This is a post in progress. I am trying to come up with a (somewhat) basic argument that shows the pointlessness of the irreducible complexity argument. Please leave comments, questions, and ideas for improvement.

Let us suppose a biological system. Gene A performs action X. Gene A evolves to function as a tetramer.
In the format:
Gene group -> action

AAAA -> X

Now, suppose gene A duplicates in the genome (see the case of the Hox cluster). Gene A evolves into genes B, C and D while AAAA is still performing job X. Meanwhile ABCD now performs action Y.

AAAA -> X
ABCD -> Y

As ABCD evolve, gene A duplicates again and the gene combination evolves to EFGH evolves doing action Y.

AAAA -> X
EFGH -> Y

Now, over time the evolution of EFGH leads no molecular signal showing relationship to gene A or to each other, thereby leaving no visible evidence of phylogeny. So, while A -> B,C,D -> F,G,H and also A-> E, no evidence is visible.

Now, E, F, G and H perform no function on their own, and none seem to have any molecular relatives in the lineage other than direct homologous genes/activities. This gene combination is irreducibly complex. Yet, they could evolve by completely natural processes and evolution by natural selection.

Therefore, even proving irreducible complexity does not prove evolution, it only shows a lack of information due the the loss of information inherent in the molecular evolution of all systems.

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