That the design doesn't start out perfect is irrelevant. You have misunderstood my intent. Perfection is irrelevant to the process.
The reason new things are not perfect is not because the designer is unintelligent or sloppy. It is because it is impossible to predict the properties of anything that is truely new. You can rearrange things with well known properties, but when anything really novel comes along, you cannot predict how it will behave or whether it will be useful.
"The reason new things are not perfect is not because the designer is unintelligent or sloppy. It is because it is impossible to predict the properties of anything that is truely new." 
That's all fine and well, but still irrelevant. What *matters* is whether a process formed something with or without some type of aid or bias.
We know the answer to that question for computer viri. We know it again for cloning. We know it still once more for how artificially intelligent software programs were formed, and yet again for self-replicating machines.
If you'll look back somewhere around post #237/8 on this thread, you'll see that we also know the answer for DNA-computers and biological machines.
In all of the above, we scientifically *know* that an intelligent designer was required for their formation.