Ahab wrote: What you are advocating here is that people should practice science in accordance with their preconceived religious views. To apply this to your smoking example above: Theistic scientists can attribute the effects of smoking on lung cancer to the act of some omnipotent being. They don't need to understand the physical mechanism to explain the cancer casuing process. God with His omnipotent powers simply chooses to smite a large numbre of smokers with cancer. And He probably does this because he wants to discourage people from doing something evil like smoking. While atheistic scientists will have to struggle with trying to find the mechanism by which smoking causes cancer. Which method do you think is going to be of value to our knowledge of the causes and cures of lung cancer?I really don't get why you have so much trouble understanding that ID theory as a pseudo-science??? It is just a way to reintroduce pre-scientific explanations into science. You don't have to worry aboout being able to explain how something works, simply attribute it to a divine, omnipotent being - at least if you are a theistic scientist.
1) I have never seen way to demarcate the difference between science and pseudoscience, and am strongly inclined to suggest that there is none. Old joke: What is the difference between science and pseudoscience? Science is funded.
2) There is nothing preventing a theistic scientist from attributing something to a physical process if there is good evidence to suppose that there was one. But a theistic explanation makes sense to me, at least, if given my prior probabilities about God, it is more likely than not that God should want it to happen. When we are forming expectations, we operate in the context of discovery. People can discover ideas about the natural world in their dreams. But then they have to make predictions about what they expect to find true if their theories are correct, and this is the context of justification. If nature confirms their expectations, then their thesis is confirmed, theistic or atheistic. If nature fails to confirm their expectations, then their theory is disconfimed. Many first-class scientists were orthodox Christians, and they didn't always separate their religion from science.
3) Bayesian theory expectations are formed based on prior probabilities, which are confirmed or disconfirmed by experience. But there is no method I know of for assessing prior probabilities. Thus if there is a report that, say, the Virgin Mary has been speaking to young people in, say, Africa, Roman Catholic will want it checked out, but will certainly be prepared to think it's for real if good evidence emerges and it's tough to explain away. A Protestant, who thinks that there's a God and the Mary is Christ's mother, but doesn't expect Mary to be talking to people, will require a higher standard of evidence. An atheist should be the toughest of all to persuade. And the evidence may turn out to be such that Catholics are reasonable in thinking that this is for real, while Protestants and atheists are reasonable in being skeptical. For more discussion on this see www.infidels.org/library/modern/victor_reppert/miracles.html
4) If methodological naturalism is the rule, and it turned out that the bacterial flagellum did come into being as the result of divine creation, then science could never discover that, and would have to say, even though it was false, that there had to be some evolutionary process somehow that produced it, even though there really was none, and God actually did it. This is, to me, a troubling result, that some events should be scientifically invisible if they occurred.