It means just because we can pump sequences into computer and generate a nested hierarchy, it doesn’t mean the nested hierarchy was the product of random mutation and natural selection.
Having an almost correct Zinc Finger array (there are about 13 Zinc Finger in my colorful figure) is like having an almost correct computer password. There aren’t really good gradual evolutionary routes to a coherent zinc finger array that targets specific locations in the genome anymore than there are gradual routes to figuring out a computer password.
Each of the Zinc Fingers of about 30-32 residues correspond approximately to a target of 3 DNA bases, but it’s not as modular a design as synthetic chemists would like since a given Zinc Finger modifies the chemical behavior of the adjacent Zinc Fingers. This illustrates the password problem with a mere 3 Zinc Fingers:
Proteins like the KRAB Zinc Finger (KRAB KZNF in the diagram) attach to segments of DNA (often ERVs or other elements) to help recruit molecular machines:
The binding of KRAB-ZFP (KRAB Zinc Fingers) to ERVs or other elements means the Zinc Finger array must be matched to recognize a DNA target. The problem for evolutionary theory was that to have a nested hierarchy across species of KRAB-Zinc Fingers implied a corresponding nested hierarchy of targets!
I found that absurd, but nevertheless, evolutionary biologists declared this as some sort of evidence of co-evolution, which struck me as nothing more than an epicycle.
Anyway here is the related paper that talks about the co-evolution KRAB-ZFPs with evolution of a certain kind of transposon. It describes the problem I was mentioning, but I don’t agree with the “solution” of co-evolution. I’d sooner believe in miracles.