport (& regulatory) proteins may not have existed when the gene mutated, but something was there that made that mutation workable (or neutral), and in some helpful way eventually. It may have been competely unrelated to the previous function of the gene, or it may have improved on the previous function--under certain conditions.
What a gene expresses (& how much + when) doesn't need any more direction as to how or where to "fit in" than do the genes themselves. A random collection of gene products will undergo natural selection, just as will a random collection of gene mutations (or outward, phenotypic expressions).
If a particular new gene (mutant) product will only become functional by co-opting or highjacking some intermediate from a different metabolic pathway, you wouldn't say that the gene must have" known" that the particular intermediate would be available, would you?