These questions reveal two areas where you and I disagree.

First, I don’t believe that changing conditions drive most of evolution.

Second, I don’t believe that “rapid evolution” is part of the discussion about punctuated equilibria. At least not the sort of rapid evolution you are trying to account for.

Are there sufficient examples of such phenotypic subtypes to explain evolution as we know it?

Of course. Just look at our own species. If the various subgroups had remained isolated for another 100,000 years we might have split into several species. The differences between Asians and Africans are at least as great as the differences between many species.

Also if there is “Nothing special going on there”, why is punctuated equilibria controversial?

For four reasons. (1) Some people doubt that it exists. (2) Some people don’t understand it and think that it’s not an important contribution to evolutionary theory. (3) Some people understand it and recognize that it’s a threat to gradualism. (4) It’s the basis of hierarchical theory and macroevolutionary processes like species sorting. Many people aren’t ready to consider such things.

This is why I feel punctuated equilibrium is relevant to the Hsp90 story. Hsp90 promotes speciation not by creating new mutations, but by exposing existing ones, which in my mind fits perfectly with the punctuation concept. The new twist is that the existing mutations are hidden rather than exposed as a phenotypic subtype in a larger population. With canalization through Hsp90, the new phenotype is indistinguishable from the rest of the population until times of stress. This to me is a better explanation than the one arguing that species rely on the continous presence of an off-chance subtype to meet changing conditions. Wouldn’t evolution just stop if that’s the only mechanism to evolve rapidly ? Are there sufficient examples of such phenotypic subtypes to explain evolution as we know it ? Also if there is “Nothing special going on there”, why is punctuated equilibria controversial ?

My apologies if the diagram is misleading, but to me there is nothing in this diagram (exept maybe that it is two-dimensional), or in my text, that excludes the co-existence of the parent species and the new one.

The key concept in punctuated equilibria is that evolution is coupled to speciation by cladogenesis. One species splits into two. One of the species shows phenotypic change while the other one does not.

This is explained by a founder effect version of speciation where a subset of alleles is fixed in a small isolated population. Nothing special going on there. The alleles were already in the large population. There is nothing mysterious about the process underlying punctuated equilibria. The original paper even referenced Mayr and gave him credit for his work on speciation.

Let me repeat. Punctuated equilibrium is not about new mutations, it’s about speciation.

The other thing to keep in mind is that both species continue to exist side-by-side for millions of years. This is difficult to reconcile with your diagram that links phenotypic change to a “rapidly changing environment.” How do you explain the fact that the parent species seems to be very happy in this so-called “rapidly changing environment.”

Punctuated equilibria has nothing to do with macromutations and hopeful monsters.

Macromutations and Punctuated Equilibria

The changes seen during the “punctuations” are the perfectly normal kinds of evolutionary changes seen in typical speciation events. In most cases, it takes an expert to recognize that speciation has occurred in the fossil record.