Either the operating system of the universe just is what it is, or it was invented by some entity or entities. Either way, science proceeds from there and doesn't deal with the question of how our particular operating system came into being.
The existence or non-existence of a greater power has no bearing on the scientific method, which only assumes that the universe operates according to consistent laws, and that we can get increasingly reliable information about them by asking falsifiable and testable questions. There is no conceivable scientific answer to the question of whether or not the operating system of the universe had an author, or whether it just exists. Asserting the existence of a higher power does not add anything to scientific inquiry, but neither does it subtract anything from it.
The problem with creationism (and Intelligent Design is just another version of it) is not that it posits the existence of a higher power, but that it posits constant diddling with an inadequate system by said power, with the explicit intent of promoting biblical literalism at some level. Intelligent design is more appropriately called stupid design, because it assumes that a higher power smart enough to invent the operating system of the universe is nevertheless too stupid to get the job done right the first time -- the universe is still and must always be in beta test mode.
The computer analogy is modern, but the basic idea certainly isn't. Newton personally believed that God could and did intervene in the workings of the universe to keep the planets on track, but his minister friend Thomas Burnet strongly disagreed. In the 18th century they used clockwork rather than computers for the analogy.
"We think him a better Artist that makes a Clock that strikes regularly at every hour from the Springs and Wheels which he puts in the work, than he that hath so made his Clock that he must put his finger to it every hour to make it strike: And if one should contrive a piece of Clockwork so that it should beat all the hours, and make all its motions regularly for such a time, and that time being come, upon a signal given, or a Spring toucht, it should of its own accord fall all to pieces; would not this be look'd upon as a piece of greater Art, than if the Workman came at that time prefixt, and with a great Hammer beat it into pieces?"
And that's far from the oldest assertion of the concept. Augustine of Hippo and several Islamic scholars had similar notions. For a long time many theologians have thought that constant diddling with natural law by its creator would automatically imply that the creator isn't very bright-a notion very much at odds with traditional concepts of God.
The bottom line is that the proposition put forward by proponents of Stupid Design, "Biologists haven't explained everything yet," does not happen to be a scientific theory at all. George Gilder, a long-time affiliate of the Discovery Institute, has even admitted as much, being on record as saying "Intelligent Design itself does not have any content." And if you believe in a creator deity, characterizing that deity as a third-rate engineer is bad theology as well.
And it you don't, of course, the concept is unnecessary.
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