Design Framework for Evolution

That's not how software development works. When software designers pull bits and pieces from other programs as units, combine and mix them, or come up with completely novel code. Their iterations need not produce a nested hierarchy.This is not what we see in life. We do not see wholesale swapping of design units across designs like we do with software development. Instead, we see a nested hierarchy, the very opposite of what we would expect from a design paradigm.Even more, it is the physical characteristics of DNA that carry information. For example, stem-loop structures can form in DNA and control transcription. The physical interactions with DNA and transcription factors can control embryonic development. This just doesn't happen with software. Software code does not physically react with itself to produce tertiary structures.Quite frankly, software does not have a lot in common with DNA.

I'm with the others on this one. What are these mechanisms? It seems very vague and not concrete at all.

But it isn't the same, as I already discussed.First, DNA between species falls into a nested hierarchy. Software does not.Second, it is the physical interactions between bases on the DNA molecule that produce the information. This is not how software works or is designed.Those are two major differences bewteen the two.

The genome IS a molecular machine, as you are defining it. The physical and chemical interactions that DNA participates in are no different than the physical and chemical interactions that proteins participate in. DNA folds around histones, forms stem-loop structures, binds to proteins and RNA's, recombines, and contorts. Nicks in DNA serve as triggers for apoptosis. DNA is as much of the machinery as any protein or any other cellular structure.