This the second part to my series on science. Here are the other parts: Part 1, Part 2, Part 3, Part 4, Part 5, Part 6, Part 7, Part 8, Part 9, Part 10, and Bibliography.

Methodological Naturalism:

Another attempt is methodological naturalism. Its criteria are nearly the same so criticism of one will not be repeated. It posits any religious explanation of the phenomena is inherently more improbable than that of a naturalistic explanation.
(1) is not testable,
(2) is not falsifiable,
(3) does not make predictions,
(4) does not describe repeatable phenomena,
(5) does not explain by reference to natural law,
(6) does not cite a mechanism,
(7) does not make tentative claims, and
(8) has no problem-solving capability.
They have also claimed that it is not science because it
(9) refers to an unobservable entity.

i) Stephen Meyer criticisms of this are that it can’t adequately demarcate science:

The demarcation question has long been a vexing one. Historically, scientists and philosophers of science have thought that science could be distinguished by its especially rigorous method of study. But attempts to define science by reference to a distinctive method have proven problematic because different branches and types of science use different methods. For example, some scientific disciplines distinguish and classify natural entities, while others attempt to formulate overarching laws that apply to all entities. Some disciplines perform laboratory experiments under controlled and replicable conditions, while others attempt to reconstruct or explain singular events in the past, often based on field studies of evidence or clues rather than laboratory experiments. Some disciplines generate mathematical descriptions of natural phenomena without posting mechanisms to explain them. Others look for mechanisms or explain law-like regularities by reference to underlying mechanisms. Some scientific disciplines make predictions to test theories,
while others test competing theories by comparing their explanatory power. Some disciplines use both these methods, while some conjectures (particularly in theoretical physics) may not be testable at all. And on it goes…..
An episode in the history of science illustrates the problem. During the seventeenth century, a group of scientists called the ‘mechanical philosophers’ insisted, based largely on advances in early chemistry, that scientific theories must provide mechanistic explanations. Such explanations had to involve one material entity pushing or pulling another. Yet in physics, Isaac Newton (1642–1727) formulated an important theory that provided no mechanistic explanation. His theory of universal gravitation described mathematically but did not explain in a mechanistic way, the gravitational attraction between planetary bodies—bodies separated from each other by miles of empty space with no means of mechanical interaction with each other whatsoever. Despite provocation from the German mathematician Gottfried Wilhelm Leibniz (1646–1716), who defended the mechanistic ideal, Newton expressly refused to give any explanation, mechanistic or otherwise, for the mysterious “action at a distance” that his theory described. Did that make Newton’s theory unscientific? Strictly speaking, the answer depends upon which definition of science someone chooses to apply. Today one would be hard-pressed to find anybody who denies that Newton’s famous theory qualified as scientific. For example, some critics of intelligent design have argued that it fails to qualify as a scientific theory because it makes reference to an unseen or unobservable entity, namely, a designing mind in the remote past. Yet many accepted theories—theories assumed to be scientific—postulate unobservable events and entities. Physicists postulate forces, fields, and quarks; biochemists infer submicroscopic structures; psychologists discuss their patients’ mental states. Evolutionary biologists themselves infer unobserved past mutations and invoke the existence of extinct organisms and transitional forms for which no fossils remain. Such things, like the actions of an intelligent designer, are inferred from observable evidence in the present, because of the explanatory power they may offer. If the demarcation criterion of observability is applied rigidly, then both intelligent design and materialistic theories of evolution fail to qualify as scientific. If the standard is applied more liberally (or realistically)—acknowledging the way in which historical scientific theories often infer unobservable past events, causes, or entities—then both theories qualify as scientific. And so it goes with other such criteria as well. There is no specific (non-question-begging) demarcation criterion that succeeds in disqualifying the theory of intelligent design from consideration as a scientific theory without also doing the same to its materialistic rivals.

ii) What’s even more hilarious is the criticism of “it posits unobservable entities” while they use propositions to make their universal statements. Such statements are not observable by the senses. No one couldn’t even predicate if we accept this view of science.

iii) Do not be fooled by its apparent appeal to neutrality. Alvin Plantinga gives the example of a Christian practicing altruistic behavior as a genetic defect (as a possible interpretation on methodological naturalism), but, as a Christian, this is not why Christians show altruistic behavior.

iv) This is methodological instead of evidentiary. This means it only is circular. The explanation is scientific if it is natural. That entails it isn’t the evidence that leads one to the conclusion, but his definition. That his position isn’t derivative from the evidence.

v) It reduces all scientific explanation to possible explanations given the assumption that God doesn’t exist. As Hays has said “Another consequence is that methodological naturalism reduces scientific explanations to hypothetical explanations rather than true explanations. The secular scientist is merely claiming that, “This is how we reconstruct natural history if we exclude supernatural considerations.”
That’s not driven by the empirical evidence. That’s not reconstructing the past from the natural record alone. Rather, that’s a hypothetical narrative, which you arrive at by bracketing supernatural considerations.”

vi) In its attempt to avoid discussing ontology and metaphysics it ends up making statements about ontology. It really ends up a trojan horse that sneaks in metaphysical naturalism. Some have noticed this trick, for example, Steve Hays said:

But methodological naturalism generates yet another conundrum. If a “historian” or “scholar” adopts methodological naturalism, then he thereby forfeits the right to classify miracles as improbable. For probability is a metaphysical concept. It involves a claim about the nature of the world. Yet what supposedly distinguishes methodological naturalism from metaphysical naturalism is the ontological neutral of methodological naturalism.

In that event, methodological naturalism is debarred from treating supernatural events as any less probable than natural events. There can be no antecedent presumption one way or the other.

But in that case, a “historian” or “scholar” who applies methodological naturalism to the Bible can’t very well claim that any other explanation, however unlikely, is still more likely than a supernatural explanation. To do so would smuggle in metaphysical naturalism under the guise of methodological naturalism.

Yet if methodological naturalism can’t properly treat a supernaturalistic interpretation of events as any less likely than a naturalistic interpretation of events, then what conceivable warrant does it have to invariably favor a naturalistic interpretation to over a supernaturalistic interpretation? Logically speaking, it should be equally open to both possibilities.

Simple method:

Some think science is just a method. In its basic structure, it has only a few steps.
1. Make observations.
2. Propose a hypothesis.
3. Design and perform an experiment to test the hypothesis.
4. Analyze your data to determine whether to accept or reject the hypothesis.
5. If necessary, propose and test a new hypothesis.

This view is rather common: Scientists should only go into the world and collect the facts indiscriminately and come to unbiased views, and that we have a fact-theory distinction. This would seem to indicate that facts are rather brute and uninterrupted as if these facts organize themselves. There is good in this, in the sense we do have facts: the sun exists, there’s a rock, etc. The issue is that facts are theory-laden. When we start explaining these facts, we come to different conclusions. A naturalist interpretation almost always differs from a young earth creationist interpretation. The facts are always interpreted by worldviews. They do not speak on their own; they are “mute” as Cornelius Van Til called them. Imagine if I tried to convince you that a house is haunted and that Ghosts are there. As for a Naturalist, they couldn’t accept that evidence. That worldview excludes that possibility. I may tell you that there are rattling chains, people getting poked, appearances, groans of terror, etc. It doesn’t matter what evidence I provide. We have presuppositions, and they are not falsifiable by experience.

This also seems to indicate that scientists go out and collect facts indiscriminately. “Indiscriminately collecting facts” is rather odd. If I went around with a ruler, indiscriminately measuring the length of sticks out in the woods, a scientist would wonder why I’m doing this. Scientists go out and purposefully collect facts. Just like in history we find that the president giving the Gettysburg address is more important than what James Penrose, out in the crowd, had for breakfast. It’s just that facts are not all equal.

It also returns to the notion of neutrality. I will quote Dr. Greg Bahnsen to show it just simply couldn’t be the case.

Furthermore, the place where a man goes to secure or look for evidence indicates a certain prejudice toward the answer expected to a question on his part from the very outset. Also, what a man even considers ‘factual’ will be determined by his outlook or philosophy (e.g., the materialist and Buddhist will disagree from the start of an argument). Moreover, we note that the very formulation and styling of an argument require that a man has his final conclusion in sight even from the outset in order that the argument is structured to move to the proper end; the predetermination of conclusion significantly governs the formulation of premises. In The Structure of Scientific Revolutions, Thomas Kuhn clearly exhibits the non-objective character of science when it comes to foundational questions. He says that the scientist views the world through a model or arranging-picture; he has a paradigm that defines the scope and methodology of the science using it. The world becomes a totally new place when the paradigm is altered; even sense data and its interpretation are governed, qualified, and determined by the model. In 1931 Kurt Gödel pulled the rug out from under the supposed neutrality of logic in the same way that Kuhn later made scientific or factual neutrality look suspicious.
Gödel developed a theorem that demonstrated the impossibility of formulating a consistency proof for any system of logical calculus (with its signs and rules of inference) within that system.Hence different systems of logic are selected for reasons other than objective logical argument. Against this background, it should come as no surprise that the Christian and unbeliever do not and cannot approach their differences with argumentative or philosophic neutrality. Even though the Christian and the non-Christian have the facts of the objective world in common, they have radically divergent interpretations of them. For the Christian, all facts are pre-interpreted by God, created by God, and revelatory of God; they must be handled in such a way that glory is brought to God. But the non-Christian views these facts as meaningfully interpreted only by his own mind, as uncreated and free from God’s control, as ambiguous and contingent; he uses them to bring glory to man. Hence the Christian and non-Christian have different interpretative schemes. Even when the believer and unbeliever share the same rules of logical inference, they nevertheless can be said to have different “logics.” For the believer and unbeliever differ as to the use, significance, ground, and authority of these rules; basically one subordinates logic to God while the other does not. One views logic as rules of thought implanted in man’s mind by the Creator; the other sees logic as the self-sufficient, self-authenticating tool of autonomous man’s reason. One founds logic in God; the other founds it in itself. The Christian places God’s authority above considerations of logical possibility or his own human use of logic; the unbeliever places abstract possibility above God. Since the fall of man was ethical in character (not metaphysical), the unregenerate and regenerate share the facts of the world and the rules of thought, but their interpretation and use of them are far from neutral.

This very method of science is antithetical to the Christian worldview. It presupposes that God does not have an interpretation of every fact of our experience and that we are not thinking God’s thoughts after him. Dr. John Frame even shares Dr. Bahnsen’s thoughts

Though not written from a Christian perspective at all, Thomas Kuhn’s The structure of scientific revolutions is extremely helpful in destroying the myth of the alleged ‘objectivity’ of science. Non-Christian science is widely deified and worshiped, but it is more vulnerable now than it ever has been for the last four hundred years.

Frame continues and begins to criticize the scientific method, as he tells us the “check out the facts” type of view is over-simplistic and just isn’t the case. His first criticism is that the instruments scientist use are theory dependent tools. He also points out science is not just collecting facts but also “analyzing and evaluating data.” The issue, then, also is how to categorize them. What method or criterion do we use? This is where one’s subjective thoughts may be used to organize them. Dr. Frames continues to tell us that scientific theories go beyond the data. Such as when laws of science are often claimed to be universal. Lastly, he mentions that scientists don’t just throw away the theories they have when it produces contradictory results. They often adjust the theory or they call such datum a “problem” to be solved within their own conceptual scheme. Until other theories come about that look more promises, these abnormalities continue multiplying. It also does not take into account simplicity such as the gremlin story from before.
The problem also has to do with its simplistic outlook on induction. It leaves it open to philosophical problems like the “Paradox of the raven.”
This has nothing to do with Edgar Allen Poe. The problem arises that the proposition  “All ravens are black”  is logically equivalent to  “No black thing is no raven.” This is called contraposition (conversion of and all A is B to all not-B is not-A.). This problem was discovered by a Philosopher named Carl Hempel that was thinking about a purely formal theory of confirmation.

When you’re just looking at things in your room at home you are verifying that all ravens are black. Without even studying Ravens. You are looking at these non-black things and they are non-raven. This view of science doesn’t go far enough.  The study of the facts of the world has to be relevant to the thing studied. We will discuss the other problem of induction later. It is important to remember these things as I will be going to post-Kantian philosophers. That means you should look back at the influence Immanuel Kant had on the philosophy of the time.