I should note for the record that I'm not questioning whether the result of the decision was right, and I'm not commenting at all on some matters in the case (such as the ridiculous disclaimer they wanted to put on the textbooks). I'm merely pointing out that many of the arguments the opinion presents are not just bad but complete howlers. They're not the sort of thing that reasonable people can disagree about, and there are plenty of arguments that I do put in that category, including some on issues I have a very firm view on (such as abortion). To be in that category, you have to begin from different moral premises or different views of rights or justice. Many of the views defended in this opinion are simply unreasonable. Only an irrational or ignorant person could defend them. They involve misstatements, misrepresentations, ignorance of the history of philosophy, and simply fallacious inferences. I wouldn't give them a passing grade on a philosophy exam. I'll number my points to keep them separate in my mind as I go.
1. Jones says a reasonable student would see teaching ID as an endorsement of religion because religious people have said similar things. But this argument is pretty insufficient. It's true that so-called scientific creationists have talked about gaps in evolution, and one version of ID can be thought of as explaining things unexplained by evolution. But that doesn't mean ID is the same thing as scientific creationism, and it doesn't mean ID is religion. That's just a non sequitur.Saying there are unexplained things in a scientific theory isn't endorsement of religion just because one religion-derived view with scientific language uses a similar argument. You could never arrive at creation science unless you started with the assumptions of certain way of reading Genesis, a particular religion. ID requires neither a particular way of reading a particular religious text or any particular religious views at all. There's a huge difference.
2. Jones accepts John Haught's claim that design arguments are religious, citing Thomas Aquinas as someone who held the view. Yet Aquinas would be the first to insist that his design argument is not remotely based on religious revelation. He distinguishes between general revelation and special revelation, and he says you can't know special revelation is true apart from faith. You can know general revelation is true just by using reason. His design argument is the Fifth Way, and the Five Ways are five of his arguments for the existence of God starting from general revelation, using reason as available to anyone without the use of faith. The argument is much older than Aquinas anyway. It goes back to Plato at least, who does not use it to support any religious beliefs, and Xenophon puts it in the mouth of Socrates, who was put on trial for rejecting the religion of his time. Whatever Socrates was up to was more properly philosophical.
3. He makes much of the fact that Aquinas notes that the designer is the same being most people call God. Aquinas doesn't say that step of the argument can be known by reason, at least if that means concluding that this being has all the characteristics of God as revealed in scripture. Each argument he gives offers one or a few divine attributes as demonstrable, and then he concludes that you can know by reason that a being with many of the divine attributes exists. He doesn't think you can show that God is a Trinity or that God is of one essence with the human being we call Jesus. He does think you can show a necessarily existent, omnipotent, omniscient, perfectly good being who explains all the contingent things found within the universe, who designed things at some level in order to explain the purposed appearance of things. That happens to be true of the being he believes in by faith, and he thinks they're the same being, but he doesn't argue for this based on religion. His arguments aren't religious arguments. It's simple historical ignorance on Haught's part to claim that they're religious, assuming Jones represents Haught fairly to begin with.