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.
4. Jones says Aquinas and Paley offer the same argument. It's the same type of argument (a design argument), but there are huge differences between Aquinas' view and Paley's. Paley bases his argument on the apparent purpose of parts of organisms and on the complexity of organisms, to which he can't attribute any explanation but design. Aquinas bases his argument on the fact that the universe is ordered in a very predictable way. It's the laws of nature that serve as his beginning fact, not the specific data of any particular organisms. The pro-ID testimony didn't help here, but the judge shows his ignorance by accepting their testimony when a quick look at Aquinas' actual argument, which is only a paragraph in the most popular version of it in the Summa Theologica, would have disabused him of that notion.
5. He's right that most people who believe in God would make the inference from the designer to the being they believe in. After all, they already believe there's only one being who could fit the criteria. But would someone who doesn't believe in the traditional monotheistic God do so? The answer is obviously not. If I were an atheist, and I came to believe that the ID arguments were convincing, I would not necessarily start following any particular religion. In fact, I wouldn't necessarily conclude that any religion has God right. I may well do what Antony Flew did and accept only a very minimalist view of God, a being who doesn't really care about us and who certainly doesn't expect us to worship him. Flew is not religious, but he accepts fine-tuning ID. A reasonable person might think the ID proponents (at least the religious ones) are doing this in order to make a partial case for the existence of the God they believe in, which some obviously are doing (that's the point of the Wedge strategy), but to take that as a sign of ID itself being religion is to confuse motivation and theoretical basis. A rational person wouldn't confuse those two things, and it's the rational person's judgment that counts, as Jones points out.
6. Jones thinks it's significant that a pro-ID book would admit that it's outside the realm of ID to identify the designer. That must be left to religion and philosophy. I'm not sure how this counts in favor of the thesis that ID is religion in disguise. So ID proponents recognize the limits of the ID argument. How does that mean ID is more expansive than the ID proponents think it is? They explicitly recognize that you need something outside ID to get it to the realm of the religious claim that Jones thinks is hidden in ID. But he takes this as evidence that you don't need to look outside ID to get such a claim out of the ID argument. That's simply crazy reasoning. This is like observing a scientist admitting that you have to turn to religion and philosophy to explain whether quantum mechanics implies the impossibility of a predetermined future and then claiming that quantum mechanics is religion because it says that you need to look outside it to religion and philosophy to figure out its implications. That's ridiculous.
7. One particularly strange argument begins with Behe's statement that the plausibility of ID depends on whether one believes in God. Well, duh. Someone who already believes in God will find the conclusion to be true already and is thus more willing to give it credence. But Jones's mistake is to conclude that Behe thinks the argument depends on belief in God. It doesn't. Nowhere in its premises is anything about belief in God. All Behe said is that people will find its conclusion more likely if they already believe in God. That doesn't mean the argument itself depends on belief in God. Even if it did, it wouldn't make it a religious argument, as the case of Aquinas shows. Belief in God entails nothing about whether one is religious or follows a particular religion. That distinction is crucial for sorting out philosophical distinctions between different views that one might accept as a result of an ID argument. Jones would rather just lump any theistic conclusion into the religion category, despite over 2500 years of the history of philosophy that should tell him otherwise.
8. Another argument that he seems to endorse is equally faulty, although the legal question is complicated. The argument is that there's no way a supernatural explanation could be anything but religion. It's a terrible argument. Lots of people have accepted something beyond the natural world without being religious about it. Socrates accepted reincarnation based on a philosophical argument. Plato gives further arguments for a soul, as does Rene Descartes. Even if these arguments are all bad, they aren't religion. They're philosophy. Just as Flew's recent support for the fine-tuning argument is philosophical acceptance of the supernatural without religion, so too are these philosophers' philosophical acceptance of the supernatural without religion. It just doesn't follow that an argument is religious just because its conclusion accepts the supernatural.
Now this isn't an argument that ID is science. That claim doesn't have to be established, though. This case is about whether teaching ID violates the establishment clause. It isn't religion, even if it's also not science, so ID is not constitutionally prohibited.
Unfortunately, in this case, the Supreme Court has given a precedent that lower courts have to follow. They've declared the supernatural to be religion, and Jones does have to abide by that. But he doesn't have to do it by endorsing the argument wholeheartedly. He can resign himself to having to follow their standard. That shows incompetence in judgment if not in carrying out his responsibilities as a lower court judge.
9. There are several other arguments that are so terrible as to be completely embarrassing. The book used in the proposed curriculum is about ID, but because it's a Christian publisher and some of the authors happen also to be creationists it somehow follows that ID is religion. Christian publishers publish lots of things. They publish philosophy books, for instance. One very good one I know of assumes nothing religious at all. At another point he takes it as evidence that ID is religion because Phillip Johnson thinks naturalistic evolution is incompatible with biblical theism. Who doesn't think that?
The funniest is Jones's observation that some ID authors find an ID argument in the Bible. Yes, but there are also love poetry, funeral dirges, simple historical accounts, court records of political rulers, letters to friends, battle chronicles, victory songs, wise advice, stories with a moral, and even an account of primitive genetic engineering. Does Jones think things of those categories are always going to be religious just because there are examples of them in the Bible? There goes genetics in the science classroom, and history and literature are also establishments of religion by his criterion.
10. He argues from a particular book, authored by young-earth creationists that was later edited by the publisher to reflect a more general ID argument not requiring belief in YEC, to the conclusion that this particular book, as it currently stands, is religious. If he's confusing motivation with conclusion, I've already pointed out that error. It's clearly religious in motivation, but that's not sufficient. If he's not making that error, then he's confusing a former version of the book, one not published, with a current one, the one that would have been used in the classroom. Clearly the book kids would have had to read is the one that counts, not some earlier version that had things in it that are inappropriate. So why is the earlier one relevant?
11. He cites Ken Miller's argument approvingly, to the effect that ID arguments are more favorable to religion than teaching a view that's religion-neutral. It's true that ID arguments are more favorable to religion than religion-neutral science (or to the unconstitutional teaching of naturalistic evolution that is incompatible with religious views and is certainly not the teaching of science, since naturalism isn't science). OK, so it's more favorable to religion. But so is teaching the Big Bang, which accepts an origin to the universe and not the steady-state model that is less favorable to traditional theistic religion. So is quantum theory, which some have used to resolve problems with divine foreknowledge and human freedom. Being more favorable to religion is not the same thing as endorsing it.
12. Jones sees the uproar in the community as a sign that they took it to be government endorsement of religion. But this ignores the point he's already made that the person who sees it as government endorsement of religion must be a rational, informed person. If the community's view is largely based on the misrepresentations popularized by the anti-ID crowd that I've already pointed out above, then the community isn't informed. If the community engages in the fallacious reasoning pointed out above, then the community isn't rational. So the mere fact that the community believes something doesn't mean a rational, informed person would.
13. When he gets to the Lemon test, he points out that only has to establish one of the three disjuncts of the test. If it's any of them, it fails and according to the Supreme Court establishes a religion. He focuses on two of them. It violates (1) if it doesn't have any secular purpose at all. It violates (2) if its principal or primary effect advances or inhibits religion. But then he rephrases these and changes them in the process. He changes (1) from not having a secular purpose to having a religious purpose. Something can have a religious purpose and even have an effect of advancing religion as long as it doesn't have no secular purpose as well and as long as it doesn't have one primary effect of advancing religion.
Jones then proceeds to argue that the school board had religious purposes, but he never argues that there is no secular purpose for teaching ID arguments in public schools, just that there's a religious purpose. He does argue that they didn't present a secular reason, but that's still short of showing that none can exist, and all the Lemon test requires is that a secular reason be available. He also never shows that the primary effect is religious, just that some people thought they had a harder time teaching religion to their kids (whether they did or not is not addressed) and that there were conflicts over this in the community (which is not a specifically religious effect).
The worst thing about this is that if the case had been narrowly decided, they could have prevented the genuinely problematic aspects of this case while not prohibiting ID in principle and allowing that subject to be addressed in future cases. The opinion expressly cuts that off by saying it would be a waste of time. Rather than deciding this case, the opinion decides any future case without considering that other cases might be very, very different in not raising any of the legitimate concerns raised in this opinion (not that all of them are legitimate, as should be clear by now). So the Lemon test is clearly not violated by ID teaching in general, even if it might be violated in this case (which I don't think the opinion really shows, if you take the Lemon test to mean what it says rather than how Jones redefines it immediately after stating it). He couldn't write any of this in the "it is ordered that" section, but it clearly establishes precedent for other cases.