The point (made by Berlinski) is that macroevolution may be impossible by the mechanism of natural selection. There is a very good reason for this. If A is going to evolve into B, but it needs a large number of steps to get there, most or all of those individual steps have to be valuable enough in themselves to spread through the population.
What you do not seem to understand, is that A does not have to get to B, it could have been C, or D, or Z.
You keep seeing B as the goal of evolution, it simply isn't.
If we flipped a coin ten times, the chance of getting a specific sequence of 10 heads or tails would be 1 in 1024.
On the other hand the chance of getting
any sequence of 10 heads or tails is simply one.
Now evolution of a certain species tells the story of a series of adaptations, not the story of a specific series of adaptations.
This is the mistake that you, Berlinski, and all the other Discoverites make.
ID'ers are asking evolutionary biology to explain the teleology they themselves impose on nature.
Of course that does not work, not because the science is lacking, but simply because science cannot explain something that is not there.
NS only works by small steps that are individually beneficial.
Evolution does indeed work in small increments, but naming these steps beneficial, is a value judgement that illustrates a fundamental misunderstanding of what evolution by natural selection really is.
Berlinski is rubbishing a mechanism that he and others think is wholly inadequate to explain macroevolution. It is logically valid to do that without immediately providing an alternative explanation. It is better to know that you do not know something than to pretend a totally inadequate mechanism provides the explanation.
Berlinski is a senior fellow of the Discovery institute, a religious/political think tank that has it as it's only goal to promote ID/creationism.
He is not rubbishing anything, he is just repeating the old and stale, much refuted, ID/creationism arguments.
If he is rubbishing anything, it is his own reputation. By claiming to be an agnostic, while vigorously defending ID/creationism, and religion as the only source of morality, he becomes a joke.
Logically we should probably say speciation is a mystery.
Even if you were right, ID/creationism does not do that, they simply know there is an intelligent designer/creator, and work from there.