Hi Warren,
Thanks for your reply. Although many here have taken my question to further degrees, I would like to address why I see the "argument from engineering" to be misleading. Leaving aside the fact that no known engineered artifact can self-replicate (absent theoretical Von Neumann machines), an examination of those artifacts that we can definitively state were designed or engineered show that they have two basic intrinsic properties: 1) they have a "purpose", and 2) they have a causative history that can be traced directly to the actions of a known designer. A hypothetical "ID Biology" research program, if based on your engineering analogy, would have to provide an answer - or at least provide some supporting theory or observation - to address one or the other of those two intrinsic properties of designed objects. It doesn't have to do both, initially, but it at least needs to start somewhere.
1) Purpose. To get a start on this line of reasoning, I think it would be necessary to examine existing organisms, communities and ecosystems in an attempt discern purpose. Note: I don't mean functional role, I mean "why this organism occupying this niche in this habitat and not this other one". If an unambiguous purpose can't be identified in existing organisms, ID is going to have to begin working towards identifying an "end state" or final purpose for a given species. If ID can predict what the "final form" of an organism might be, then it would could make a reasonable case for the presence of teleological evolution. It might take some time, obviously, so looking at short-generation organisms might be the way to go. After all, the Grants spent 30 years watching finches in the Galapagos to map their natural history so that they could finally provide empirical support for the action of natural selection on a wild population. Alternatively, ID could make a retrodiction by stating what the final purpose of an extinct lineage would be, and hence the final form of the "ultimate" species based on the teleological paradigm, then go examine the fossil record to see if that was the case. In either case, it wouldn't necessarily prove purpose, but if you can prove teleology, that gives you a leg up on it.
2) History. One of the key things that can be said about, for example, the computer I'm typing this on, is that we can confidently declare that it was designed because we know the causal history of computers - and we know quite a bit about the designer. "We have met the designer and he R us." With most of the artifacts around us that were engineered by intelligence we can confidently make the same claim. However, consider that the further back in time we go, the less ambiguous are the engineered artifacts. Walk through a vinyard in the Vaucluse - you'll see a myriad of sharp flakes of flint. Most of them are natural pieces formed by the random processes of nature. Occasionally you'll find some that are ambiguous. Very very rarely, you'll find one that was in fact worked by the hand of humans ~30,000 years ago. However, the determination (engineered/natural) relies on external factors not related to the flint itself: to wit, knowledge of purpose (tool), process (flint knapping leaves specific marks readily identifiable by an expert), and the designer (humans). In the absence of those three components, a piece of flint is just a piece of flint. Even with two of the three, the resulting piece of flint is ambiguous at best - not enough to hang a world-shattering paradigm from. Extrapolating to ID Biology, it isn't sufficient to proclaim that "eubacterial flagella couldn't evolve" (Behe's claim from "Darwin's Black Box", f'rinstance). On the other hand, it isn't necessary to have all three ducks aligned at the beginning. If ID can show observations or even at least a testable theory for at least two of the three, even though the results might be ambiguous, it would be enough to get things started - and get real research started.
This, I think, goes along the lines of what your pseudonymous friend "Mike Gene" was on about in the most recent cut-and-paste you made. Until ID can provide something resembling substance on either of the two points I mentioned above, it will most likely remain on the outermost fringes of science - with crystal channelers, astrologers, and magnet therapy proponents.