Manifest “question-begging” fallacy

Browsing through the common questions section of this website, I was startled to come upon a description of the Biologos approach (or philosophy) that manifestly reveals the “question-begging” fallacy that has bothered me about the approach for so long. In the section comparing EC to ID, the site states unapologetically:

“…we do not see scientific or biblical reasons to give up on pursuing natural explanations for how God governs natural phenomena.”

But this is a textbook “question begging” fallacy. No one (Discovery institute, Ken Ham) would dispute that there must be natural explanations to natural phenomena. The very question is as to whether or not particular phenomena are or are not “natural”. It simply begs the question to state we should seek a natural explanation for natural phenomena.

Methodological naturalism has always been my biggest qualm with EC, and the core reason for my continued skepticism… The method always seemed a question-begging approach that would preclude anyone from recognizing intelligent agency if it were in fact there and detectable.

Now, I’m afraid it simply confirms my suspicions that methodological naturalism is at core an unreliable and fallacious question-begging method, to see it so clearly embraced yet described in such textbook-clear “question-begging” language right on the main Biologos FAQ page.

Can anyone appreciate my concern? Am I missing anything obvious?

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You got all that (see posting at bottom of this post), from one sentence in a FAQ?

I think you should re-calibrate. Let’s go back to that clause:

“… we do not see scientific or biblical reasons to give up on pursuing natural explanations…”

Firstly, I see some balance here: they look at both Science AND the Bible for feedback…

Secondly, when a Creationist says “… animals were created from nothing … End of Story…”, they might reason “we believe we can discover the how of God’s creations…”

This is a simple and straightforward link to the very core of the BioLogos mission: to demonstrate that while God can create things through the miraculous or super-natural way … he can also use natural processes (not SUPER-natural ones) to create the Universe, Earth and even Life.


If phenomena are not natural, then they are outside the realm of science. I don’t see how this is begging the question so much as operating within established parameters and definitions. You think it is “begging the question” to presume methodological naturalism in scientific investigations? Others would just say it is accepting the scientific method when doing science.

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It is question begging to assume (conclusively) that something is in fact a natural phenomenon at the beginning of the investigation, rather than investigating it and then concluding it to be the result of natural phenomena.

For atheist/naturalistic scientists, this is of course the inevitable result of their worldview, they could not choose to conclude some biological phenomenon as the result of intelligent/supernatural agencies without changing their core beliefs.

But for Christians that acknowledge God can and has so acted, it seems contrary to open-minded investigation to “conclude” (conclusively?) at the beginning of any investigation that some phenomenon is decidedly, without question, a natural phenomenon, and therefore demands a natural (“scientific?”) explanation.

On a side point, I have trouble with any definition of “science” that de facto would rule out SETI, archaeology, forensics, or even the examination of humanity’s role in global warming as “outside the realm of science.”

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No, it’s the result of the research method, which does not entertain supernatural explanations as part of scientific hypotheses, by definition.

I think I understand where you’re coming from. The problem with “methodological naturalism” is that different people have completely different ideas about what the phrase even means. Some people understand it to mean that miracles don’t happen, period. Other people only understand it to mean that some things that were previously thought to be miraculous turned out to have a natural explanation after all. Other people take it to mean … oh, spare me, my head is beginning to hurt …

I personally take the line that we should focus instead on factual accuracy and technical rigour. If someone wants to look for evidence of miracles, irreducible complexity, or even modern sauropod dinosaurs, then by all means let them. The only times we should object are either (a) if they are claiming that evidence supports them when it does not, or (b) if their appeal to miracles is first and foremost a get-out clause to let them reject conclusions from the evidence that they don’t like – for example, “appearance of age” type arguments for a young earth. The first is dishonest; the second makes God out to be dishonest.

I explain it in more detail here:



I didn’t get all that from one sentence. As I thought I explained…

I got it from years of reading Biologos and constantly being struck with what always appeared to me to be an underlying fallacy of question begging (or assuming the conclusion) which was for years the core reason I remained skeptical of any conclusions… when someone begs a question in their methodology, they arrive at a predetermined conclusion. It always felt to me for years that the Biologos approach was one of, “we already know this is a natural phenomenon, so we will not consider any other possibility.”

It was just very striking to read the fallacy stated right in black and white in their own self-description… and it confirmed the suspicion I have harbored for years… acknowledging in effect, “we here at Biologos beg the question, concluding phenomena a priori to be natural.”

Hence my objection is not that Biologos says that “God can also use natural processes to create the Universe, Earth and even Life,” (who would object to that?) Rather it is the a priori (i.e. question begging) conclusion that God has used these natural processes to create the Universe, Earth, and even Life, to which I philosophically object. A conclusion that is embraced prior to completing the investigation, and which a priori rules out any competing hypotheses even from consideration.

Christy, it may also be a result of their methods, but my point was simply axiomatic philosophy… I don’t mean to argue the point, but I think it self-evident: If an atheist witnessed a bona fide miracle, they simply could not conclude that phenomenon as the result of a supernatural agency without changing their core beliefs. This isn’t a result of research methods, it is simply self-evident fact. They simply could not conclude supernatural cause without changing their core beliefs and posting the possibility of the supernatural, hence ceasing to embrace atheism.

This fact (and I do maintain this as a self-evident fact) is what makes me simultaneously suspicious of their research methods, which conveniently are also guaranteed to arrive at a naturalistic conslusion.

If someone sets out to look for natural explanations, how are they supposed to avoid assuming they exist? You can look for an natural explanation while also assuming supernatural explanations exist, you just can’t look for those supernatural explanations using science.

Thanks for the link. I’ll read further when I have time, but I generally agree in essence with what you wrote here about “factual accuracy.” I personally am interested in what is “true”. And if some research method, or demarcation of what is or isn’t considered “science” actually gets in the way of being ale to follow the evidence wherever it leads, then that is my core objection. Thanks for the thoughts and the link.

I think God reveals himself in relationship, in person to person encounters, not in chemical codes and microscope slides. Even though I believe in supernatural realities, science isn’t how I can “investigate” God. I investigate God by approaching him as a Person and relating.


Ma’am, appreciate the thoughts… One can certainly use a “working” assumption as a working hypothesis, with a willingness to allow the data to prove or disprove said assumption and follow the evidence wherever it leads. that is standard scientific method. I object to Biologos’ instance of the “unguided” natural hypothesis as the only one allowed to be considered, and what seems an unwillingness to even consider ever allowing that “hypothesis” to be questioned. It seems not a working assumption, but rather an assumed conclusion. This seems contrary to basic scientific method to me.

Agreed - one can’t look for “supernatural” causes with science, this again seems self-evidently true. Science by definition can only explore or examine the natural.

But it simultaneously seems self-evident to me that science (or at least common sense?) can determine if something is the result of “unaided” or “unguided” natural phenomena, or if some phenomenon can better be explained by intelligent agency interacting with said natural phenomena. Hence SETI, archaeology, forensics, etc.

I’ve discussed it here before, but no one objects to SETI as unscientific due to its methods to determine intelligent agency. If SETI actually received a message (say, a long message, clearly in Hebrew), it would be exceedingly odd to maintain Biologos’ version of methodological naturalism and refrain from concluding it as having an intelligent source. They are still examining natural phenomena (radio signals), but can legitimately conclude intelligent agency without making any claim as to the “nature” of that intelligence: natural, supernatural, or otherwise.

Now, if the content of the message claimed, e.g., that the author of the message was the God of Abraham, Isaac, and Jacob, then that, science, as science, could not examine, or how God, if it were God, had supernaturally interacted with said natural phenomena… that would enter the realm of theology/metaphysics. But determining that the message was clearly the result of an intelligent agency rather than unguided natural phenomena, say, a random pulsar, seems to me should unambiguously be within the realm of ”science.”

I can understand how it seems that way, and no doubt scientists are blinded at times by their preconceived ideas and confirmation bias. However, none are more blinded in that fashion than those who automatically exclude as valid anything that does not fit their model.
How would you alter an investigation to fit your ideal? Have you seen this done successfully? I’m not sure in what way it would look different.

It seems to me, methodological naturalism is the way we make sense of the world. When we have a clogged pipe, we call a plumber, if he checks the plumbing and says it is clogged by a demon and he will be praying about it, we call another plumber. If the auto mechanic says the check engine light is miraculously illuminated, we find another mechanic. If the computer tech says the computer is possessed, we agree, shut it down to remove the demonic power and re-boot after saying a little prayer… or maybe not.
Not to be flippant, as prayer does have a part in how we approach problems like these in life, but in the course of daily life we look for and find natural causes for natural occurrences. The same is true in biology, though somehow we as a culture have spiritualized science in ways we have not spiritualized plumbing.


You can call me Christy. :slight_smile:

Yeah this is where I am confused what kind of alternative you are imagining.

If we have a scientific hypothesis, we are pursuing a natural explanation, because that is the kind of explanation science equips you with the tools pursue. I don’t understand how one could possibly have a scientific hypothesis that was open to both natural and supernatural explanations, because, by definition, science is not equipped to investigate the supernatural or entertain supernatural explanations. You cannot arrive at supernatural explanations via science, science is limited. That doesn’t mean that a person pursuing a natural explanation via science must deny that potential supernatural explanations exist. You just can’t arrive at them via science. Are you saying you can?

BioLogos isn’t a person and doesn’t have beliefs, but most people affiliated with BioLogos don’t insist that only unguided natural explanations be considered when talking about all facets of reality. They would probably say that supernatural explanations rely on a different epsitemology and are part of different discourses than science. That doesn’t mean that supernatural explanations can’t be part of our knowledge of the world, it’s just knowledge that is not obtained through science.

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Phil, thanks for the thoughts… certainly concur with your plumber analogy… but on the other hand, appropriate recognition of intelligent agency is also the way we make sense of the world, no?

If your hypothetical plumber was inspecting my house, and I asked him if the plumbing system had been optimally designed, and he said, “there is only an appearance of design, this house and its plumbing just happened to come together by unintentional natural causes,” I would also take issue with this plumber. We appropriately recognize intelligent agency in the design of computer software, house plumbing systems, automobiles, submarines, even rudimentary stone tools and arrowheads. Why am I somehow forbidden from recognizing it, or even postulating it, when I examine a valve, a database, a digital video camera, or an active high-frequency sonar system?


Perhaps I can clarify… I think there is confusion of
whether by natural we mean “as opposed to supernatural”, or if we mean simply “unguided.”

Is a stone arrowhead a “natural” phenomenon? Well, In the sense that it is made of stone, molecules, etc., then sure; just as my iPhone or my collection of Shakespeare on the shelf is a “natural” phenomenon… I could take the book to a lab, they could do chemical and spectrographic analysis, and there is nothing “supernatural” about the book. In this sense of “natural,” I agre with you wholeheartedly… science doesn’t do “supernatural.”

But I mean by “natural” the sense that nature by itself… in its unguided, undirected “natural” process, doesn’t produce arrowheads, or iPhones, or works of plays and poetry. Shakesepare’s sonnets are not a work of “unguided, undirected” nature, they were produced by intelligent, purposeful agency, not by “nature.”

So the alternative I see isn’t between seeking a “natural” explanation vs. seeking a “supernatural” explanation, so much as allowing competing hypotheses of “unguided natural process” and “directed natural process.” If there was supernatural process behind the design of living things, that is certainly logically inaccessible to us, I wholeheartedly concur on that point. But this is different than recognizing it can or can’t be the result of blind, unguided natural processes.

For analogy, if God were hypothetically to supernaturally cause a pulsar to emit frequencies that were received by SETI which unambiguously stated, “I am the God of Abraham…” then I would agree wholeheartedly that the manner by which God supernaturally affected the pulsar would be quite out if the realm of science. All SETI would have “access” to would be the radio waves themselves… a clearly natural phenomenon in the sense of it not being “supernatural,” but just as clearly not “natural” if by that we mean “unguided” or “unintended.” They ought not touch the question of whether it was “supernatural”, but they can and certainly ought to be able to recognize - scientifically - it was intentional and not a product of blind nature.

True enough. And SETI looks for patterns like that, I understand. ( Though truthfully my knowledge of SETI is mostly through The Sparrow, so take it with a grain of salt. )
The question remains, how would you set up an experiment to determine design or intent following something other than natural cause and effect? I think we are left with the philosophical, and certainly on a purely intellectual basis would agree with you, but think it is beyond science to determine.

Not sure if I would say SETI, forensics, archaeology, etc., are “not scientific but philosophical,” but that’s not so important to my thoughts.

As for some scientific method or experiment to determine… one thought… The observation (if correct) that the rarity of functional proteins is in the neighborhood of 1 in 10^70 is certainly compelling to me, and certainly mimics the method used by SETI to distinguish something intentional from the random. If, in fact, there aren’t enough opportunities in the visible universe throughout its entire history to have any remote chance of coming up with one functional protein, much less the hundreds (thousands?) required for life, then there seems very good (empirical? Scientific? Statistical? Mathematical?) reason to believe there is more than simply “natural processes” at work there.

One more thought… if I invited you over to play poker, and after we played 24 hands you noticed that every one of the 12 times I dealt, I dealt myself a royal flush, you’d probably believe I was cheating.

Now, would you say that was strictly a “philosophical” belief? Or would it be something you could say you could back up by some sort of empirical, scientific, or mathematical means? I would suggest it to be the latter, no?

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Well, NOW you are talking.

You will get much further if you stick to the facts… instead of trying to pose some kind of “tragic flaw” or “corrupt” mentality.

I see the complaint you have described as an anxiety that they will get labeled as a bunch of superstitious or airy headed dreamers.

They aren’t “begging the question”… they are avoiding the question.

“Let your conversation be always full of grace, seasoned with salt, so that you may know how to answer everyone.” -Colossians 4:6

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