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Sometimes, as here,

But what I believe instead is that the vast majority of the complexity we see in biological systems actually has its origin in the purely abstract fact that among randomly chosen programs many give rise to complex behavior….

I suspect Wolfram has just independently discovered neutral mutations and is needlessly agog. But then I read things like,

Third, whenever the overall behavior of a system is more complex than its underlying program, almost any mutation in the program will lead to a whole collection of detailed changes in the behavior, so that natural selection has no opportunity to pick out changes which are beneficial from those which are not.

and think that Wolfram does not appreciate the way in which natural selection sculpts a population. Although of course the genetic composition of a population changes under selection pressure, individual genes are not often directly selected in or out. Individual organisms are.

In sexual species, just about every organism is genetically unique. A species is a swarm of similar genomes. A species under pressure to change its adaptation is being sculpted by selection in that those best able to get along in a new way are the most likely to make it. The pruning is continuous so long as the selection pressures stay the same. It's done at the organism level. Nothing is operating at the level where Wolfram is imagining the difficulty.

You need to read the book. He is a mathematician looking at how complexity arises from simple computer programs. His results may eventually be applied to many areas of science, perhaps all areas of science. Such applications and extentions will need to be done by others, he is merely reporting his research into computations done on cumputer.