Thank you so much for your excellent post, r9etb!
You wrote that I may not be entirely correct with respect to my comments about non-phenomenal reality. Maybe you are correct about this, r9etb. Certainly the examples you give of "system-level" relations seem to entail phenomena. For as you wrote, "the 'undirected DNA change' has to be accompanied by a mechanism that can reliably translate the mutation into something useful, such as the pancreatic beta cell for the production of insulin, plus the various pieces of the metabolic process that rely on insulin."
The point I was trying to get at, however, is that the ultimate system-level is the universe itself: The universe appears to be ordered and purposeful. That is, it is "lawful," and its laws may derive from yet deeper principles. (People have been known to vehemently disagree with me over this issue, as it is their right to do.)
It seems to me the ultimate system-level cannot be an object of intentionalist consciousness, however, since the intending consciousness is part and participant in it. To put it crudely, to my understanding, non-phenomenal existents cannot be subjected to the type of tests for which the scientific method is famous. Since the universe itself cannot be reduced to fit the intentionalist method, I think it partakes of the non-phenomenal with respect to this particular aspect. Likewise history is "non-phenomenal" in this sense: We do not know its future course, so we clearly do not have an object for intentionalist consciousness about which reliable propositions can be advanced. Likewise the concept of "human race," for another example, partakes of the non-phenomenal in a certain fashion. And then there is the case of the individual human person, who also partakes of the "non-phenomenal" as a "component" or dimension of his being.
Maybe I'm just splitting hairs here....
Thank you ever so much for writing, r9etb!
Doubtful.... ;-) It appears to me that you're basically extending Goedel's Incompleteness Theorem to physical reality. I have no clue if that's permissible, but your approach does seem consistent with Schroedinger's complaint about the difficulties facing an observer trying to get "outside" of the quantum system one is trying to observe. (I can't recall the exact context or wording, nor have I any idea whether his complaints still have weight; but I do recall its similarity to what you're saying....)
OTOH, for the sorts of physical phenomena being discussed in the ID vs. Evolution debate, the "evolution" side must assume that there is nothing except "phenomenal" reality of the sort they can observe. From their perspective, any of the system-level questions must be answerable strictly in phenomenological terms.
In terms of your comment, and the topic of this thread, the question is: is it possible for scientists to "get outside" of evolutionary processes to the point that they can correctly describe the development of something like an endocrine system? That turns out to be an interesting question.
The first possibility is that the process does end up being fully describable in a way that doesn't require an inordinate number of multivariate "happy accidents" and coincidences. In that case, the scientific approach will have triumphed on the topic of "systems evolution." Still, one would have to wonder whether an evolved intelligence could escape the constraints you've laid out to the point where one could understand the evolution of intelligence.
Another possibility is that design actually played a role at some point, for some things. One way to approach this possibility is through the example of my son's insulin. It's manufactured using recombinant DNA techniques, using bacteria and/or yeast. It's an example of intelligent design, albeit ID of a fully human character. The question is: can one use scientific processes, applied "in the blind," in such a way as to properly infer the presence of designers in a process where we a priori know them to have been involved?
I've had answers all over the map on this question ... but in any case, it seems to me that the question itself is perhaps an example of the issue you're raising; and it also seems to offer a way to test your idea on a specific example: does the presence of even a human designer take us into this "non-phenomenal" realm? Or would we expect that an agent's actions on physical objects always leave a mark of some sort, even if we cannot have access to the full characteristics of the agent by which those actions took place?
As it stands now, the "standard" scientific position is apparently that it would be impossible to detect, much less test, the physical traces of design -- apparently even human design -- without having some additional pieces of information besides the products of design. (At least, that's the claim one typically sees on these threads.)
The scientific implication of this position is to place "design" into your "non-phenomenal" universe at a surprisingly close distance. (Of course, the fact that we can easily detect many sorts of design makes me think this stance is not correct, but that's a different discussion.)
On the other hand, if it turns out that one can use scientific methods to infer the presence of a human designer in the test case, then the horizon of the "non-phenomenal" is pushed back somewhat -- and it would also naturally raise the corollary question: "why wouldn't design be detectable, at least in theory?" Of course, one would still be required to provide scientifically acceptable tests whenever a design hypothesis was made, but there would be at least a chance for science to detect design if in fact it had occurred.