Science has never spoken on this, since it can’t do that. But scientists have. Here are just a few examples from places I know well.
Design Principles of Regulatory Networks: Searching for the Molecular Algorithms of the Cell
Defining the Design Principles of Skin Epidermis Postnatal Growth
Quantitative Operating Principles of Yeast Metabolism during Adaptation to Heat Stress
I don’t see that as closely aligned, because I don’t assume that design requires a designer. “Appearance of design” downgrades ATP synthase to an “appearance” of something I consider obvious. I understand why people do this, and especially why naturalism leads people to do it (that infamous quote about a “divine foot in the door”) but I’m with Dan Dennett here. The biological world is overflowing with design. Calling it “apparent” just encourages the madness of attempting to find the “real” design that isn’t just “apparent” design. Does this give some kind of comfort to ID creationists and their propaganda machines? Maybe, but that just means that they didn’t read to the end of the sentence: “…without a designer.”
But here’s the thought experiment. Suppose I sit down at my supercomputer to predict ways to build a much better version of enzyme Z; let’s even say that my enzyme has a new substrate specificity and is orders of magnitude more stable than enzyme Z. I synthesize the gene and insert it into bacteria. Does this enzyme evince design? Or only apparent design? Is there any way to tell the difference, without knowing that I designed the new enzyme on my supercomputer? Are we going to actually say, “well I can’t tell whether this is design or apparent design until I investigate supercomputer user patterns?”