Of Science and Faith: The Scientific Method, A Positive Look

by Jim Pemberton

We often hear about how science is based in reason, but we aren’t often taught precisely how this works. We know something of the scientific method, but we don’t know how it relates to logic. We only have some sense that it does. We have come to the part of this series on Science and Faith where I will discuss how the scientific method is based on deductive logic in general.

Of Science and Faith

There’s no need in this series to handle all the various forms that the scientific method takes, so this will only be a general discussion. It will involve the common steps and how each works together to produce a reasonable conclusion.

I had planned to discuss the limitations of the scientific method, indeed the process of scientific discovery, in this article as well. However, it occurred to me that there is simply too much material for one article, so I decided to split up the material.

The scientific method that you all learned in grade school is a good summary of it. The basic steps are as follows:


Preliminary Remarks

The word evidence is used for any of these, but evidence is a broad term that is part of both the Observation and Experiment categories. One thing that evidence isn’t is the conclusion. Evidence contributes to the conclusion, but it is not the conclusion. Many people refer to evidence as being proof of the conclusion. Evidence never leads to conclusion on its own and is never “proof” of anything. It is nevertheless important.

The conclusion is always the last thing. The reason I mention this in the preliminary remarks is to point out that many are tempted to start observations with a conclusion in mind. In fact, most scientific endeavors have a desired conclusion in mind. The good scientist is able to keep a desired conclusion from inadvertently skewing observations and experimentation. Not all scientists are good scientists.


We all experience the world around us. Given training in certain fields of science, scientists are trained to make educated observations in their fields. These observations follow a couple of patterns. One is calculated observations. For more mathematical sciences, this may involve simply sitting down with paper and pen and make formulaic theories. A scientist might also sit down and plan a structured observational event. A zoologist might plan a trip to the field to observe a certain type of animal and obtain data on its migratory habits for example. This leads to a more organic kind of observation. Something happens to be discovered and scientists are contacted to make trained observations on it or a scientist happens to be in the field gathering random data and notices a pattern (s)he wasn’t expecting.

The education of a scientist is important here. In making educated observations assumptions from the education, training, experience, and worldview of a scientist will be employed in order to categorize the observations accurately and effectively. These assumptions will be used throughout the process of following the scientific method.

Using the example of the light and the light switch from before, observation entails walking into a room and carefully looking at the things in the room. A window might be open, a chair turned to the side, the room illuminated from something other than the window, a rug on the floor, a switch on the wall, etc. A scientist might notice that the illumination of the room, aside from what is coming through the window, is coming from some devices on the ceiling. Some debate might ensue as to the source of the light from the devices on the ceiling. A careful observer will notice that the switch on the wall is able to be manipulated. When it is manipulated, the light from the devices on the ceiling changes its state.


From the observations a scientist makes, a sense of related occurrences can be noticed. From these occurrences, a relationship can be speculated. This relationship will be stated in a specific way. This specific way is called a hypothesis.

The hypothesis from our light switch example may be something like this: Whenever the light switch is up, the lights from the ceiling are on. This can be expressed in terms of a syllogism, although scientists don’t necessarily take the step to convert it to a syllogism. Since we have already used it as an example of a syllogism from last time, we know that the syllogism is something like this: If the light is on, then the light switch is up. As explained before, this is how a causal relationship fits into a conditional syllogism.


The scientist will then set up an experiment to test the hypothesis. That is to say that the logical correlation will be noted carefully. Not always will a scientist be able to manipulate one or both of the events, but as those events occur, their occurrences are noted for patterns of correlation. In setting up the experiment, a quantifiable measurement of success must be built into the experiment.

In our example, the scientist notes that the light switch can be manipulated and there are multiple devices on the ceiling, 4 to be precise. Success is determined when each device shows light whenever the switch is manipulated to the ‘up’ position. As a ‘control’, the windows are also monitored to see if the state of light coming from them changes when the switch is manipulated. The manipulation is set up to occur, say, 25 times. Any observation that the lights are on when the switch is not up are also catalogued.


The experiment is conducted as planned and the results noted for each light in the ceiling and for each window. These results are analyzed using the criteria established from the beginning. So what comes up is generally a percentage representing a likelihood that the hypothesis is true. Very low percentages are typically deemed to be proof that the hypothesis is false. Very high percentages are typically deemed to be proof that the hypothesis is true.

In our example, we have no observation that any of the lights are on when the light switch is down. We have no observation that the light from the windows changes. However, we observed that each time the light switch was manipulated to the “up” position, the lights in the ceiling usually came on. (Interestingly, it was noticed at this time that when the light switch was manipulated to the “down” position the lights in the ceiling went off. This was not part of our original experiment, so we can’t count it, but we can include it in a future experiment.) The exception that occurred is that after 11 times, one of the lights stopped turning on. So there are 14 counts of the light switch not affecting one of the lights. The conclusion therefore is that we have 86% likelihood that the light switch affects the lights.

Final Remarks

In order to be seen as acceptable science in the scientific academy, two or three other things must happen. It should be published with peer review, and in accordance with continuing peer review, it must be confirmed by another group of scientists repeating the experiment to verify the same results.

Now this was a ridiculously simple experiment. There were some key concepts that it didn’t cover. Nevertheless, we covered the basic nuts and bolts such that what I hope is understood is that the scientific method follows the pattern of deductive logic, that the testing results in a likelihood that the deductive syllogism is set up.

In the next article, I will discuss some of the limitations of scientific discovery.


About jimpemberton

Christian, maverick minister, husband, father, jack of all, master of none. I pay the bills controlling production for a laboratory casework manufacturer.
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10 Responses to Of Science and Faith: The Scientific Method, A Positive Look

  1. parsonsmike says:

    When a conclusion is put forth as a truth, it isn’t necessarily a truth. Sometimes, the observation stage is incomplete, and the evidence is therefore incomplete, leading to a false assumption, or to a hypothesis that is skewered by a bias or biases, known or unknown.
    To use the light switch analogy. Let us say that a scientist comes to my house. There is a light switch by my driveway door that turns the kitchen’s overhead light on. Every time he flips it up, the light goes on. Every time he flips down, the light goes off. He confidently declares that whenever the switch is up the light is on. And whenever the switch is down, the light is off.

    He assumes he has all the evidence he needs. he has made his observations [stage 1], he has put forth a hypothesis that the light is always on when the switch is up [assuming there is power from the breaker box and a working light bulb in the socket], stage 2. He has tested his hypothesis by flipping the switch up and down on various days and at different times [stage 3] and so he concludes his hypothesis is correct [stage 4].

    But he is wrong.
    After reading his paper, I invite over one last time to my house. I show him my kitchen overhead light and he observes it is off. So he declare the switch is down. He walks from my front door, through my kitchen and is dismayed to find the switch up. “Is there power?” Yes. “Is there a working bulb”? Yes. “Then there must be a short in the line.” Nope. “Nope? Did you rewire the switch?” Nope. And then I turn the light on with the other switch. The OTHER switch.

    Now any decent scientist would not be fooled by this way of setting up a circuit. Most would be familiar with it. So in reality, this example would probably fool no one. But it is an analogy to what scientists are doing with evolution and age of the earth theories.
    They do not have all the evidence, and in fact are finding new evidence all the time. They can’t observe the actual event, they can’t repeat the event. And yet they stand DOGMATICALLY on their “scientific conclusions”!

    And in my opinion what is worse, is that Bible believing men and women, who declare the Bible to be God’s Word, stand DOGMATICALLY with them.

  2. jimpemberton says:

    That’s a great observation, parsonsmike, and well said. You already see the direction I’m going with this and I’m going to discuss some of these things in the next article.

  3. Ken Hamrick says:

    This is very educational, Jim. I have a friend named Fred who is a genetics scientist of some sort, and a professed Christian (although he believes in evolution). Somewhere in grade school I had been taught that a hypothesis, if it proves correct, gains the status of a theory; and a theory, if proven correct, becomes a law. Fred insists that a theory such as evolution is a proven fact and a theory at the same time. Since he’s a scientist, then the misunderstanding about the progression of “certainty” of these categories must be mine. but maybe you can explain it better for us.

    Thanks for putting the time and effort in to produce this series.

  4. Pingback: Of Science and Faith: The Scientific Method, Limitations | SBC Open Forum

  5. One of the problems that I encountered with the scientific method, when I was writing my Master’s Thesis in American Social & Intellectual History, was that it did not cover all bases. In other words, it was lacking what I call a synthetical approach. By that I mean that the method is ill equipped to deal with a situation involving more than one situation, e.g., where both the thesis and the null hypothesis are true, that is, truly reflect given situations and conform to the requirements of verifiable truth. In other words, when the rule is true, and the exceptions are also true, then the truth consists of both the rule and the exceptions and it must reflect that reality. Our present day scientific method suffers from the paralysis of analysis; it needs a synthetical element, an element which allows for at least two seemingly diverse matters to be considered as true and reflective of the next step in further understanding. I remember about eight years ago telling a science educator, a lady who was head of science education of a county school system and who was working on her Ph.D. in that field at the University of North Carolina, Chapel Hill, about the problem, and she looked at me in amazement and asked: “How did you know that?” In other words, how did a dumb Baptist preacher know about something they were only discussing in her science education classes? I explained, of course, that some forty years earlier I had run into the problem. We need to be more sensitive and aware of the developments in thinking, especially as they involve such basic realities as the present day scientific methodology which has such an impact on our lives. We are now living in the Information Age, and knowledge is beginning to increase at an exponential rate. We are also on the verge of going to the stars. Indeed, the late Ben Rich, former head of the Skunk Works of Lockheed which developed the stealth aircraft, stated that if E.T. should visit us and need a way home, we are equipped to help him. He even spoke of vehicles that are faster than the speed of light, and that a year before a physicist came out with a theory for such travels. One science educator even spoke on the matter of exceeding the speed of light by a factor of 200. All of which means that we need an intellectual understanding commensurate with our presently developing society. Our Lord said, Mt.24:31, He would gather His elect from one end of (The. Definite article in the Greek) heaven to the other.. and the promise in Rev.7:9 is that the number of the redeemed will be a number that no one can number. Such numbers suggest that mankind could and, indeed, might well be already expanding to the stars and that we might have as many as a thousand generations and as much as 900,000 years before the curtain comes down. Perhaps, the most neglected doctrine in the Bible is the Present Coming, the Spiritual Coming of our Lord, to His people (Jn.14:18,28).

  6. jimpemberton says:

    Dr. Willingham,
    Thanks for your comment. Any philosophical error in formulating the preconditions for scientific discovery will result in conclusion that aren’t logically supported. The way that two apparently contradictory things can be both true are because misconstrued categories are applied to understanding the issue. This happens enough in theology, but scientists typically lack the training to identify these things.

    The availability of information on the Internet seems to be an inverse ratio to people being able to employ it wisely if they understand it at all. Perhaps the reason is that poor reasoning and bad information is made at least as available good information. In fact, I would argue much more so. It is often difficult and time consuming to sort through the mounds of baloney to get to the nuggets of prime cuts when doing investigation on the Internet. It requires much discernment that seems to be in short supply.

  7. Dear Brother Pemberton: I am aware of the arguments for logical consistency. Dr. Gordon Clark was perhaps one of the most salient advocates of such a view. However, the beginnings of the scientific method trace back to a fellow who, I understand, stated that if both the rule and the exceptions are true (the latter proven so by observation, etc. and the former perhaps by revelation or reason), it follows that both the rule and the exceptions constitute the truth. Whether he was responsible for that statement or not, it is noteworthy that a number of Calvinists (i.e., R.B. Kuiper, J.I. Packer, et. al.) have presented instances of paradoxes, and as I discovered from six years of research in church history that the biblical truths are, indeed, paradoxical and, hence, have a built in correction system for God’s people, a feedback system, to borrow language from one of the fields of engineering. In any case, it was my finding that a both/and approach to a truth which has two parts, apparently contradictory, fits nicely with the right and left hemispheres of the brain, providing for the objective and the subjective, reason and intuition and/or emotion which enables the believer to be balanced, flexible, creative, constant, and magnetic or, in short, God’s best subliminal advertisement for the Gospel, a mature Christian believer. Even when the believer is in the situation of utmost humiliation, being mistreated, tortured, and even executed, he or she might well have the winsomeness that converts the person administering the torture.

    I might further observe that my view developed from writing a thesis in intellectual history in which I found that the null hypothesis was also true, that is, could be supported and confirmed by observable facts, and, hence, the truth was both the hypothesis and the null hypothesis. The like was confirmed in my researches in church history, concerning various doctrines that consist of two poles. While I like logic and note that it is used in the Bible, even to the point that a technical term is set forth in Roms.12:1 which could almost be transliterated, it is not logical consistency that the Bible sets forth as the final understanding. Indeed, because it has this both/and methodology, believers have often failed to grasp the truth presented and have made a mess of things. Forcing a seemingly opposed idea to be consistent with the one rather arbitrarily selected (the one that appeals to a person’s mental make up the most) will, in effect, produce differences which eventually bring down the original position, producing, this pendulum swing effect that troubles human history (from one extreme to the other). There is a five step process for avoiding such a mistake, and it involves the recognition of the rule and the exceptions, avoiding the trap of the paralysis of analysis which inevitably brings on the reaction leading to the other extreme.

  8. jimpemberton says:

    Dr. Willingham,
    I agree with your assessment of logic in that its usefulness is limited by our ability to use it. There are perhaps two areas in which we fail. One is sin. That is I agree with Van Til regarding our propensity as sinners to suppress the truth by intellectual means. Although the Holy Spirit enables us to acknowledge the truth of the gospel and recognize the glory of God, we do struggle with many tangential issues as we plod along in our sanctification entertaining sins we are both aware of and are not yet aware of.

    The second is the limitations of our feeble minds. We could submit ourselves to careful study for the entire history of the world and still lack something that would help us understand God more fully. I don’t think God is unreasonable, only that we lack the ability to reason well enough to understand fully. Nevertheless, God has presented himself well reasonable enough that we can understand what we need to of him in this life.

    A Muslim apologist I spoke with at length in London turned to the common objections to the Trinity. One challenge he made was that Allah was simple to understand and the Christian God was not. It occurred to me to point out to him that simplicity was no proof of truth. We believe the revelation of the Trinity because it was important enough for God to tell it to us, not because it is easy or difficult to understand. He had no answer to it for he paused to think of an answer and instead changed the subject.

    It occurs to me that God gives us certain theological tensions, paradoxes if you will, for at least a couple of reasons. One is to focus our attention on what is important. If we find a paradox and struggle on the debate one to another then we miss the only possible harmonization between the two. Indeed, God has used debate between theological movements throughout history to help us mature in our thinking and lock in on precise definitions. The Arian and Nicean controversies are a great example of this. The tension between the sovereignty of God and human responsibility is dissolved when we realize that our responsibility is to submit to God’s will precisely because we haven’t been.

    The second is to train our minds. That is to say that we are a people of many different cultures and schools of thought. One of the things that helped the spread of the gospel in the Roman empire was that the communication of the one gospel could be adapted to all manner of cultures. The result was that a core identity that transcended the immediate culture was established through the gospel. When the gospel is syncretized with local religions, it loses both the ability to be adapted and the ability to unify. It is the truth of God revealed through the gospel that trains the minds of those who believe when it encounters people who struggle to understand it from a lesser worldview. Worldly cultures pass on sets of categories that perceive some of the revelations of scripture as paradoxical. Accepting apparently contradictory facts as both true requires one to adopt a different way of thinking. This different way is not illogical, though it may seem so in one’s culture of origin. Learning a different system of categorization has a cascade effect on one’s thinking and it influences his or thought regarding other things that are seemingly unrelated. In today’s secular culture, for example, it is commonly believed that people are basically good (except, ironically, those of us who understand that people are basically sinful). Of course, we understand this to be a suppression of the truth, especially when unbelievers demonstrate that they don’t believe this when they call for the punishment of someone they think is basically evil. Nevertheless, they think it’s contradictory that a good God would cause evil in a world that is basically good. What they call good and what they call evil are different than what the Bible calls good and evil. When their good and evil categories become redefined according to the Bible, the contradiction disappears for them.

    And so in these ways logic is above us, but is also incrementally accessible. We may reason, and should, for that was the pattern of the Apostles. However, it was also the pattern of the Apostles to carry God’s authority and we are called to do the same. Authority as a practice (not our authority, but that we point to the authority of God’s special revelation to us) is for more pragmatic than mere logic. We seem to be built innately to understand authority more than logic though good reason is always warranted.

  9. jimpemberton says:

    There is some relationship between theory and hypothesis. However, hypotheses aren’t necessarily explanatory. Theories are explicitly explanatory. There is a claim that theories are well-substantiated, but that claim often overlooks the fact that well-substantiation in science is often synonymous with consensus. The dirty little secret is that consensus is often driven by political motives, both from the need to obtain funding as well as through academic enforcement of a worldview that relies on unsubstantiated presuppositions. Take the big bang theory, for example. By definition a theory must be testable. Do you know anyone who can test the big bang? I don’t. So why do scientists hold the big bang as a theory? The reason is because they have been academically cowed into it. Let a scientist challenge it and see if (s)he gets funding.

    Laws are a different story. My physics professors all taught that laws were self-evident and scientifically unprovable. The distinction between “self-evident” and “scientific proof” is perhaps lost on most people, even science teachers.

    As for the theory of evolution being a proven fact, it’s such an interdisciplinary school of thought that a) there’s no way it can be tested as a theory, and b) there’s no one scientist that understands it. Fred’s specialty being genetics might gain him understanding of genetics, but he hasn’t studied the other disciplines like he has genetics. He’s relying on the experts in geology, paleontology, physics, etc. He’s been told that it’s been proven by the sum of all these experts and that he needs to organize his efforts and analyze his data assuming that it’s a fact. If he looks at how much the field of genetics knows compared to how much it doesn’t know, he would have to admit that it doesn’t necessarily add up to evolution. In fact, the thing that genetics hasn’t demonstrated in any measure is that random genetic mutation by the means we have observed is in any way sufficient to explain the creation of information necessary to account for the diversity of life that we have. In his own discipline, he doesn’t have the evidence. He’s been told that when added to the other evidence, molecules-to-man evolution is proven. The problem is that we actually have compound doubt. In each field there is enough doubt that the evidence that proponents of evolution say should support evolution should be held in enough doubt to question the explanation of evolution to account for it.

  10. Pingback: Of Science and Faith: Resuming the Series | SBC Open Forum

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