Can we backengineer a bug?

I’m been reading Sean B. Carroll’s book Endless Forms Most Beautiful: The New Science of Evo Devo, which is thoroughly fascinating. One can almost understand the response of proponents of intelligent design to the marvels of the workings of our genes, which mirror the workings of logic circuits. But of course, this is a reaction appropriate to someone who hasn’t read the whole book, and ID proponents are very much in that situation. It was rather ironic that, upon the suggestion being made that “junk DNA” might not be mostly junk after all, the ID crowd claimed this as a prediction of intelligent design. What should not be ignored is the fact that, even though this may have been an expectation of theirs, they were not doing the scientific research necessary to test it. Yet they still want to claim that they are doing scientific research.

The truth (although a thought-provoking one) is that, when we created artificial logic circuits, we were actually creating something alot like the ‘machinery’ that created us. So in a sense, it is ultimately the case that natural logic circuits produced artificial ones.

The question now is whether we can create software that will replicate all the logic circuits in a particular organism’s genes – perhaps the fruit fly, although it might be better to start with something simpler. Not only would this allow a fast-running computer to speed up simulated evolution and test its workings, but we might even be able to get it to work backwards, through all the possible paths that would have viable organisms, to get a clearer sense not only of the course evolution may have followed, but perhaps it might even be able to simulate the course back all the way to its beginnings. Is it too much to hope that the computer circuitry that the creations of DNA have created might actually be able to return the favor in reverse and show how DNA got us to this stage of computer-constructing organisms?