Either I did not explain myself clearly enough or you are avoiding my point. The question is not, as you imply at various points, whether scientists assume design, to what extent they do so, how often they do so, etc., but whether they can to the extent you want them to IF as you say there may not yet be a right way to handle design issues in scientific research.
So I ask the question again: if in fact there is as yet no right way to handle design issues in scientific research, what do you expect scientists to do? Whether you like either/or options or not, the only options I can see is for scientists to suspend all research so as not to rule out possible design explanations or to keep on going as normal and wait for future scientists to offer possible design explanations that can be tested and perhaps verified.
It also seems that you confuse "design" with functionality. Just because scientists assume an entity has a function (they couldn't study it if it didn't, so this is in fact a very basic, almost fundamental, scientific assumption) doesn't mean they believed, or even assumed, it was designed. Since that functionality could also have come about through evolution, it is in fact fallacious to claim an unconscious presumption of (intelligent) design. As for those scientists who do assume "intelligent" design, the fact that they occasionally can prove that an entity thought to have no function actually has one is in and of itself not proof that "intelligent" design is real. Scientifically, all it means is that those who thought it had no function were wrong, regardless of why they thought it, were wrong. And it doesn't take a scientist "committed" to (intelligent) design to make these kinds of discoveries. In my own work I have postulated that a protein no one else believed played any
role in any known metabolic system in plays a significant role in the onset of articular cartilage degradation. As you said, I am not "committed" to (intelligent) design, yet I could not believe that this protein had no useful function whatsoever. What matters in science is imagination, regardless of its source; the best scientists have always been those with the ability to imagine something different from convention, and then prove it. Under those circumstances, prior commitment to (intelligent) design is not necessary.
Kevin L. O'Brien