This post is intended to brush away the foundational strawmen in the EvC debate and explain exactly what Science is and what it is not; what a theory is and what it is not; what the theory of evolution claims and what it does not. Hopefully, after reading this post, it will be clear that some creationist arguments are against strawman claims, and others are irrelevant as a challenge either to science in general or evolution in particular.
Science is an attempt to understand the universe. We do this by constructing intellectual models of the universe. We call these intellectual models "theories." Theories are not the universe, nor do scientists believe that they are.
The universe is made up of things (particles, waves, forces, objects, etc.) with properties (mass, frequency, force, etc.) which interact with one another. Call the information about these things, properties and interactions "facts." A series of facts connected in time is an "event."
We look at things in the universe and define these facts and events. We notice that certain events occur over and over fairly regularly. Sometimes exactly the same, sometimes with occassional variations. We notice which facts seem to control these events. We define a rule that says that whenever certain (initial) facts occur, certain events occur. This rule is a theory.
So, the universe is made up of things, and science is made up of rules. They are connected only by the idea of facts and events.
Science is the collection of all accepted theories. The practice of Science is the elimination of bad theories. What makes a bad theory? A rule that does not work is a bad theory: "I can fly if I tie a towel around my neck" is a bad theory. An unprovable rule is a bad theory (not because it is necessarily false, but because it is useless in terms of the principles of science): theories about paranormal phenomenon are bad theories as long as they are untestable under scientific conditions.
An overly complicated theory is bad if there is another simpler theory which explains the same events. Scientists call this KISS (Keep It Simple, Stupid) principle
Occam's Razor. This is not because it is less likely to be true, but because the purpose of a theory is to model the universe -- to set down rules to allow us to understand what to expect. The simpler the rules (provided they work) the easier it is to understand.
Because of the preference for simpler rules, and also because of the fact that Science is built up imperically from observations rather than being handed down from on high as a completed reference tool, Science is incomplete. Not every "thing" in the universe is explained by an accepted theory. There are anomalies.
There are two kinds of anomalies. The first kind is a "thing" whose facts are not impossible, but for which there is no "likely" explanation. An example is a snowball in an active volcano. There is no scientific reason why a snowball cannot exist in a volcano, but there is no reasonable explanation how it could have gotten there. If it has been there, why hasn't it melted? If it has been melting, how large was it to begin with that there is still a remnant. If it just got there, how? Did someone toss it in? where did he keep it until then? Did it just "magically" or "miraculously" appear? The fact that we can't "scientifically" explain its presence does not negate its existence. Neither does its existence negate the general usefulness of the theory it appears to defy.
The second kind of anomaly is an "event" which violates the rule or theory. The "failure" of the
Michelson–Morley experiment is this type of anomaly. This kind of anomaly actually leads to an advance in Science. First, there is an understanding that the current theory has limitations, and that outside those limitations it may not be valid. Second, there are advanced new theories to explain the anomaly. The new theory must not only explain the anomaly, it must explain why the results given by the old theory are correct within its limitations and incorrect outside them, and ideally it should describe other situations outside the limitations of the old theory and predict events that would be anomolous to the old theory. In the case of the Michelson–Morley experiment, the new theory propounded by Einstein is the one we call "Special Relativity."
So pointing out anomalies of the first type is totally irrelevant to the validity of the theory, and pointing out anomalies of the second type only defines the limits of the theory; it does not invalidate it.
Remember, an accepted theory is the simplest theory that works. It does not claim to be the complete set of rules. When you are teaching someone chess, you explain the normal movement of each piece. The more unusual moves, such as castling or
en passante capture of pawns is left until after they have learned the basics. These rules correspond to "event" anamolies. Likewise, chess puzzles usually start in mid-game. But it might be difficult or even nearly impossible to re-construct the earlier moves that lead up to the position. These correspond to "thing" anamolies. Neither of these anomolies invalidate the basic rules of chess.
So Science leaves out God and miracles not because it is an "atheistic religion," but because even if it is conceded that they exist and that they affect the "things" in the universe, to try to include them in the rules is to introduce a complication that is not necessary in understanding the vast majority of events.