On Methodological Naturalism...

Methodological Naturalism- "Science can only appeal to natural laws and physical entities as explanations of observable phenomena."

As a skeptic, I usually find many anecdotes of all sorts of strange phenomena. From alien abductions, to ghost stories, to faith healers, etc., people love to make up all sorts of extraordinary claims for very simple every day things that happen to them. For example, a person may be feeling a bit sick one day, so he decides to go to church and be prayed for. He then returns home, goes to sleep, and finds that in the morning, he's feeling much better. Would it be reasonable to say that it was the fact that he was prayed that which made him feel better? Is it simply ok to jump to the conclusion that God miraculously healed him? Not really. Take him to a doctor and you will more than likely get a perfectly natural explanation. Most diseases/viruses, etc. are self-terminating. Your body's immune system naturally fights them off, if given enough time. No need to invoke any sort of supernatural entity in order to explain your sickness going away.
And this is the nature of science, it deals with the known, physical world. Appeals to the supernatural are simply unnaceptable, and for good reason. One simply does not invoke miracles in order to explain anything, because a miracle is not an explanation at all. It is what Dawkins calls "A non-answer". The problem of appealing to the supernatural, or to the extranatural is that you are simply answering a mistery with a mistery. For example, in my home island of Puerto Rico, there have been reports of animals found dead with two 'vampire-like' holes in their necks. Many people then have invented a creature to explain these mysterious deaths, they call it "El Chupacabras"
The problem with using this as an explanation is that no one has ever confirmed the existence of this Chupacabra creature. So when you ask "What is going on here with these animals", the reply is "We dont know, but we think it may be this creature called El Chupacabra.", which then begs you to ask the question "What is el Chupacabras?", to which they will reply "We dont know". So in essence, you're back to square one. Nothing has been explained at all.

For every day, common things, we should all be extremely weary of appeals to the supernatural or appeals to the extraordinary for explanations. When someone tells you the reason you got Pink Eye is because a Demon has entered your body, you're better off ending the conversation right there and going to a doctor. It doesn't mean that the supernatural does not exist, it just means that science does not deal with that area, science is confined to the observable and testable, something which clearly the Supernatural is not, and so in the scientific way of doing things, the natural explanation is always the best one.
However, what happens with much 'bigger picture' type questions about the nature of the universe?

"Given the limitations placed by methodological naturalism, science is sometimes pushed into odd corners. Consider the discovery of finely-tuned cosmological constants, including each of the coupling parameters for the four fundamental forces. If any of these twenty or so constants had been slightly different, life would impossible anywhere in the universe. Most agree that this discovery requires an explanation. Under methodological naturalism, when physicist Lee Smolin explains fine-tuning by positing a vast multiverse of possible universes each with different values for these constants, he’s doing science. When astronomer Owen Gingerich explains the very same observations by means of purposeful design, he’s doing religion. This is at best an artificial demarcation. As archeology and the search for extraterrestrial intelligence (SETI) project show, design is an explanatory concept already used in science. Nonetheless, the only scientifically acceptable explanation of fine-tuning at present is an undetectable multiverse. Cosmologists must therefore pursue this hypothesis to win grants, publish papers, and get tenure, even if supernatural design happens to be the right answer. As this example shows, methodological naturalism is actually in conflict with realism. In order to hold scientific realism, one must believe that theories are generally reliable indicators of truth. But if there is a choice between naturalism and truth, methodological naturalism forces science to choose the former. Once science is limited to certain kinds of entities, it can no longer follow the data wherever it leads. It is forced instead to beat the data until it offers a naturalistic confession."

"Another problem for methodological naturalism is that no one knows what sort of explanatory resources science will need in the future. One can bet that we will never need to use design, but that’s a prediction, not a discovery or an inference from established truths. Many of the expectations of late-19th century physicists were dashed by general relativity, quantum mechanics, and chaos theory. Instead of limiting our explanatory resources, we should allow scientists the latitude to employ whatever entities best explain the phenomena. " (Kopersky)

My opinions on this are mixed. Firstly, it seems to me like holding a dogmatic naturalist position in the sciences would eventually mean that science would completely be of no help if it indeed does turn out that it was God who created the universe. By simply saying "Science deals with the natural, not the supernatural", science has confined itself to a box, and as Kopersky says, it would mean scientists would no longer be able to follow the evidence wherever it may lead.

However, I have an issue with his statement "we should allow scientists the latitude to employ whatever entities best explain the phenomena."
Whatever entities? This takes me back to the first part of this blog, in which I explained that appeals to the supernatural seem to not ever bee adequate explanations for anything. Up to this day, the very best explanations for everything we know about the universe have been perfectly natural explanations. We no longer need to appeal to the 'Chariots of the gods' in order to explain why the planets revolve around the sun. We no longer need to attribute 'the god's anger' whenever there's a thunderstorm or a tornado, but instead, we can adequately explain these things by our observation of weather patterns, etc.
My main argument against this is simply that we should use history as a guidepost in order to judge the adequacy of a type of ‘God of the Gaps’ argument. Every single known instance in which the supernatural has been invoked as an explanation for any sort of phenomena has been wrong, thus, why should we believe any appeal to the supernatural will ever be right in the future?

"What if the right explanation for some phenomenon is supernatural? It doesn’t matter. Under methodological naturalism, the best naturalistic explanation is the best scientific explanation, and via realism, we take that explanation as true. Given that there is little if anything that science does not purport to explain, methodological naturalism plus realism implies that nearly every phenomenon has a true, naturalistic explanation, at least in principle."

If we are going to be honest about finding truth, wherever it may lead, we should recognize when it is that we are letting our metaphysical assumptions about the universe get in the way of investigating. If we assume a priori that there is no God, is it possible that we will then develop a method of investigation (the Scientific Method) that because of its very nature, will exclude the very possibility of finding evidence for a deity? In essence, won't we be finding what we're already looking for in the data, rather than letting the data speak for itself?

What are your thoughts?