Life-Altering Fallacies and How to Avoid Them: Science and Critical Thinking

For many years, I lived under a misconception — perhaps even a delusion.

I believed that scientists commit to pursuing the truth in an objective and unbiased way; that they strive to apply critical thinking in the scientific process.

Boy, was I wrong!


Eye-Opening Experiences

My confusion was understandable, considering my early love for mathematics and the sciences. Having studied electrical engineering and medicine, I developed a working knowledge in several scientific disciplines, including mathematics, physics, chemistry, biology, and medicine; throw in amateur astronomy just for fun. Throughout my training, I had learned to think of science as an objective pursuit of knowledge.

Things started to unravel during the two years before medical school. While studying biology, I had trouble understanding how natural selection could explain big gaps in the development of different species. Additional courses in biochemistry and genetics uncovered complexities at the molecular and cellular level that could not be explained by natural selection. I checked book references and looked for evidence, but I could find none. The uncomfortable part was that while I saw these inconsistencies, my teachers and fellow students accepted them without question.

During my years practicing medicine, I found a shift occurring in how critical thinking was applied, or rather, not applied, in areas that were politicized: abortion, birth control, euthanasia, and child-raising by same-sex couples.

While attending a family medicine review course, I was astounded to find the presenter, a physician representing the Academy of Family Physicians, spoke of pregnancy as a disease state. Somehow, in the previous years, I had missed the transition in medicine that took us from thinking of pregnancy as a natural, healthy process by which a child came into the world, to a condition that increases morbidity and mortality over the non-pregnant state and requires suppression through the use of birth control. I realized, then, that we were in a major philosophical shift.

A year ago, I watched Ben Stein’s Expelled: No Intelligence Allowed! This film revealed how scientists and administrators have worked to destroy the career of any colleague who even considered intelligent design as a valid area of inquiry. Those who did so would lose funding for research and their faculty position. I had never read any of the intelligent design literature, but from my own perspective, it seemed like a reasonable hypothesis. Regardless, I had trouble understanding the degree of hostility. What was going on here?


Intelligent Design

Intelligent design is not difficult to understand. We process and recognize intelligent design unconsciously all the time. We identify it whenever we recognize an order or arrangement that suggests purpose. For example:

  • You find a bracelet with engraved designs when digging in the garden in your back yard. Do you assume that this jewelry is man-made or the result of a natural process? Why?
  • You’re walking in a canyon in the Southwest and come across carvings in the canyon wall that look like hunters and animals. You interpret these as petroglyphs created by an ancient native people rather than due to the random action of wind and water.
  • An archaeologist uncovers square, block-like structures in the clay. Is he more likely to assume these are natural formations or something designed by people?


Scientist Michael J. Behe, the author of Darwin’s Black Box, further defines intelligent design:


Design is simply the purposeful arrangement of parts.1


For discrete physical systems, if there is not a gradual route to their production—design is evident when a number of separate, interacting components are ordered in such a way as to accomplish a function beyond the individual components.2


Here are some observations:

  • The intelligent design concept does not come from religion.
  • The concept does come from our brain’s ability to distinguish order and patterns and interpret these through our experience.
  • Intelligent design is not creationism — a belief that the earth was formed only about 10,000 years ago and arising from the interpretation the Genesis account of creation as a scientific record.


Critical Thinking

Critical thinking is the discipline of forming concepts, analyzing observations, and developing reasoned arguments in a way that is clear, accurate, relevant, logical and fair.

The Foundation for Critical Thinking outlines nine elements one can use as a standard for assessing the quality of one’s analysis: clarity, accuracy, precision, relevance, depth, breadth, logic, significance, and fairness.3

Critical thinking is common in everyday life, but for most of the routine decisions we make, it’s not exercised to a high degree.

Some things, however, call for higher levels of critical thinking, such as:

  • Scientific studies that lead to conclusions about the laws of nature.
  • Information that can lead to policy changes in business or government.
  • Legal cases that result in judgments and penalties.


Critical Thinking about Intelligent Design

Because intelligent design seemed a reasonable concept, I decided to investigate how and why it has drawn such a critical response from the scientific community. I have searched out professional articles and books offering criticism of intelligent design, and I’m still looking, as the volume of material is enormous. As yet, I have failed to uncover a single argument that would stand up against the criteria of excellence for critical thinking.


Here is a summary of the kinds of errors I’ve uncovered:

1. False assertions and premises.

2. Irrelevant assertions.

3. Favoring opinion over an examination of the data.

4. Using the possibility of an alternative pathway as justification to reject

a hypothesis. (If this were a valid approach, no hypothesis could stand.)

5. Circular reasoning.

6. Applying different standards to similar data.

7. Using methodological naturalism to exclude any data that does not fit with its

philosophical position.


It’s this last error, I believe, that is THE main reason why scientists do such a poor job of exercising critical thinking in certain areas. What is methodological naturalism?


The Fallacy of Methodological Naturalism

To understand methodological naturalism, we first need to understand the scientific method. The scientific method is the systematic observation and measurement of phenomena in nature and through experimentation where one forms hypotheses and then tests their accuracy. It is open to any observable reality. If a scientist observes something that does not appear to follow natural law, he does not assume it is supernatural (acting outside of known natural laws), but he also does not exclude it.

Methodological naturalism begins with a position that excludes supernatural causes, regardless of observations. It’s inherently atheistic, based on a philosophical position or worldview that there is no God who can influence the natural world. While one cannot decisively prove or disprove an infinite God’s existence through direct observation and experimentation, we can discover evidence of his action. Methodological naturalism decides to ignore this evidence without examination. Restated, current scientific philosophy requires scientists to ignore certain data. How is that objective?

What we are seeing here is the modern day version of the trial of Galileo. Galileo asserted a heliocentric solar system, with the sun, and not the earth, at the center. He was placed on trial and told to recant because his findings did not agree with the philosophy of the day — that the earth was at the center. Today, scientists are placed on trial and branded heretics if they bring forth data that does not support the atheistic position.

Of course, indoctrination by a system based on this bias can blind one to its influence. For my part, I believe it is better to consider all the data and possible scenarios rather than to exclude the ones you don’t like, and in this case, the ones that could strengthen one’s recognition and belief in God’s action.


1 Michael J. Behe, Darwin’s Black Box, New York: Free Press, 2006, p. 193,

2 Ibid, p. 194.

3 Linda Elder and Richard Paul, “Universal Intellectual Standards,” The Critical Thinking Community, October, 2010, accessed July 8, 2017,




2 thoughts on “Life-Altering Fallacies and How to Avoid Them: Science and Critical Thinking

  1. Very enlightening! I also have wondered about the way we practice some medicine. For example, why do doctors in med school never learn NFP methods, even though it would prepare them for problems in women’s health? I’ll definitely have to look more into things like you mentioned!


    1. In principle, physicians are not opposed to NFP. However, they take a pragmatic approach, thinking birth control as easier and more effective. They also have a bias against NFP, so that no instructor will make more than a passing mention of it. The same kind of bias, sadly, has eliminated discussions about abstinence. You would be shocked to hear pediatricians in adolescent health ridicule abstinence discussions while they express great enthusiasm for pushing birth control on pre-teen girls. My own experience has been that about 5% of women show interest in pursuing NFP. Conversations with my pediatric patients are quite positive as long as I broach the subject before they become sexually active. I think the percentage of women interested in NFP would be much higher if the medical field and our culture did not push artificial contraception so vehemently.


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