Posted by: N.S. Palmer | August 15, 2013

A Short Course in the Scientific Method

By N.S. Palmer

Let’s have a short review of the scientific method, shall we?

Most people have heard the phrase but have only a vague idea of what it means. It’s something about men and women in lab coats fooling around with test tubes, torturing white rats and such.

Fortunately for white rats, that description is almost entirely inaccurate.

Even scientists, however, often misunderstand the nature of what they’re doing and its limitations. Popular science writers are even worse. So a review of the basics is in order.

How the Scientific Method Works

The scientific method is a process consisting of observation, hypothesis (“suppose that X is true”), testing (“If X is true, then we’ll see Y”), and repeated testing (“Yes, in this case, we see Y” or “No, in this case, we don’t see Y”).

Here’s an example of the scientific method in action:

  • I observe that an apple is red.
  • In the next five cases, I observe apples and they are all red.
  • I form a hypothesis: “All apples are red.”
  • I and other people test the hypothesis under different conditions, in different places, at different times, and with different types of apples.
  • We find one of two things: Either (a) all the apples we look at are red, which confirms our hypothesis; or (b) we find at least one non-red apple, which disproves our hypothesis.

As long as we’re on the subject, notice the different words used in cases (a) and (b). If we find only red apples, that confirms the hypothesis. It doesn’t prove it. There could still be some non-red apples, but we just haven’t found them yet. On the other hand, if we find even one non-red apple, that disproves the hypothesis that “all apples are red.” Then we know that the hypothesis is false.

When a hypothesis has been confirmed by all known observations, we consider it well established. At that point, we might promote it to the status of a generalization, law, or theory. A theory differs from a generalization or law because it doesn’t just summarize observed facts: it also tries to explain them in terms of other facts that we haven’t yet observed. When we go looking for those unobserved facts, we’re testing the theory.

But whether something is a generalization, law, or theory, it’s still only been confirmed, not proven. Even a “law” can be revised or rejected in the light of new evidence or a more insightful analysis.

Human Nature Distorts the Process

Sometimes, new observations aren’t even needed. For broad theories, there are often little observations at the margins that don’t quite fit the theories. In those cases, most people tend to follow the theory. They either ignore the observations that don’t fit, they dismiss them as unreliable, or they try somehow to cram them into the theory so that they fit.

What most people don’t realize is that human beings, even scientists, are not purely dispassionate thinking machines. If they’ve spent years researching and confirming a theory, they’ve got both their egos and years of their lives invested in it. So do other scientists. To question conventional wisdom is to question the validity of one’s own work and risk ostracism by one’s peers. Understandably, and quite reasonably in terms of their own mundane self-interest, most people just don’t want to do that. So even if they have private doubts, they defend conventional wisdom against all comers.

This human tendency isn’t a new thing. You’ve probably heard of the Pythagorean theorem: in a right triangle, the square of the hypotenuse (the longest side) is equal to the sum of the squares of the other two sides. What you probably haven’t heard is that Pythagoras and his followers believed everything could be explained by integers (whole numbers) and ratios of integers (fractions). “Ratio” is where we get the word “rational,” so in other words, the Pythagoreans believed that the world was rational. Note that any whole number can also be expressed as a ratio, such as 15/15 or 1/1.

But Pythagoreans had a terrible shock when they discovered that some quantities could not be expressed as whole numbers or ratios. In particular, if a right triangle’s shorter sides each have length 1, then the hypotenuse length is the square root of 2. The square root of 2 cannot be expressed as a whole number or as a ratio: it is irrational.

And the Pythagoreans did what most scientists do when they run into an observation that conflicts with a cherished theory: They ignored it. They still believed that they could explain the world entirely by rational numbers (integers and ratios), but there was also this “other thing” (irrational numbers) that they just tried not to think about.

The same thing happened at the end of the 19th century. With classical mechanics, essentially a more sophisticated and developed version of Isaac Newton’s worldview, scientists — and pretty much everyone else, if the truth be told — thought that they had the world completely figured out. But there were these little observations at the margin. Odd things that the theory couldn’t quite explain: for example, that according to observations based on the theory, the earth wasn’t moving through space. But even the greatest scientists of the era, such as Lord Kelvin, tried to ignore those results on the assumption that someday they’d be explained.

And Albert Einstein did explain them, but he explained them in a way that the scientific community didn’t like: He said that classical mechanics was wrong.

Einstein didn’t do any new experiments. He just took the marginal observations seriously and came up with a new way of looking at space and time. Most scientists thought he was a crank.* Einstein’s theories didn’t gain wide acceptance until the old generation of physicists died off: I still have a book from the 1930s called Back to Newton, by an old-guard physicist who tried to debunk Einstein’s view. After that, a new, more open-minded generation embraced Einstein’s ideas.

Paradigm Shifts

What happened when mathematicians finally accepted irrational numbers, and when physicists finally accepted Einstein’s relativity theories, is called a paradigm shift. It’s not just a little change in this theory or that theory. It’s a change in our whole way of looking at the world: that is, it’s acceptance of a new worldview.

That worldview provides the context for development of theories about more specific aspects of reality. It provides a foundation for new theories, but it also biases them in the same way as the Pythagorean view and classical mechanics biased people when they were the dominant viewpoints. So even under the new paradigm, there will still be little observations around the margin that don’t quite fit. The process starts all over again.

Sooner or later, those marginal observations lead to a new paradigm that’s slightly more accurate, and then to another, on and on. Reality is infinite, so we never get to the end. What would be the fun in that?

What the Scientific Method Does Not Tell Us

Let’s get back to the example of the apples:

  • I observe that an apple is red.
  • In the next five cases, I observe apples and they are all red.
  • I form a hypothesis: “All apples are red.”
  • I and other people test the hypothesis under different conditions, in different places, at different times, and with different types of apples.
  • We find one of two things: Either (a) all the apples we look at are red, which confirms our hypothesis; or (b) we find at least one non-red apple, which disproves our hypothesis.

So far, so good. That’s all entirely justified and reasonable. But what if we then wanted to draw a further conclusion:

  • We’ve observed apples.
  • Therefore, only apples exist. Grapes, bananas, and oranges are figments of deluded people’s imaginations. Those observations aren’t reliable at all.

In the case of grapes, bananas, and oranges, the suggestion seems ludicrous. But when our reigning scientific paradigm is at stake, it seems much more reasonable:

  • We’ve observed the physical universe.
  • Therefore, only the physical universe exists. Thoughts, feelings, near-death experiences, and psychic phenomena are figments of deluded people’s imaginations. Those observations aren’t reliable at all.
  • Oh, and by the way, you’re an idiot if you take those things seriously.

That last point is usually implied rather than stated explicitly. But it’s clear from scientific materialists’ hostile response that more is at stake than just facts and theories. Their egos are involved. They’ve spent years of their lives looking at the world in a certain way. They’ve written books and articles about it. They’ve taught it to their students. Their professional reputations and their self-respect are on the line.

What if they were wrong?

That’s a very uncomfortable thought, so in fear and frustration, they push it away and denounce anyone who brings it up.

Our Current Paradigm Misleads Us

Our current paradigm sees the world as matter and energy. Period. Nothing else exists. Thoughts, meaning, and “information” are redefined out of existence, cast instead as configurations of matter and energy. For doing physical science, that paradigm has a certain utility. But there are those observations around the margin: first and foremost, the fact that each of us is conscious and knows it. There are also things like near-death experiences and psychic abilities. Under the reigning, materialistic paradigm, you can “explain those things away,” but you can’t really explain them adequately.

So for the most part, people who are committed to the reigning paradigm — who have invested their self-esteem and years of their lives into the reigning paradigm — simply try to ignore conflicting observations. And they get rather upset when people suggest that the reigning paradigm might be mistaken.

The stakes are high. Remember the earlier discussion about observations to test a hypothesis? No matter how many observations you make, you can never conclusively prove a theory, once and for all time. But even one single conflicting observation, if you take it seriously, can disprove a theory. If any of the little observations around the margin are true, then our dominant materialistic paradigm is wrong.

What the scientific method tells us is valid and important. It describes, analyzes, and enables us somewhat to control the physical universe.

What the scientific method does not tell us is that “only apples exist.”

If someone believes that only apples exist, or that only matter and energy exist, that conclusion is not based on the scientific method. It’s based on an act of faith. It should be recognized as such.

  • Einstein won a Nobel prize not for his relativity theories, which most people didn’t believe, but for his work on the photoelectric effect.

Copyright 2013 by N.S. Palmer. May be reproduced as long as byline, copyright notice, and URL ( are included.


  1. Hm. It seems you’ve also described how most people cling to their political views.

    • I hadn’t thought of that connection, but you’re right! Thanks, Jim.

  2. Reblogged this on artsy sciency intrigue.

  3. The method that you refer to seems very similar to the syllogisms used in traditional logic.

    • David,

      An interesting idea. I confess that the similarity eludes me, but maybe I’m taking the word “syllogism” too literally.

      If you mean the general methods of informal logic, yes, I can see that. Thanks!

  4. […] A Short Course in the Scientific Method ( […]

  5. Noah,

    Thanks for this thought provoking post. As a Christian I believe in a spiritual reality that overshadows the physical world we live in. Initially I believed this because that is what I was taught. Since then I have had many experiences that defy scientific explanation which have confirmed the reality of a spiritual dimension. These experiences have led me to truly believe in God and in a spiritual realm.

    For example: I spent several month in Africa. During that time I participated in several crusades/meetings in very remote parts of Kenya . During some of those crusades I saw things that defied scientific explanation. One time we prayed for a man who was obviously blind. He had a obvious blue/gray film completely covering his eyes. As we asked Jesus to heal him his eyes cleared. He started excitedly talking about all the things he could see including details from a Paw Paw tree several hundred feet away when minutes before he had to be led to the front of he crowd by someone else. I still struggle to believe what I saw happen even though I physically saw it (I am an engineer by trade so tend to think logically to a fault). Can this be explained “scientifically?” No, but it did change that man’s belief system as well as strengthen mine. Just because we only see a limited part of something doesn’t mean that that is the only “thing”/reality that there is.


    • Jet,

      It’s great to hear from you again! Thank you for that wonderful and inspiring story.

      I also have seen too many things I can’t explain to accept the conventional wisdom of a materialist worldview. And I sense an underlying goodness in this world that reassures me in the face of so much horror and evil that we see with our physical eyes.

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