In at least 2 of the examples, Pax6 and Neural Crest Cells I'd say it was the role of the developing nervous system as an organising centre that was the cause of that involvement since the key developmental timepoints involved are well before the CNS starts acting as a central interpreter of environmental information.
I am not a specialist in the field but in the article Cabej writes:
The neural control of recruitment of Pax6 in the regulatory network of lens crystallin during the early individual development strongly suggests that the nervous system must have also been responsible for the initial recruitment of lens crystalline in metazoan evolution.
Concerning the neural crest cells, based on other published works, Cabej writes that hindbrain (neural tube) provides the neural crest cells with epigenetic patterning Dynamics information’. He quotes Trainor . ‘‘the proper program of events governing the migration of crest may need first to be established in the hindbrain to allow migratory crest cells to interpret and respond to environmental signals set up through a series of tissue interactions.’’
However, it seems to me that examples on the direct involvement of the CNS in producing evolutionary innovations are to be found in his book. Don’t worry I find the $150 a bit steep myself. Maybe go to the author’s site?
*Note: Are are block quotes done on this site? Thanks
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