Intelligent Design, the best explanation of Origins

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Intelligent Design, the best explanation of Origins » Philosophy and God » Historical sciences, and methodological naturalism

Historical sciences, and methodological naturalism

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Historical sciences, and methodological naturalism

January 9, 1997
Our willingness to accept scientific claims that are against common sense is the key to an understanding of the real struggle between science and the supernatural. We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door. The eminent Kant scholar Lewis Beck used to say that anyone who could believe in God could believe in anything. To appeal to an omnipotent deity is to allow that at any moment the regularities of nature may be ruptured, that miracles may happen.

Historical science, experimental science, and the scientific method
Historical research is sometimes said to be inferior to experimental research. Using examples from diverse historical disciplines, this paper demonstrates that such claims are misguided.

Richard C. Lewontin who is a well-known geneticist and an evolutionist from Harvard University claims that he is first and foremost a materialist and then a scientist. He confesses;
“It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, so we cannot allow a Divine Foot in the door.”(Lewontin 1997)

Materialism regards itself as scientific, and indeed is often called “scientific materialism,” even by its opponents, but it has no legitimate claim to be part of science. It is, rather, a school of philosophy, one defined by the belief that nothing exists except matter, or, as Democritus put it, “atoms and the void.” 2

Methodological naturalism is necessary for science because science requires that as a precondition of investigating natural things. It is not necessary to elucidate historical facts however. History does not investigate by empirically determining anything. Although history does seek to answer questions about the past, it requires only that the past is rational. Rational simply means that there is a reason. So if something did happen that were an act of God in the past, then as long as that act had a reason, history can investigate it.

The specific complex information of living systems as, well as fine-tuning agents of a life-permitting universe and immaterial truths, etc have causal materialistic dead ends. However, intelligent design is a current observable mechanism to explain the design, thus are an adequate simple causal mechanism to explain these realities of our universe, its fine tuning improbabilities, information, immaterial abstracts, etc. Intelligence can and is a causal agent in the sciences such as forensics, archeology engineering, etc., thus there is no reason to rule out a priori the unobserved designer scientifically. We only rule him out by philosophical or anti-religious objection, which anybody has the free will right to do, but it isn't necessarily true or right to do so, and we can't use science to do so, if we are unbiased, correctly using the discipline. Additionally, to argue non-empirical causes are inadequate would rule out many would be mainstream secular materialistic hypothetical causes as well. It then becomes a matter of preference to the type of causes one is willing to accept and one's preferred worldview has a lot to do with that.

There are basically 3 possible  causing agents of origins and the universe as a whole:

1. The universe and the physical laws: an intelligent creator, or random unguided natural events
2. The fine-tuning of the universe  and the origin of life: an intelligent creator, random unguided natural events, and physical necessity
3. Biodiversity: above three, and evolution

This result means that intelligent design cannot be removed entirely from consideration in the historical sciences.
They are a division of history rather than science, and what applies to history, in general, applies to them. However, evidence must be found to support them.

Let's suppose you have a crime scene. So you call an investigator, He comes, and wishes to start his investigation. The victim has a bullet in her chest. No fire arm nearby. Then you say to him: Friend, in your county its only permitted to infer that the victim died of natural causes. No inference that a murderer shot the victim is aloud. Now write your report  What would you say?

This illustrates why I am against methodological naturalism applied in historical sciences because it teaches us to be satisfied with not permitting the scientific evidence of historical events to lead us wherever it is. Philosophical Naturalism is just one of the possible explanations of  the origin of the universe, it's fine tuning, has no answer about the origin of life, explains very little about biodiversity, and what it explains, it explains bad, has no explanation about essential questions, like the arise of photosynthesis, sex, conscience, speech, languages, morality. It short: it lacks considerable explaining power,  which attracts so many believers, because they think, they do in their life whatever pleases them, no interference from above.

Sean Carroll, in his  book The Big Picture: On the Origins of Life, Meaning, and the Universe Itself.

Science should be interested in determining the truth, whatever that truth may be – natural, supernatural, or otherwise. The stance known as methodological naturalism, while deployed with the best of intentions by supporters of science, amounts to assuming part of the answer ahead of time. If finding truth is our goal, that is just about the biggest mistake we can make.

Scientific evidence is what we observe in nature. The understanding of it like micro biological systems and processes is the exercise and exploration of science. What we infer through the observation, especially when it comes to the origin of given phenomena in nature, is philosophy, and based on individual induction and abductional reasoning. What looks like a compelling explanation to somebody, can not be compelling to someone else, and eventually, I infer the exact contrary.

In short, the imposition of methodological naturalism is plainly question- begging, and it is thus an error of method.

A typical misconception about science is that it can tell us what will definitely happen now or in the future given enough time, or what would certainly have happened in the past, given enough time. The truth is, science is limited in that it does not grant absolute truth, but only yields degrees of probability or likelihood. Science observes the Universe, records evidence, and strives to draw conclusions about what has happened in the past, is happening now, and what will potentially happen in the future, given the current state of scientific knowledge—which is often times woefully incomplete, and even inaccurate. The late, prominent evolutionist George Gaylord Simpson discussed the nature of science and probability several years ago in the classic textbook, Life: An Introduction to Biology, stating:

We speak in terms of “acceptance,” “confidence,” and “probability,” not “proof.” If by proof is meant the establishment of eternal and absolute truth, open to no possible exception or modification, then proof has no place in the natural sciences.

Luke A. Barnes writes:
Theory testing in the physical sciences has been revolutionized in recent decades by Bayesian approaches to probability theory.
Wiki: Bayesian inference is a method of statistical inference in which Bayes' theorem is used to update the probability for a hypothesis as more evidence or information becomes available. Bayesian inference is an important technique in statistics, and especially in mathematical statistics. Bayesian updating is particularly important in the dynamic analysis of a sequence of data. Bayesian inference has found application in a wide range of activities, including science, engineering, philosophy, medicine, sport, and law.  .......and......... historical sciences, including intelligent design theory which tries to explain how most probably past events occurred. That is similar to abductive reasoning :
Wiki: Abductive reasoning  is a form of logical inference which goes from an observation to a theory which accounts for the observation, ideally seeking to find the simplest and most likely explanation. In abductive reasoning, unlike in deductive reasoning, the premises do not guarantee the conclusion. One can understand the abductive reasoning as "instant-deduction to the best explanation".
No one can know with absolute certainty that the design hypothesis is false.  It follows from the absence of absolute knowledge, that each person should be willing to accept at least the possibility that the design hypothesis is correct, however remote that possibility might seem to him.  Once a person makes that concession, as every honest person must, the game is up.  The question is no longer whether ID is science or non-science.  The question is whether the search for the truth of the matter about the natural world should be structurally biased against a possibly true hypothesis.

For, we did not – and cannot -- directly observe the remote past, so origins science theories are in the end attempted “historical” reconstructions of what we think the past may have been like. Such reconstructions are based on investigating which of the possible explanations seems "best" to us on balance in light of the evidence. However, to censor out a class of possible explanations ahead of time through imposing materialism plainly undermines the integrity of this abductive method.
Methodological naturalism is the label for the required assumption of philosophical naturalism when working with the scientific method. Methodological naturalists limit their scientific research to the study of natural causes, because any attempts to define causal relationships with the supernatural are never fruitful, and result in the creation of scientific "dead ends" and God of the gaps-type hypotheses. To avoid these traps scientists assume that all causes are empirical and naturalistic; which means they can be measured, quantified and studied methodically.

The first difference is that historical study is a matter of probability. Any and all historical theories are supported by evidence that is not deductive in nature. We might consider them to be inferences to the best explanation, or Bayesian probabilities but they cannot be deductions. historical theories are not based on experiments, – repeatable or otherwise – nor are historical theories subject to empirical verification. The evidence for a historical theory may be empirical, but the theory itself is not. These differences mean that one cannot simply treat science and history as similar disciplines.

Stephen Meyer, Darwin's Doubt pg.162:
Studies in the philosophy of science show that successful explanations in historical sciences such as evolutionary biology need to provide “causally adequate” explanations—that is, explanations that cite a cause or mechanism
capable of producing the effect in question. In On the Origin of Species, Darwin repeatedly attempted to show that his theory satisfied this criterion, which was then called the vera causa (or “true cause”) criterion. In the third chapter of the Origin, for example, he sought to demonstrate the causal adequacy of natural selection by drawing analogies between it and the power of animal breeding and by extrapolating from observed instances of small-scale evolutionary change over short periods of time.

“Methodological naturalism destroys the truth-seeking purpose of science, dooming it as a game with an arbitrarily restricted set of possible outcomes.” Dr. Paul Nelson  

International Committee of Historical Sciences

In science there are no “facts”, just observations (observations and laws), and explanations (hypotheses and theories). “Fact” is a apologetic or legal term. As far as explanations go in science: “hypotheses” are educated guesses, but “theories” are close enough to the actual mechanism being studied to make accurate predictions. Peter Medawar (AD 1915-1987) Biologist/ Agnostic/ Physiology or Medicine Nobel AD 1960. My favorite Medawar quote is “I cannot give any scientist of any age better advice than this: the intensity of the conviction that a hypothesis is true has no bearing on whether it is true or not”. (Medawar, AD 1979, p. 39). In preparing this dissertation, it struck me that even, the intensity of my conviction that a God hypothesis is true has no bearing on whether it is true or not. There MUST be evidence! Hence, the title of my nearly complete dissertation in Biblical studies: “The Imprimatur Of Our Triune God Is Seemingly Everywhere On A Fundamental Level In Science”. And what is becoming one of my favorite Bible verses: “For since the creation of the world God’s invisible qualities—his eternal power and divine nature—have been clearly seen, being understood from what has been made, so that people are without excuse.” (Romans 1:20, NIV).
Medawar, Peter B. (AD 1979) “Advice to a Young Scientist” (Alfred P. Sloan Foundation Series) New York: Basic Books, Perseus Book Group.

1. Credit to: Steven Guzzi

Last edited by Admin on Tue May 21, 2019 8:20 am; edited 22 times in total


Operation Science and Historical Science

      Yes, historical science can produce reliable conclusions.
      Earlier, I say that scientific methods "vary from one area of science to another."  Some variations in methods are due to differences between operation science (to study the current operation of nature, what is happening now) and historical science (to study the previous history of nature, what happened in the past).  Both types of science are similar in most important ways, especially in their use of scientific logic, but there are minor differences.   /   Although some young-earth creationists try to contrast historical origins science with experimental empirical science (i.e., science based on observations), this is wrong because historical origins science is based on observations so it is empirical.
      Although repeatable controlled experiments can be done in operation science, this is not possible for historical events.  Sometimes, the limitations of historical data provide a reason for caution about conclusions.  But this challenge has inspired scientists to develop methods that reduce the practical impact of data limitations, and historical sciences — in fields such as astronomy, radiometric physics, and geology — are authentically scientific.
      In historical science, one way to "reduce the practical impact" is to use repeatable uncontrolled experiments to gather data.  For example, other pages explain how observations of many Cepheid stars from many parts of the universe have shown that all Cepheids have similar properties, allowing them (and supernovas, which have their own consistencies) to be useful for measuring astronomical distances.  These consistencies let scientists develop reliable descriptive theories, which can become explanatory theories that usually are related to (and are consistent with) explanatory theories in operation science.

Eugenie Scott, director of a pro-evolution watchdog group and a leading critic of intelligent design, makes the case for methodological materialism this way:

Most scientists today require that science be carried out according to the rule of methodological materialism: to explain the natural world scientifically, scientists must restrict themselves only to material causes (to matter, energy, and their interaction). There is a practical reason for this restriction: it works. By continuing to seek natural explanations for how the world works, we have been able to find them. If supernatural explanations are allowed, they will discourage—or at least delay—the discovery of natural explanations, and we will understand less about the universe.

But what if the “natural explanation” for something isn’t the true explanation? What if the true cause for, say, the origin of the universe was a creative intelligence at work? Scott’s case for methodological materialism just assumes that the correct explanations for everything in nature will turn out to be purely material explanations, blind forces. But that’s the thing at issue. Scott is committing a logical fallacy that students are taught to avoid in freshman English—begging the question.

In Darwin’s time, scientists thought the origin of life and the existence of matter were easily explained within the confines of methodological materialism. Now, 150 years later, methodological materialists are at a loss: they can give no adequate, purely material cause for the origin of life or for the origin of matter.

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Methodological naturalism? 31 great scientists who made scientific arguments for the supernatural1

(1) Nicolaus Copernicus (1473-1543), the founder of modern astronomy.
Who was he and what was he famous for? Nicolaus Copernicus was the first person to formulate a comprehensive heliocentric cosmology which displaced the Earth from the center of the universe.
How did he violate the principle of methodological naturalism?
In his scientific writings, Copernicus referred to God as “the Artificer of all things.” The motivation for Copernicus proposing his heliocentric hypothesis in the first place was a theological one. In his great treatise on astronomy, De revolutionibus orbium caelestium (On the Revolutions of the Celestial Spheres, 1543), Copernicus voices his conviction that anyone who diligently contemplates the movements of the celestial bodies will be led thereby to a knowledge of God. In Chapter 8 of the same work, Copernicus even puts forward theological arguments in favor of his scientific theory that the Earth rotates on its axis once a day.



Why Exclude Design as an Explanation?

"Why then the expectation," asked Meyer, "that we will find the answer to the question in naturalistic terms?" Why no consideration, whatsoever, for the possibility of a scientific theory of intelligent design?

"For most scientists," he continued, "there is a perception that the 'rules of science' forbid those types of inferences -- that is, inferences to a pre-existent intelligence." Philosopher of science Nancy Murphey casts the issue in terms of what she thinks science itself seeks, namely, naturalistic explanations for all natural processes. "Christians and atheists alike," Meyer quoted Murphey as arguing, "must pursue scientific questions in our era without invoking a creator." Any reference to a creator ipso facto leaves the realm of science and enters that of metaphysics and theology.

"This is the answer to our question," said Meyer. "Our era is one which proscribes the possibility, which outlaws the possibility of talking about creative intelligence as an explanatory entity within science." But when exactly did this proscription arise? Nancy Murphey, noted Meyer, admitted that the naturalistic definition of science has dominated for only about 130 years. "It's historically contingent," he continued. "Most of biology prior to Darwin was in a creationist framework. Newton and Boyle, during the period of the Scientific Revolution, were quite fond of making design arguments, and not just on the basis of biology, but in optics and astronomy as well."

The issue can be framed as the "categorical opposition" of the philosophical doctrine of methodological naturalism versus intelligent design. Methodological naturalism simply does not admit the possibility of intelligent design. One can accept the theory of intelligent design, of course, but not as a scientific proposition. "Or, as I've heard many times," joked Meyer, "it might be true, but it can't be science."

But is methodological naturalism, asked Meyer, "purely an arbitrary convention?" If so, some people may no longer feel themselves bound by it. On the other hand, if good reasons ground methodological naturalism, "perhaps the 'rules of science' ought to continue as they are."



Scientific research tries to find out what particular hypothesis is correct. In the study of historical events and processes, the scientist’s worldview will influence some types of predictions in fields such as biology, astrophysics, chemistry, or geology

Science always begins with some worldview (or paradigm), even though many  are not much aware of this. Predictions are made, based on the foundation provided by the worldview. This process puts the researcher’s worldview or theory on the line, to be tested. Of course worldviews are not directly tested, but the theories or hypotheses derived from them are tested, one at a time, according to whether accumulating evidence supports them and the predictions are supported.

To use design as a basis for scientific predictions is compatible with the scientific process because it does exactly what science is supposed to do. It puts our theories and hypotheses out in the open to be discussed, to be supported by accumulating evidence, or refuted by the evidence. Some may object to this, but if we  are seeking for truth, why should we not  do it?



Its remarkable that creationism is often accused to put the horses in front of the cart. That is, it pressuposes the bible to be true, and from there, it tries to interprete reality and history to conform with Genesis. Does methodological naturalism not do EXACTLY the same ? It is based on the assumption that only natural causes can and shall be tested. All hypothesis and theories are based on the assumption that creation by God is not a method of causing things into being worth to be considered, because the supernatural is involved, and the supernatural cannot be tested. That is true in regard of operational science, where science tries to find out how something works. But in regard of events of the past, its not justified to consider only a naturalistic world view to formulate hypotheses, and exclude creation a priori.

In many fields, predictions cannot be made. But new phenomenas are discovered, and incorporated into the existing predictions. That are post-dictions. The account of Genesis has been proven true over and over. Archaeology confirms locations and artifacts described in the old testament. Astronomists have concluded that the universe most probably had a beginning, which corroborates Genesis 1. Biologogy confirms that animals produce after their own kinds. Common ancestry has been disproven. Anthropology confirms by way of genetics that there is one human race, and its young. ( thousands , not millions of years old ) Geology confirms that many rock layers were deposited catastrophically, burying fossils within only minutes or hours, which backs up Noah's flood.

All of these are fields of science that confirm the Genesis account. Though the Bible isn't a scientific textbook, it claims to be 100% true and accurate in its account. there is context and culture, so one must employ proper hermeneutics to understand the writers intentions and audience, but the Genesis narrative is written as a historical account and should be read as such, imo.


Butterfield, Herbert. The Origins of Modern Science, 1300–1800, p. viii

Until the end of the Middle Ages there was no distinction between theology and science. Knowledge was deduced from self-evident principles received from God, so science and theology were essentially the same field. After the Middle Ages, the increasingly atheistic rejection of God by scientists led to the creation of materialist secular science in which scientists will continue to search for a natural explanation for a phenomenon based on the expectation that they will find one, instead of settling on a supernatural explanation. This rejection of faith and revelation and the paradigm shift towards the modern evidence-based secular science involving methodological naturalism correlated with a rapid acceleration in scientific discovery that is responsible for the shift from alchemy to chemistry and from astrology to astronomy and developed our comparatively vast knowledge base about that natural word.

It is remarkable how the author creates a false dichotomy. As if Alchemy and astrology would be related to design/creationism, while chemistry and astronomy to science, and as such, implicitly stating, why one is not trustworthy, while the other is. There is no dispute between science and religion. There is a dispute between worldviews. Between the claim that no agency explains our existence, and on the other side, that a creator is the best explanation of origins. Both views can be inferred and deduced perfectly after scrutinizing the evidence observed in the natural world.


Thank you for your kind words. Actually, the article in an earlier form was submitted to two different journals. They were quickly rejected, even as I expected.

About 150 years ago Thomas Huxley and members of a group called the “X Club” effectively hijacked science into a vehicle to promote materialism (the philosophy that everything we see is purely the result of natural processes apart from the action of any kind of god and hence, science can only allow natural explanations). Huxley was a personal friend of Charles Darwin, who was more introverted, and aggressively fought the battle for him. Wikipedia has an interesting article worth reading titled, “X Club.” It reveals a lot about the attitudes, beliefs, and goals of this group.

Huxley said that it was a waste of time to dialogue with creationists. The discussions always went nowhere. His approach was to attack the person, not the argument. He never discussed their evidence in an open manner. Establishing public understanding that science and God were incompatible was his major goal. To discuss anything in an open venue with those looking at science from a religious perspective would only give them credibility. 

Huxley and the X-club members had exclusive control of the British Royal Society presidency for thirteen consecutive years, from 1873 to 1885. Their goal was to convert the society into a vehicle to promote materialism. They succeeded in this even to this day. As such, they were actually pseudo-scientists, placing personal philosophical preferences above honest scientific analysis.

Modern evolutionary science has come to follow this example. If something challenges materialism, it is rejected as false science regardless of its strength. As a “sales tactic” this approach has been effective. Materialists discuss all of the well-known advances and understandings from legitimate science and then claim that they also apply to the results of evolutionary dogma. To challenge evolutionary dogma in any manner is to go against the understanding of the vast majority of scientists across many fields of study. Therefore, evolutionary science is understood to be fact and it is false science even to acknowledge that challengers have anything legitimate to say. Hence, my article is outright rejected, even though it does not mention God, because it clearly indicates that materialism is inadequate. This challenges the true heart of this philosophy that has hijacked science for the past 150 years and continues to this day.

By contrast to the above approach, one proper subject matter of investigation is to determine the scope of a task to be accomplished. Another is to determine the scope of the natural processes available for the task. However, because of the materialistic bias of modern science, it is forbidden on the one hand to talk simultaneously about the biochemical and genomic information requirements to implement a natural origin of life and on the other hand the scientifically observed capabilities of natural process to meet these needs. The chasm is virtually infinite. This is obvious to anyone who looks at it without bias. But, since the goal is to support materialism at any cost, this discussion is forbidden. If the article Dr. Matzko and I authored were to be published in a standard journal, it would open the door for discussion of all of the weakness of evolutionary theory. This possibility terrifies materialists, because they know the scope of the unexplained difficulties they are facing and which they do not want to be known publicly.

Incidentally, I have written a collection of five articles discussing these issues. It is available free online at Article 4 is an 18-page discussion of how Huxley and the X Club turned evolutionary science into a vehicle to promote materialism at the expense of honest scientific investigation. I believe that almost everyone reading this article will be shocked at the deception materialists use by design in their tactics. To them, this is warfare. The easiest way to win a war is for your enemy to be ignorant of your tactics and agenda. So, they disguise their agenda of materialism to make people equate it with science. They have been successful in this.

I also have an active blog online at It challenges anyone who disagrees with anything presented in the Five Articles to explain their basis. In general, I expect very few legitimate challenges. So far, there have been none. 150 years ago Huxley established a policy of refusing to discuss science with creationists in a venue not under his control (i.e., he could attack but they weren’t allowed to respond). Huxley would then viciously attack the creationist personally in an effort to get attention off of their comments. Materialists today still follow Huxley’s approach. Notice the difference: I welcome open discussion. The major science journals run from it.

Materialism vs. Supernaturalism? “Scientific Naturalism” in Context

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