It's been a while since I spared with my old friend John "buy my book" Loftus, yet I found him on the Dangerous Idea Blog spouting stuff about methodological naturalism, so I thought it would be fun.Loftus distinguishes between Methodological naturalism and Metaphysical.
Paul de Vries described the difference between “methodological naturalism,” which is a disciplinary method that says nothing about God’s existence, from “metaphysical naturalism,” which “denies the existence of a transcendent God.” [Paul de Vries, “Naturalism in the Natural Sciences,” Christian Scholar’s Review 15(1986): 388–96]. The method of naturalism assumes that for everything we experience there is a natural explanation, whereas metaphysical naturalism is a worldview that denies the supernatural realm exists. 
He writes a piece intended to move the reader from commitment to one to acceptance of the of the other. There is significant commitment among theists to Methodological naturalism because that is nothing more than the approach that says only deal with natural causes in scientific statements. Then we are supposed to see the consistency of metaphysical naturalism and feel cognitive dissonance and go "O well I accept it as a method I guess I should ,make it my metaphysic's." Since it is such a transparent approach the answer should be transparent too, but we will get there in a minute.
He establishes the importance methodological naturalism (MN) in science: "Methodological naturalism is the backbone of science. We cannot have science without it. To see this, just think of the extreme position where every question is settled by saying “only God knows,” or “the Bible says it; We believe it, that settles it.” But this importance only emerges as a methodology, whi9ch assumes it's special use contextually. The context we are talking about is science. As long as we can maintain a distinction between science and metaphysics or science and the rest of reality we can maintain the distinction. That's the real problem because the ideology of atheism seeks to reduce knowledge to one thing, their spin on science.
The question of naturalism only arises when it comes to the gaps in our knowledge. Why does it only apply to the gaps? There are many thousands of scientific experiments taking place every single day. In previous centuries those experiments would’ve been testing something on the cutting edges of the science of that day. But because the science of today is considered normal science (ala Thomas Kuhn) Christian defenders don’t raise the question of methodological naturalism about them. 
We don't raise it because we have settled the issue. We understand the distinction between methodology for science and metaphysical/ontological understanding and it's a problem for us. It only entails gaps where atheists fail to understand that if you allow other kinds of knowledge everything is not a struggle with scientist ideology. He's ignoring theology as always so he has no idea of reasons exists for other views. Ironic that he appeals to Kuhn because he somewhat misuses the allusion. It is not that Kun considered science in this age in particular "normal science" as in exemplary form of Science. The science in any age ,however primitive. is "normal science." For Kuhn science is a social construct and works by paradigm shifts so it's not going to supply any kind of metaphysical truth.
Lofuts,,,, ,,,,,,,,,vs,,,, ,,,,,Meta
Loftus makes the assertion that early scientists were Christian:b "Most early scientists were Christians and they used this method in order to discover the facts about the world. Ronald L. Numbers tells us:"
"By the late Middle Ages the search for natural causes had come to typify the work of Christian natural philosophers. Although characteristically leaving the door open for the possibility of direct divine intervention, they frequently expressed contempt for soft-minded contemporaries who invoked miracles rather than searching for natural explanations. The University of Paris cleric Jean Buridan (a. 1295-ca. 1358), described as “perhaps the most brilliant arts master of the Middle Ages,” contrasted the philosopher’s search for “appropriate natural causes” with the common folk’s erroneous habit of attributing unusual astronomical phenomena to the supernatural. In the fourteenth century the natural philosopher Nicole Oresme (ca. 1320-82), who went on to become a Roman Catholic bishop, admonished that, in discussing various marvels of nature, “there is no reason to take recourse to the heavens, the last refuge of the weak, or demons, or to our glorious God as if He would produce these effects directly, more so than those effects whose causes we believe are well known to us.
Enthusiasm for the naturalistic study of nature picked up in the sixteenth and seventeenth centuries as more and more Christians turned their attention to discovering the so-called secondary causes that God employed in operating the world. The Italian Catholic Galileo Galilei (1564-1642), one of the foremost promoters of the new philosophy, insisted that nature “never violates the terms of the laws imposed upon her. .
Loftus should stop here and consider this a good reason to think that science and religion are compatible. Why should there be any further discussion? Because the ideology atheist fundamentalism can't rest until it's the only outlook in the world. Orwellian atheism must conquer all. It is this telos that drives John to ask silly questions: "Why would God create a world where scientists must adopt such a method in order for us to discover the facts of science, which would in turn eventually lead them to think the only causes that exist are natural ones, that supernatural explanations are unnecessary?" Because God never meant for science to be the only form of knowledge?" Perhaps because God is not obsessed with science. If God created us with brains to think and curiosity to spur discovery why would he then turn around and make they job too obvious? That would cheat humanity out of the experience of growth as a species. In fact the rational for my theodicy argument would also answer this question. God wants us to make a personal search for truth so we cam internalized the values of the good.
At this point Loftus falls back on the notion that there is no empirical evidence (he says "objective"). "Even with methodological naturalism God could still overcome it with sufficient objective evidence. The problem is that the evidence doesn’t exist. Christian defenders refuse to admit this." That's a deceptive argument. There is no direct scientific evidence that "proves" God or "disproves" God. In fact it's not clear such evidence would be possible. Any evidence that pointed to God would contradict metaphysic naturalism and thus if method supposedly leaded to meta then no such science evidence for God would ever be coherent. That is not the same as saying there is no evidence for God. There is it just requires a different paradigm. I hate to say it but my book (buy my book) offers that approach and data. 
He tries to rub a little salt in the wounds saying "Just think of the failed repeated attempts to test prayer." I've never seen an atheist answer the empirical evidence of Lourdes. That's been reinforced over the years by new academic work. We knew the double blind approach was wrong for the question because you can't control for outside prayer but the empirical approach has not been answered.
Then he tries to turn the alleged problem into an overall paradigm indictment of faith:
This point is extremely important for to see. Just think if there existed sufficient objective evidence to overcome the method of naturalism and it's clear this is what they are doing. Their problem is that this kind of evidence does not exist, and it should. So in order to maintain their faith, Christian defenders have to complain about it even though scientists have amassed a massive amount of knowledge from using it, knowledge that changed our world. 
To overcome the method of naturalism. "The Method" like there's only one. See the bait and switch? He starts out talking about two methods and now it's one. Somewhere along the way you are supposed to do this black is white slide where Methodology becomes metaphysics. But he has not justified collapsing method into metaphysics for the reasons ai spelled out above. In a metaphysical frame work that is not limited to the ideology of science as the only knowledge there other reasons to believe in God and reasons to understand the major questions about God, reality existence, and knowledge as transcending. This is why it is a true black is white slide because Method and Meta have one thing in common ( both about science) but they are really opposite ends of a spectrum.
The view from within the ideology looks very different, as Loftus says:
It's knowledge gained about things that were once on the cutting edges of science, about things that, if Christians defenders were alive in a previous era, they would've complained how methodological naturalism doesn't leave room for faith, in those very areas where science rolled over faith-based thinking.
Obviously not true since it did. Methodological naturalism left room for faith in Newton's day and Newton's life. He never made such a complaint. The difference is in John's world there is just one form of knowledge, science viewed through atheist lens. In my world there is a large framework that allows for many forms of knowledge and science is in come compartment and in that compartment Methodological naturalism works fine. But it's limited to that compartment. In that sense it helps provide some evidence that ,while it doesn't "prove God," does offer rational warrant for belief.
there were comments on DC I will answer a couple in the comments here.