The program(s) is(are) still being "decoded" so I must rely on those who are working on it.
A 21st Century View of evolution
Molecular genetics has amply confirmed McClintock’s discovery that living organisms actively reorganize their genomes (5). It has also supported her view that the genome can "sense danger" and respond accordingly (56). The recognition of the fundamentally biological nature of genetic change and of cellular potentials for information processing frees our thinking about evolution. In particular, our conceptual formulations are no longer dependent on the operation of stochastic processes. Thus, we can now envision a role for computational inputs and adaptive feedbacks into the evolution of life as a complex system. Indeed, it is possible that we will eventually see such information-processing capabilities as essential to life itself.
It'd be more correct to say that the codes are still being decoded, but I see we're talking past each other again. I was talking about genetic programming, not genetic engineering.
I took a look at the article you linked. Tough reading (too technical, not enough explanation) but I got the gist of it. Here's my guess. As we understand more and more of the genome we'll see more and more complexity, more and more mechanism, cycles impinging on cycles in crazy ways. That is not a hallmark of design at least as practiced by humans.
But that's just a guess. Time will tell.