Darwin’s vision of what he mistakenly calls natural selection might be more rightly characterized an imagined or fantasized version of selection, not what really happens and nature.
Thus his theory of “Natural Selection” is an equivocation, where his word “Natural” isn’t really what happens in nature, but rather how he and subsequent evolutionary biologists have imagined what happens in nature.
It may be said that natural selection is daily and hourly scrutinizing throughout the world, every variation, even the slightest; rejecting that which is bad, preserving and adding up all that is good; silently and insensibly working, whenever and wherever opportunity offers, at the improvement of each organic being in relation to its organic and inorganic conditions of life.
Quoted also in:
But selection doesn’t improve each organic being when it sends them to extinction, and selection often selects for damage, not for improvement as in numerous cases of reductive evolution, and Behe would rightly argue DE-volution is more the natural norm than the exception.
But beyond that, natural selection would be in impediment to evolution of complexity in many cases. Complexity as in more integrated systems. And Darwin somewhat understood the problem of extravagance and rube goldberg complexity when he quipped that the Peacock’s tail made him sick.
The problem of NS preventing evolution emerges in numerous places in the evolution of Eukaryotes. For example consider these prokaryotic and eukaryotic system from textbook biochemistry:
Granted the eukaryote might not necessarily evolve from exactly the system depicted for the present-day prokaryote, but whatever the ancestor looked like, it would pose comparable problems to hypothetically evolving a prokaryote to the eukaryote.
Because there are several proteins involved, there are thousands of ways to break the prokaryotic system, but even a few would immediately be lethal (and thus selected against). Consider the IF-3 connect to the E and the IF-1 connecting to in the 30S subunit. That is the reverse situation in the corresponding Eukaryotic system. There is no gradual path to this, and it has to work instantly and adequately, otherwise the system dies. And there are numerous other problems as there are so many more complexes involved in the Eukaryotic cycle that have to pop in and be functional from the start.
Natural selection would preclude such evolution, and the evidence of this is, ironically the supposed conservation of the Prokaryotic architecture over hundreds of millions of years. I mean, one should not be saying, “selection conserves this feature” and then simultaneously arguing selection evolved away from this feature! That is a logical contradiction.
Selection preventing evolution by constraining or “conserving” an architecture is related to the problem of fitness peaks in evolutionary algorithms. Now someone could say “fitness landscapes change”, but those claims are unjustified in light of mechanical considerations of life critical systems such as those above, not to mention it is inconsistent with insisting something is “conserved” for hundreds of millions, if not billions of years.
I will post a few other examples of things that caught my eye. I won’t immediately say the differing operation of helicases is un-evolvable, but still this gives me pause: