C. Schwartz,
You're missing the point of Gould's article. Biologists assumed that the phenomenon they understood (a gene coding for a protein) represented the entire underlying mechanism of biology. The reductionism was biology as an expression of the known gene-for-protein phenomenon. Now it's clear that while genes code for proteins in general they do so in a way or ways that we don't understand. They may do so in ways that may be subject to complexity and irregularity. They may do so in ways that may not even be consistent among all species. They may do so in ways that cannot be predicted from looking at the genome. Therefore the reductionism of the genome as the predictive mechanism for biology is lost.
Up to now evolution was reduced to the increasing of complexity in the genome itself. Now we see that's not true as such. Therefore evolution (and Gould really equates evolution and biology) represents two processes: the increasing of complexity in the genome and the increasing of complexity in the expression of the genome. When your reductionism has failed to include the entire second process, it has failed. Or, more correctly, it may have failed. That is, if the complexity involved in gene expression cannot be predicted by looking at the genome. Reductionism has to be predictive. It's not enough to say that genes code for proteins.
peace
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