Methodological Naturalism Revisited

As requested, I’ll outline my objection, please let me know if/where you would be interested in further expounding or where you might push back.

So, regarding methodological naturalism (MN)…

  1. Simply, I find it is begging the question. If one starts by excluding from consideration anything but a strictly naturalistic conclusion, it is unsurprising that one will arrive at a naturalistic conclusion.

  2. It interferes with a straightforward pursuit of truth. Does anyone object, in principle, that “follow the evidence wherever it leads” is a better scientific methodology rather than “follow the evidence if it leads to certain conclusions but certain other conclusions are verboten”?

  3. If there is any doubt that this is simply a classic, textbook “question-begging” fallacy, I direct you to Biologos’ own self-description on the main page… I see no way around this, the wording of the fallacy is obvious and textbook to me. As I discussed on another thread…

“…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.

This is clearly begging the question, i.e., “sneaking” the conclusion into the premise. Many here seem to think it justified, due to limits of science, etc., but it remains question begging nonetheless. Perhaps it is clear to illustrate: If I were a detective investigating a death, and proposed it to be an intentional homicide, rather than by natural,causes, I would object if a colleague suggested, “I see no reason to give up on pursuing a natural explanation for this natural death.” This would be obvious begging the question, similarly.

  1. This fallacy seems pretty obvious when committed by creationists … others have noted it about AIG or other creationist approaches. In a previous discussion with Dr. Swamidass, I noted the following…

You observed that the AiG scientist “promises to ignore any evidence that points to an old earth. That is not “science” as we understand it.” And I absolutely appreciate the difficulty of trusting an approach that affirms an a priori commitment to avoid certain conclusions. But I observe that the BioLogos position, with its explicit commitment to methodological naturalism, similarly “promises to ignore any evidence that points to a special creation.” That, similarly, is not science as I understand it. And I have a similar difficulty in trusting an approach that affirms an a priori commitment to avoid certain conclusions.

  1. I further find MN to be special pleading… it is readily employed to rule out consideration of intelligent agency in biology, while it’s use is clearly not utilized in similarly scientific pursuits such as archaeology, forensics, and most significantly, search for extraterrestrial intelligence.

  2. If we humans ever get to the place where we can intelligently design genes, scientists far in the future could examine a strand of DNA and legitimately determine it to be the result of human intelligent design, no? If so, then the approach to examine biology for evidence of design is entirely legitimate.

  3. Given #6 above, it would lead to special pleading, as a scientist could detect design in biology if and only if he believed said biological phenomena to be a product of human intelligence. If he believed a certain complex phenomena to be the result of human tinkering, he could recognize design… but If he thought, even possibly, that it was designed but not the result of human intelligence, then his ability to recognize said design would magically vanish? This also seems special pleading to me.

  4. So given all the above, when a scientist committed to MN examines any phenomena, I know in advance that any conclusion they arrive at will be a naturalistic one. No less than I know that in advance that a scientist committed to biblical creationism will find intentional intelligent agency behind biological life. For those of us, like me, that are in principle open to entertaining either conclusion based on the evidence, both of these approaches are wanting. I do not see the benefit of any method that will arrive at a foregone conclusion to my basic and core question.

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If I may, I wonder what your reaction is to this short article I wrote a few years ago during the #creatorgate “scandal” about using the word creation in a scientific journal? Preview: I think it is historically indefensible to take MN as some sort of timeless essence of what science is; but I also think MN has the virtue of limiting science to a particular sphere, rather than being allowed to expand into the only game in town.

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(I should add or clarify, that as I am using the term, I mean by “natural” the undirected and unguided, acting according to the basic, “natural” laws of physics and chemistry.

I entirely, 100%, totally, completely, fully, and in every conceivable way, agree that detecting, or concluding that something is “super natural” is simply not in any way within the realm of scientific inquiry.

However, as noted with the examples of forensics, archaeology, and SETI, detecting that something is the work of intelligence agency, while making no claim about the identity of said agent, is certainly and clearly within the realm of science.)

Sir, thanks for that link. “Creator” is certainly a loaded word that is practically synonymous with God. I generally don’t hear the word creator in the context of an artist or the designer of a computer program or a machine (Star Trek: The Motion Picture notwithstanding). As such, if the word in fact did carry a theological connotation, I would similarly object to its use in a strictly scientific journal in this context.

I have used the following analogy: If SETI actually received some clearly intentional radio transmission that certainly originated outside of our solar system, and oddly enough, when decoded, the signal unambiguously read, “I am God, and in the beginning I created heaven and earth,” I would maintain that the specific identity of the sender remains a matter of philosophical, metaphysical, or theological discussion, and not science. It in theory could have been God himself, or some other intelligent alien being impersonating God: an intelligent but naturally evolved alien life form, an angel/demon, a hyper intelligent shade of the color blue, or all sorts of possibilities. The specific identity of the message’s sender Would be outside the realm of science at that point, I would maintain. Anyone who affirmed, in faith, that this message was sent by “THE creator” would be exercising a matter of faith and metaphysics. Not science.

However, simple recognition that the message clearly had some intelligent source, and was in fact not a serendipitous result of strictly natural and unintelligent causes, I think would clearly and obviously be within the realm of science.

I think there are different perceptions about how this (MN) may have historically unfolded. Did science (or even just “modern science” of the last few centuries) start with a premise of “No God”? One can certainly make the case that the “godless” approach certainly has ancient pedigree (Thales and his “ascribe nothing to the gods”) - a line of thought that gathered much steam as the enlightenment drew near. But apart from the Humean-style skeptics or Deists up and down history, most of mass culture (which would include most scientists historically) were not of the mindset to think that God never affects the material world. I.e. - apart from a few deists (or others we might now call secularists) the philosophical world could hardly be accused of harboring this starting assumption of supernatural exclusion.

So where did it come from? Today’s defenders of MN would say it arose as a descriptive result of many centuries of scientific observation that there are things about creation that can be counted on to remain regular - to a fault. Does that ever shift into being prescriptive in ways that now raise the hackles of those who feel it is being unfairly excluded? Probably. But don’t accuse them of manufacturing this out of thin air from an historical vacuum. It was (and has been) solidly descriptive of what we observe about the world before it got venerated into any sort of prescriptive status.

It is as if a mechanic discovers that she can effectively solve automechanical difficulties by exploring measurable things about the engine … what is the oil pressure? Does it have enough oil? Is it running hot? She experiments with its performance in various driving situations. A religious person might fairly ask her if she has prayed over it to cast out any demons. If she says she hasn’t, do we hold it against her that she had ruled out that possibility from the outset? Well, maybe - but she probably had good reason. How many successful “exorcist mechanics” do you see billboard signs for? It isn’t that people decided ahead of time that they would never ever consider the possibility of supernatural explanations for everything - it may well be (I argue that it is) the case that people have historically gone with what works. Once they have decided that attending to things like oil or thermostats is more generally effective, then don’t fault them for trying those things first [… or even stubbornly persisting in them!]


It seems to me that the method used to determine agency in those cases is …methodological naturalism.


(Clarification again, I mean natural as opposed to intelligently guided, not natural as opposed to supernatural)

Good thought, let me return your one illustration to you as I think it gets to the crux:

I completely agree that science, as science, as in the case of your mechanic, Ought to start with, examine, and defer to natural explanations where reasonable.

What I object to is the entire, categorical Prohibition that forbids ever concluding or even considering intelligent agency in any case whatsoever.

So let us follow this illustration a bit further… you see something odd on your engine, so you take your car to this same mechanic…Your mechanic opens your hood and sees, seemingly scratched into the engine block, a face with the words “Kilroy was here”.

A MN-devotee might fairly ask If she has explored all possible natural causes for that natural phenomenon. that it is premature to conclude intelligent agency before ruling out any and all entirely natural alternatives. If she says she hasn’t, do we hold it against her that she so quickly recognizes intelligent agency? Perhaps she has good reason for concluding that those words are the result of intelligent agency, and not the coincidental result of Differential pressures in the engine causing fortuitous cracking that coincidentally resembled those English words? Ought we tell her “we do not see scientific or biblical reasons to give up on pursuing natural explanations for how God governs this natural phenomenon.”?

it also may well be (And I also argue that it is :wink: ) the case that people have historically gone with what works in recognizing intelligent agency. Once they have recognized that, for certain phenomena, attending to things like intelligent purpose, rather than oil or thermostats, is far more explanatory and effective, then we likewise don’t fault them for trying those things first.

And given that for some phenomena, one option or the other may not be readily apparent or glaringly obvious, I think it is appropriate to entertain or further explore either and/or both options as legitimate, valid hypotheses.


I don’t follow…?

Say SETI receives a digital / binary message, from Alpha Centauri, That begins with the listing of the first 100 prime numbers, Then decodes to the unmistakable message, in English, that says, “We are the xglobef creatures from what you call Alpha Centauri. We have been able to receive your radio transmissions and are returning your message in your language.“

And the scientists at SETI will be methodically exploring every conceivable natural, unintelligent, and unguided explanation for this phenomenon, stubbornly refusing to ever conclude intelligent agency?

So I think we must be talking past each other, or somehow I am not being careful with my terms.

I’ll admit that I’m a bit confused. In the case of SETI, there is a natural explanation. There are physical, extraterrestrial creatures sending the message.

In your forensic example, you said murder isn’t a natural cause, but that would technically be natural in the fact that a physical being murdered the person. What we couldn’t detect is if God smote someone in a supernatural event.

Likewise, when the ID movement says there is a designer that science needs to include, I scratch my head. That designer most of them have in mind is a supernatural being. I agree with them that a supernatural being designed everything, but I don’t see any way that science can tell anything about that?

So yes, I wonder if we have different definitions of “natural” and “design”. :woman_shrugging:


Perhaps we are. My observation is that with SETI for example, the instruments physics and technology was developed by MN, the astrophysics to differentiate natural causes of repetitive signals is a result of MN, and the linguistics used to differentiate intelligent vs natural transmissions rely on MN. In fact everything on our end I can think of in those examples are dependent on MN. Maybe I have a blind spot. Could you give me an example of how forensics, archeology, or astronomy/SETI can be done without MN? Maybe I am just missing it.
Perhaps your point is that MN should be allowed to reach conclusions that are not defined of as "natural " origins. I can understand that, but have a hard time visualizing how it could do so. Any help there?

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And for @jpm , @Mervin_Bitikofer, and anyone else interested…

I’ve noticed this is indeed a point of common confusion. Let us indeed clarify terms. I will start by drawing on various authorities to clarify eactly what I mean in this context by “natural.”

First, I appeal to the great authority of google. When I type “nature” or “natural” into google images, I get such images as…

index index2 index4

Notice I do not get such images as…

index index2 index3

These would not be what people typically think of if they think, generally speaking, of “nature” or “natural.” This gives a sense as to what I mean by “nature” and “natural.”

Secondly, let me consult my other source of inerrant truth, C. S. Lewis…

I begin by considering the following sentences (1) Are those his natural teeth or a set? (2) The dog in his natural state is covered with fleas. (3) I love to get away from tilled lands and metalled roads and be alone with Nature. (4) Do be natural. Why are you so affected? (5) It may have been wrong to kiss her but it was very natural. A common thread of meaning in all these usages can easily be discovered. The natural teeth are those which grow in the mouth; we do not have to design them, make them, or fit them. The dog’s natural state is the one he will be in if no one takes soap and water and prevents it. The countryside where Nature reigns supreme is the one where soil, weather and vegetation produce their results unhelped and unimpeded by man… In all the examples Nature means what happens ‘of itself’ or ‘of its own accord’: what you do not need to labour for; what you will get if you take no measures to stop it.

Thirdly, I appeal to my dictionary…

natural --adj. 1. existing in or formed by nature (opposed to artificial.) 2. based on the state of things in nature; constituted by nature.

And finally, I can appeal to no greater authority than Phil himself, who perhaps unintentionally acknowledged…

So, in all these contexts, as Phil also so wisely observed, “natural” is to be distinguished from “intelligent.” (artificially contrived, purposefully planned, designed, or artificial). This is the sense of “natural” that I am using here. Natural, meaning not artificial, designed by intelligence, etc. So let me touch on this on one other angle, and I’ll put in a separate post…

Phil, not to pick on you specifically, but your earlier quote is just too perfect as it illustrates exactly the confusion in language I find here. So yes, let us visualize how we can be allowed to reach a conclusion that is not defined as of “natural” origins…

I propose that SETI scientists should be able to analyze radio signals and conclude that a signal either A) has a natural origin, or that B) certain characteristics of a signal suggest that said signal does not have a “natural origin,” (rather, it has an intelligent source or origin).

Seriously, though, this is the crux of too much confusion on this topic. There is an unfortunate, and I believe, entirely unintentional equivocation on the terms used in these debates. “natural” in these contexts, as the examples and counterexamples have tossed out above, usually is believed to mean “as opposed to supernatural,” when I mean it to mean only “as opposed to intelligently caused.”

I, for one, would totally completely, totally, fully, 100% embrace methodological naturalism if by that we strictly and exclusively mean that science cannot appeal to the supernatural. I could go into great detail about why I would affirm this most strongly.

If that was all there was to it, I would wholeheartedly agree, and there would be no issue whatsoever. However, ID (in theory) should be able to make the same category conclusions about a certain biological feature as SETI scientists do about a radio signal, and legitimately make a determination (not unlike the SETI scientist) between the two choices that you so wisely outlined above… that a certain biological feature either:

A. Has a “natural” origin, or
B. Has an “intelligent” origin.

And either conclusion should be a legitimate possible conclusion upon studying some phenomenon, and neither conclusion need require in any way invocation of the supernatural… Whether done by an archaeologist, a forensic scientist, a SETI technician, or a biologist.

So in short, we have to be very careful - by “naturalism” in “methodological naturalism,” do we mean
A. “excluding supernatural agency from our scientific method”, or
B. “excluding intelligent agency from our scientific method.”

–If the former, I am in complete agreement with that scientific method. And any method that proposes intelligent agency while refraining from making any metaphysical appeals or claims falls nicely under the umbrella of “science,” be it forensics, SETI, or ID.

–if the latter, then I disagree most vehemently with that scientific method. And we can safely reject any appeal to intelligent agency from science… thus excluding intelligent design from “science,” along with archaeology, forensics, and SETI.

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Okay - very good. So we all here agree it would be silly for the mechanic to not attribute the graffiti to an obviously intelligent agent. But once again - isn’t this because we have experience with people who do that sort of thing? It is within our corpus of human experience to see messages such as “Kilroy was here” carved on a tree, painted under a bridge, or perhaps even scratched into an engine block. And because that explanation [intelligent human agency] would not yet appear to have let us down, it is naturally our first and only “go to” on finding such a message.

You may fairly respond … “but haven’t people experienced God and the divine grace and generosity at work in their lives - and isn’t this also part of our corpus of human experience?”

To which the reply may come … sure! I easily speak that language and understand and accept that appraisal of reality. But when I engage in various specific activities within that reality, those sets of activities tend to come with their own little “rule sets”. For example, as a baker or a chef, we generally accept that we will follow a recipe and labor to have all the necessary ingredients and equipment at hand to complete the task. If we discover we have no eggs, it is not an accepted part of our “baking activity rule set” that I should pray for eggs or some equivalent egg substance to appear in my batter. I could do that - but generally, we resign ourselves to needing to borrow a couple eggs from the neighbor or make a special trip to the grocery store. We wouldn’t lambast the beleaguered cook for presuming God doesn’t exist because he didn’t first try getting on his knees for the eggs. The very Christian cook would rightly retort - “sure God can do whatever God wants - but I’ve never seen God just make my needed eggs appear! It’s just never worked that way in any of my own vast cooking experience.” And so scientists “doing science” have their sets of expectations about how things generally work which represents a well-worn and tried thread all through history of what has proven fruitful and what hasn’t towards our desired scientific goals. And those goals are to cultivate understanding of the way things physically and dependably work in our material world.

These scientists (believers and unbelievers alike) can rightly invite the IDist or MN critic to make use of their wares and show their stuff. If what they have on offer helps explain something even better leading to insights and predictions, then great! Or put another way, if there was a mechanic out there somewhere that enjoyed stunning success by casting demons out of cars, that mechanic would become an instant success. She could charge a tenth the price, and who wouldn’t jump at that rather than pay for a ring job or an engine rebuild. News would spread like wild fire, and the proof would be in the pudding. And if that caught on and worked dependably and widely, vo-tech schools everywhere would rapidly be converting their shop courses with all their expensive tools into bible classes instead.

I know I’ve repeated this before - but not recently; so here it is again. It understandably bothers some Christians that God would be dismissed as “not a part of this or that”. A young skeptic is said to have remarked: “I prayed hard for a bicycle. Soon I discovered that God doesn’t work that way; so I stole a bicycle and prayed for forgiveness instead.”
To which we should reply … that young man will eventually come to the realization that God doesn’t work that way either. In short, to fail to find a god in the universe who will do your bidding tells you exactly and only one thing: apparently there is no god in the universe who is at your beck and call. That may make liars out of a whole lot of what passes for Christian messaging out there, but it doesn’t come near to even touching any real Christian thought.


True, it is unnatural to have intelligence.:wink:

I actually thought about that when I wrote the sentence you quoted. I, as most of us, do tend to use words loosely, and without context, meanings can be confused. In the quote “intelligent vs natural” I was trying to use the terminology you were using, though of course the opposite of natural would be either supernatural or perhaps unnatural, which is really not what either of us mean. I suppose we could use : “intentionally fabricated by a third party” vs. “arising spontaneously without input from a living being.” That is not good either, though. Is a spider web the result of intelligence, or is it natural? Do we credit the spider or the spider’s maker? Why are they always face high in the dark?

I had a car once that I would have taken to the exorcist mechanic. It would just die in the middle of the road and would not start, but 10 minutes later would fire up just fine. Dealer could not fix it. I am sure the electronics were possessed.

Still, back to the subject, how could you determine something was not the result of natural causes (here defined as something not subject to the usual laws of physics as we know them or as your dictionary defines " based on the state of things in nature")?

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Good thoughts. Now, where I’m kind of going with this is as follows…

There are obvious things that would be downright stupid to even bother spending time to ask if they were intelligently purposed as opposed to of “natural” origin. An acorn just fell on my skylight. Leaving aside questions of God’s general guidance or providence, I simply and automatically put that in the category of “natural” (not intelligently purposed). I attribute the sound to gravity, mass, wind, etc., and I don’t need to look for any direct intelligent agency.

On the other hand, there are obvious things that would be downright stupid to even bother spending time to ask if they were “natural” (unintelligent, undesigned, the result of unguided and unintended natural forces.) Such as a child’s chalk drawing on the sidewalk. I am not going to spend even the slightest time considering if the house with the shining sun above it in orange chalk might have been the result of the fortuitous falling of pollen.

But somewhere in the middle, there simply are things that, at first glance, we can’t tell - and I suggest it is problematic science to automatically exclude either possible conclusion from consideration. So you and I are out hiking, and I find an oddly shaped rock. “You know, that looks like an arrowhead.” You say. “Yes, it coincidentally appears in the shape of an arrowhead, but that doesn’t mean it was intended or designed as such,” I say.

So, what do we do? Do we automatically reject the possibility that it was designed under the principle of “methodological naturalism”? It is a natural object, after all, no? A simple, natural, rock. But it is shaped just the way an ancient native would have shaped an arrowhead. We have two possible hypotheses… Let’s call them:

A) the “natural” hypothesis, and
B) the “design” hypothesis.

I propose that, if we have no further information, we ought withhold judgment, but allow both options as potential avenues of exploration. Neither ruling out the natural nor the design hypothesis a priori, but further examining our phenomenon, and following the evidence wherever it leads, whether that might lead to us concluding it is strictly natural, or concluding it was intelligently designed.

We may examine it more closely, determine that, while approximating an arrowhead, it is neither the right weight or exact shape to be likely intentionally designed as such.

Alternately, we may examine it, find it to be the near identical weight and shape as other arrowheads, and further, close examination reveals scrapes and small marks consistent with intentional carving.

My only plea is that true science ought allow either hypothesis and allow consideration of either possibility. Further data and testing may lead to conclude one or the other, but neither, I plead, ought be excluded a priori.

And so yes, for other reasons we can discuss further if you so desire, I find certain (though certainly not all) biological features to similarly be similar enough to carefully and intelligently designed purposeful engineering systems that I think it at least worth asking or exploring the question of whether they might, like our arrowhead, have been designed, or whether it only bears the appearance of design.

Whether or not we conclude they were or weren’t designed is not so much my concern… my only plea here is that I don’t think we ought exclude either possibility, either hypothesis as being illegitimate by certain rules, even before we have examined all the data.

In other words, to your suggestion above, I plea that ID be judged on its merits (or lack thereof), not ruled out from consideration because it is “not science” because it doesn’t follow some particular definition of MN.

I still don’t see how science can be used to either support or rule out ID, just as with other theological claims. While it is fine to go on building a case for ID, this effort should not be thought of as “doing science”.

I’m sure swine farmers in the area would be nervous about any possible exorcist activity. Probably would unite to get zoning ordinances in place keeping the exorcist mechanics out!

The arrowhead example is an excellent one - nice middle ground here. And you’re absolutely right that neither possibility should get excluded up front.

So just thinking out loud here along those lines … we can at least speak of arrowheads and have some conception of what they are because of clear examples (and accounts of them) where we have no doubt. So we have some basis of comparison - some reservoir of expertise on which we could call. If we presented the possible arrowhead to somebody who knew nothing of native history or weaponry and knew nothing of arrowheads; would they (with an otherwise scientifically acute mind) be able to determine if intelligent agency was involved to form our rock? Perhaps - but their chances of accurately doing so are probably reduced. And here is why the “supernatural” keeps getting dragged in (frustratingly to you, I know - so I won’t dwell). But it is where our knowledge of “how it works” or “what all it does” becomes increasingly scant. And hence it is where “the rubber really meets the road” and the real challenge arises as to what could be identified as “intelligent” in complete ignorance of what sort of agent it might be.

Seti questions are fascinating to me too. Mathematics and broadcasts of simple prime number sequences aside (the ‘smoking gun’ that got her attention in the movie “Contact”) I’m not convinced that we would recognize “intelligence” if we were to encounter a completely alien version of it. For one thing, we already run into problems even just defining intelligence within our own species of which we now at least know a few things! Witness our disputes over how intelligent animals are or how intelligent any of our evolutionary ancestors were. We already run into problems trying to decide what is or was human or not human - or how intelligence ought to be measured. It’s a vague and nebulous concept - and would surely not get any less so when applied beyond our parochial corner of any populated cosmos. Sci-fi authors have (I think) performed the valuable service of poking at our standard pre-conceptions for how things ought to look “out there”. And as commendable as movies like “Arrival” were in showcasing the difficulties of communicating with a totally “other” culture, it would still only have been scratching the surface (and the successful outcome of that story was only made plausible by having aliens which helpfully already knew quite a few things about us.) I see SETI as a nearly hopeless project, not because I’m convinced the cosmos around us is all necessarily empty, but because I have nearly zero confidence we would recognize any such cosmic “arrowhead” even if it fell into our lap.

[Don’t misconstrue this as me throwing dirt on SETI - I support those efforts. Often such labors yield unintended dividends. Having open eyes is always a good thing.]

[And just to pound home a bit more on the difficulties of discernment … try this thought experiment on for size: An alien who knows nothing of any earth life lands on earth and finds our same arrowhead (the one that you and I were unsure about, even despite our knowledge of native cultures and historical weaponry!), and then the alien also finds a honeycomb from a beehive. Wouldn’t the alien immediately drop the nearly ordinary looking rock and fixate all its attentions on the much more mathematically interesting honeycomb with all its regular hexagonal patterns? We can imagine our alien thinking ‘aha! -Surely here I finally have evidence of intelligence’! ]

The point would specifically be that recognizing design in biology is no more or less inherently or automatically theological than recognizing design in a extra-solar-system radio signal. If it bears hallmarks of design, and or if intentional design is a better explanation than any natural alternative, then we can conclude design, regardless of any hypothesis, speculation, Or personal, metaphysical, or theological beliefs about said designer.

I think of the Star Trek: The Next Generation episode where such intentional design was recognized in DNA, but yet no theological claim was made…

After studying the ambiguous number blocks for hours, the discovery is made that these fragments are compatible DNA strands which have been recovered from different worlds all over the galaxy. The crew eventually believe that they have discovered an embedded genetic pattern that is constant throughout many different species, and it is speculated that this was left by an early race that pre-dates all other known civilizations. This would ultimately explain why so many races are humanoid.