At issue is what constitutes science itself, with the court deciding that:
...[R]igorous attachment to "natural" explanations is an essential attribute to science by definition and by convention. We are in agreement with Plaintiffs’ lead expert Dr. Miller, that from a practical perspective, attributing unsolved problems about nature to causes and forces that lie outside the natural world is a "science stopper."Of course, what the ruling doesn't mention (nor do atheistic scientists often mention) is that this "rigorous attachment to natural explanations"--otherwise known as methodological naturalism--is itself a presupposition based on a particular kind of faith, and is neither empirical nor testable. Thus, as an arbitrary rule placed on science, it actually violates itself, though we are all expected to pay it unquestioning fealty or else be labeled flat-earthers (or worse).
Incidentally, this view of science would have been completely alien to all scientists before the 20th century, most of whom believed the science was only possible because a creator God had made an orderly world. Absolute naturalism is not the sine qua non of science, but is rather an untestable philosophy smuggled relatively recently into science by those with a particular metaphysical agenda.
In reality, a reasonable mind can see the silliness of this without the benefit of years of training designed to drum out common sense. Say you put a deck of cards on the coffee table and walk out of the room. Later you return to the room and the cards are scattered haphazardly all over the floor. What do you conclude? The anti-ID zealots would caracature ID by claming ID-ists would look at a scenario and say "Well, angels must have done it." This kind of portrait earns big points with their fellow atheists who find it quite clever (and with more than a few dim judges, too), but it utterly fails to address what ID actually says. Just as anyone else, the ID theorist would conclude that something knocked the cards off the table (not necessarily intelligent; it could have been the cat) and then gravity caused the cards to fall and land randomly.
Now let's suppose an alternate scenario. You put the cards on the coffee table, walk out of the room, and when you return, they are lying on the floor in a pattern that spells out "We fell down." In order to remain "scientific," would you apply your "methodological naturalism" and conclude that no intelligent force had acted on the cards? Or, without having to give it more than a nanosecond of thought, would you conclude that your spouse (or someone else with intelligence) was having some fun with you?
We know the answer intuitively, and the fact is that "science" makes these kinds of obvious conclusions every day. Perhaps the most popular science there is (if television ratings are any indication)--forensic science--deals with only discerning intelligent design in the natural realm. It's an entire science based on the clear fact that if two metal bullet-shaped objects with a spiral pattern are found in someone's head, they are not natural deposits produced by the brain, nor are they things that the wind put there.
What ID is trying to explain, and what naturalistic science is utterly at a loss to explain, is that the scattered deck of cards from the analogy is most emphatically not what we find in nature. What we find is the cards arranged into a message--only it's a message far more complex than "we fell down."
The atheist has gotten around this by jiggering the definition of science so that anything "scientific" (by which he means, and means us to mean, "true") has to have a natural, purposeless, undirected cause as an explanation. So when he finds the message spelled out by the cards, he concludes with absolute certainty--scientifically--that they got that way on accident. As the eminent atheistic Darwinist Richard Dawkins once wrote, "Biology is the study of complicated things which give the appearance of having been designed for a purpose." They appear to have been designed, but ultimately they cannot have, because we've already decided that any recourse to an intelligent cause cannot be true because it violates our definition of science. Any other explanation wouldn't be scientific, you see.
And so the methodological naturalist stands inside a wonderfully comfortable little circle he's drawn for himself, where he knows the answers to all of life's questions because he's decided beforehand what he's willing to allow those answers to be. None of this, of course, has anything to do with pursuing actual truth, but he's not too concerned with that anymore because he's published a lot of papers and has a lifetime of hypotheses to defend and social respectability to protect and tenure to gain.