The logical simplicity of the scientific method
In the debate and discourse involving the theory of intelligent design (ID), we inevitably run up against a difficulty in the definition of science. Intelligent design advocates hold, among other things, that historically, the institution of science has relied upon ‘the inference to the best explanation’ as the criteria for determining which theory best explains a given body of evidence, and is thus given reasonable consideration and treatment. As a result, in some of my own debates, I have heard ID proponents being accused of opening the door to all manner of metaphysical nonsense. This is not the case.
In my opinion, what the leading proponents of ID have failed to do is offer a clear alternative definition of science that incorporates the legitimate aspects of the current convention, as well as consistently incorporating new evidence within a design paradigm. If that is to be accomplished, we must re-examine science so as to uncover what science actually is. In the process, I propose that there is a clear and distinct definition of science that has always existed. This proposed definition satisfies both of these requirements.
Rather than expanding the definition of science to allow a more liberal methodology prone to philosophical abuse, the proposed definition would actually be a conservative motion which restricts science to more rigorous and disciplined criteria, particularly where the empirical world relate to our philosphical lenses.
Etymology: Middle English, from Anglo-French, from Latin scientia, from scient-, sciens having knowledge, from present participle of scire to know 1: the state of knowing : knowledge as distinguished from ignorance or misunderstanding ( http://www.merriam-webster.com/dictionary/science )
log·ic Pronunciation: \ˈlä-jik\
Etymology: Middle English logik, from Anglo-French, from Latin logica, from Greek logikē, from feminine of logikos of reason, from logos reason — more at legend
Date: 12th century 1 a (1): a science that deals with the principles and criteria of validity of inference and demonstration : the science of the formal principles of reasoning (2): a branch or variety of logic <modal logic> <Boolean logic> (3): a branch of semiotic; especially : syntactics (4): the formal principles of a branch of knowledge ( http://www.merriam-webster.com/cgi-bin/dictionary?logic )
The law of contradiction (also known as the law of non-contradiction) is the philosophical foundation of scientific methodology and where science begins. As such, the law is our only basis for the bricks and cornerstones by which we proceed. It is also the capstone by which we can look back and examine our progress and thereby detect missing or misplaced stones. With the law of contradiction we begin, build, and test our theories regarding our empirical impressions of the natural world.
In this way, science is accomplished only when a test for contradiction has been performed. If, for example, scientific testing reveals a contradiction, then the accuracy of our ideas is held to be in question. We are forced to believe before we begin the journey, that the empirical world is ordered logically and coherently and is intelligible to us only if our analysis is also coherent and therefore compatible with the assumed order. This point begs to be repeated; if nature is ordered in an intelligible, logical, and coherent fashion, then our philosophical constructs (theories) regarding it, must also be coherent if they are to be compatible with the assumed empirical order.
Many in the scientific community claim that science is primarily a search for empirical evidence. Susan Kruglinski, the editor of Discover Magazine reported that, “since the scientific revolution of the 16th and 17th centuries, science has been limited to the search for natural causes to explain natural phenomena. This revolution entailed the rejection of the appeal to authority, and by extension, revelation, in favor of empirical evidence. Since that time period, science has been a discipline in which testability, rather than any ecclesiastical authority or philosophical coherence, has been the measure of a scientific idea's worth”.
That is fascinating since coherence is both the authority that founds science, and the revelation given by the scientific method. Natural science is the application of the law of contradiction to the empirical world. Science itself is really only our faith in logic and coherence. The term empirical is a corruptive and deceptive label that conjures images of material certainty. This is not the case! The empirical world is only one of the entities in a natural science equation, and it must be measured against our ideas in order to provide a tested result. Empirical evidence just is. If we interpret it without the lens of philosophical coherence (i.e. logic), then we are only declaring our bias by ecclesiastical declaration.
Listen to further commentary by Susun Kruglinski in explaining the scientific validity of intelligent design theory: “After a searching review of the record and applicable caselaw, we find that while ID arguments may be true, a proposition on which the Court takes no position, ID is not science.” 1
That is also fascinating! How can something true be unscientific, unless science is not true, logical, or coherent?
Scientific testing is done with the assumption that ‘cohering two or more entities into a systemic whole is a reliable scientific method’. Coherence is the only objective revelation and authority. Logic does not give us the prerogative to smuggle in our own bias. Scientists cannot simply assert by ecclesiastical authority that empirical evidence is proof of anything without first having faith that our philosophy (theory) is coherent. I am afraid that the only cure for this situation is omnipotence (which we dare not claim).
C.S. Lewis pointed out the illusion of a purely empirical or natural science in his book’ Miracles’.
He said, “…Unless human reasoning is valid, no science can be true. It follows that no account of the universe can be true unless that account leaves it possible for our thinking to be a real insight. A theory which explained everything else in the whole universe but which made it impossible to believe our thinking was valid, would be utterly out of court. For that theory itself would have been arrived at by thinking, and if thinking is not valid that theory would, of course, be itself demolished. It would have destroyed its own credentials. It would be an argument which proved no argument was sound -a proof that there are no such things as proofs- which is nonsense.” 
Logic was the first science, and upon this rock we build our towers and move mountains. Natural science came after the acceptance of the validity of logical reasoning by which to study the natural world.
Scientific Reasoning vs. Religious Reasoning?
The conflict between science and religion is not over the existence of God because the terms God and reality are synonymous. Both are absolute, ultimate, and sovereign. The question is really one of God’s (or reality's) characteristics. Is reality a living being or merely an impersonal material force? Whatever or whoever reality is; reality is God by definition. It is what it is or I am who I am. The only difference between the philosophies of naturalism and monotheism is the nature of God. All reasoning is philosophical. Whether we use inductive or deductive reasoning (and we rely almost exclusively on deduction) contradiction and coherence are what we seek in order to verify or refute premises and conclusions.
Definition of God / 1capitalized : the supreme or ultimate reality 
It matters not whether our philosophy is monotheistic, pantheistic, polytheistic, atheistic, etc. The deist philosophizes that Theo (God) has left the building. All philosophy is theistic. Even the agnostic is in the same boat, since his philosophy purposely excludes deciding the question of Theo. To put it plainly, without theism, there is no such thing as an agnostic. The absolute character of reality (irrespective of its/his other qualities) does not give us the option of excluding ourselves from philosophizing about Theo.
Moving on to more difficult terrain, our current definition (or convention) of science is called Methodological Naturalism. It says that ‘only material explanations are scientific'. It asserts and exalts this philosophical position, yet is itself not a material explanation, and thus, cannot be stated with internal coherence. In fact, it is imposed without any logical authority whatsoever. It is an ecclesiastical proclamation.
Our current definition of science says that 'only material explanations are scientific' though that definition is itself only a philosophical proposition. So, if philosophical propositions are not scientific, then neither is the philosophy of ‘methodological naturalism’. Can a naturalist prove that methodological naturalism is scientific? Actually the answer is yes; but, only if he/she uses the law of contradiction. But as C.S. Lewis points out, it is not coherent and self destructs.
More from Susan Kruglinski’s report: “This self-imposed convention of science, which limits inquiry to testable, natural explanations about the natural world, is referred to by philosophers as "methodological naturalism" and is sometimes known as the scientific method. Methodological naturalism is a "ground rule" of science today which requires scientists to seek explanations in the world around us based upon what we can observe, test, replicate, and verify.” 1
Naturalists cannot predetermine where logic can and cannot lead us without contradicting themselves. The objective authority of scientific revelation is found in the power of logical coherence. The whole purpose of science is to lead us wherever logic will go without bias. If logic is valid, and science is logical, then methodological naturalism cannot be what science is.
Listen to how Paul Davies (theoretical physicist / Arizona State University) admits the real history of science, yet still dodges the implication. “The worldview of a scientist, even the most atheistic scientist, is that essentially of Monotheism. It is a belief, which is accepted as an article of faith, that the universe is ordered in an intelligible way.
Now, you couldn’t be a scientist if you didn’t believe these two things. If you didn’t think there was an underlying order in nature, you wouldn’t bother to do it, because there is nothing to be found. And if you didn’t believe it was intelligible, you’d give up because there is no point if human beings can’t come to understand it.
But scientists do, as a matter of faith, accept that the universe is ordered and at least partially intelligible to human beings. And that is what underpins the entire scientific enterprise. And that is a theological position. It is absolutely ‘Theo’ when you look at history. It comes from a theological worldview.
That doesn’t mean you have to buy into the religion, or buy into the theology, but it is very, very significant in historical terms; that that is where it comes from and that scientists today, unshakably retain that worldview, as an act of faith. You cannot prove it logically has to be the case, that the universe is rational and intelligible. It could easily have been otherwise. It could have been arbitrary, it could have been absurd, it could have been utterly beyond human comprehension. It’s not! And scientists just take this for granted for the most part, and I think it’s a really important point that needs to be made.”
So science is faith. And it is faith in logic. And that is a very interesting observation since now we must remember that, any logical equation or test requires at least two entities (or witnesses). The coherence of at least two entities becomes the third element in the equation. Assuming the entities involved achieve coherence, then theory + evidence = knowledge. All scientific observation is therefore triune in principle. There is no escaping this reality. No claim is scientifically valid without the testimony of at least two witnesses or variables. If an idea is not testable, repeatable, observable, and falsifiable, it is not considered scientific. All of those qualities assume the law of contradiction to be valid and are dependant upon its application.
 C.S. Lewis / Miracles / Chap 3 The Cardinal difficulty of Naturalism pgs 21,22
 Paul Davies / The Privileged Planet Q&A segment