Does a commitment to methodological naturalism mean you have to ignore evidence of special creation

Sir, thank you for your thoughtful response. I am in large agreement with many of your observations here. If I may, you made one observation that touches on the core of my skepticism with the BioLogos position - I have been wanting sometime to craft the question somewhere, but since you touched on it I hope it appropriate to ask it here to you:

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.

Hence my difficulty… if, by some chance, God had intervened in a direct way- a manner that would be at least reasonably recognizable by empiric methods, the BioLogos scientist is all but guaranteed to misinterpret the data. He will forever be seeking some naturalistic alternative. I tongue-in-cheek compare it to a SETI scientist committed to a similar methodological naturalism, who is forever seeking naturalistic alternatives, unwilling to conclude any intelligent agency for the message he received, in English, stating “yes, we have received your transmission.”

So I appreciate your critiques of much of the execution (or lack thereof) of the actual science executed by proponents of ID. But at core, I simply trust their philosophical approach, one that (however badly executed) is at least committed, in principle, to an approach that “follows the evidence wherever it leads” - with no conclusion considered off limits. This, in contrast, to AiG’s approach to “follow the evidence unless it points to an old earth” or biologos’ approach to “follow the evidence unless it points to special creation.”

Thus why I am unimpressed when an AiG scientist says he finds no evidence for an old earth… but am equally unsurprised when a BioLogos scientist says he finds no evidence for special creation. This is what their philosophical pre-commitments guaranteed they would discover. However badly the ID approach may be in execution, I at least better trust their philosophy which, at least in theory, will allow them to follow the evidence whenever it leads.

Would appreciate your thoughts, and my apologies if this is not the best place to post this.

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This is false.

I am a BioLogos scientist and affirm methodological naturalism (though it is incorrectly named) as the rule of science. It has its roots in Pascal, Bacon, Kepler, and Boyle’s theology, so I am good company. Perhaps we call it methodological theism for this conversation (abbreviated MN/MT).

Any how, I do acknowledge evidence for special creation and have for years.

The best evidence is Scriptural and philosophical. Specifically, because of MN/MT science is blind to special creation. It is silent about it. Therefore we cannot say for sure whether or not it happened. It is always a possibility. And if one is so convinced from Scripture, it is a certainty regardless of the scientific evidence.

This means it is reasonable to believe in the special creation of the origin of life or in the RTB model. However, this is not a belief that can be said to be within science itself. One has to adopt this view, perhaps with evidence and reason behind you, but admit it is not a fully scientific notion. In the scientific discourse, however, we do not consider the possibility.

To leave you with a quote from my last article on this point:

Therefore, entirely consistent with the genetic evidence (Figure 1), it is possible Adam was created out of dust, and Eve out of his rib, 6,000 years ago in a divinely created garden where God might dwell with them, the first beings capable of a relationship with Him. Perhaps their fall brought accountability for sin to all their descendants.17 Leaving the Garden, their offspring blended with their neighbors in the surrounding towns.18 In this way, they became genealogical ancestors of all those in recorded history.19 Adam and Eve, here, are the single-couple progenitors of all mankind.20 Even if this scenario is false or unnecessary, nothing in evolutionary science unsettles this story. So, evolution presses in a very limited way on our understanding of Adam and Eve, only suggesting (alongside Scripture) that their lineage was not pure. Any case claiming that evolution itself requires more dramatic rethinks of Adam is in scientific error.

You can’t get more explicit than that.

This is not true. They have specified as movement what they know the answer to be before they do the inquiry. If you doubt this, read Darwin on Trial and the Wedge Document. They are not open to following the evidence where it leads. Usually this is because they are convinced evolution is not compatible with Scripture.

False. If this happened, I would gladly acknowledge it. It would not be a scientific claim, but it still could be a valid evidential claim. This has not happened clearly yet, except in the Ressurection. Read here: Dr James Tour and the Great Pascal

Nonetheless, I do acknowledge some weak evidence supporting God’s intervention in human evolution, the origin of life, the origin of consciousness and the origin of the universe. This weak evidence though. Not enough for certainty, and it cannot be considered this way in science. Though if we take the evidence from Scripture into account, that does tip things considerably (but not in science).


Sir, again, thank you for your thoughtful reply, you’ve given me much more to contemplate and read. It may be that your approach differs at least slightly to the BioLogos perspective on methodological naturalism as I have understood it, that it is never right to conclude anything but a naturalistic explanation for all aspects of creation. But this does not seem to be quite your position, if I understood you rightly.

Nevertheless, I still find an odd inconsistency in how methodological naturalism is applied… SETI has never (to my knowledge) been criticized on the grounds that “detecting an intelligent agency” is outside the realm of science, or that any claim to have detected intelligent agency in cosmic radio signals would be an unscientific claim. Similarly when an archaeologist determines that certain scratches on a rock are not the result of blind natural forces but reflect purposeful arrangement by an intelligent agent.

I struggle to understand why it is within the realm of science to detect intelligent agency when studying rocks or cosmic radiation, but not when examining biological structures.


I find an easy distinction between these other cases and Intelligent Design:

It is only with Intelligent Design discussions that you most consistently encounter resistance to the evidence of Old Earth (at the minimum) … and/or resistance to evidence for Speciation as found in Ring Species (or both).

It’s very hard to convey one’s credentials to do science while rejecting another well accepted realm of Science.

I’m not sure if my perspective is different. Can you help me why you think that?

Perhaps @Kathryn_Applegate or @jstump can clarify, but we commonly point to the fine tuning argument, the origin of life, beauty and morality as evidence for design. This was in Francis Collins book, and these arguments pre-exist the Intelligent Design movement.

I’ve heard @jstump eloquently describe four mysterious transitions. From nothing to something. From non-life to life. From non-conscious to conscious. From non-human to human. None of these transitions appears inevitable, yet here we have them all. That is a strong “hint”. From evidence, but outside science, many of us think it is warranted to posit or wonder about God’s action at one or all of these moments.

However, those that hold to MN do not think these arguments for God’s design fit in the scientific discourse. They are held as philosophical, theological or poetic reflections on science, but not science itself. As Christians, we place high value on things outside science, so this is not some sort of demotion in value or trust. We can look at the evidence, and perhaps draw the warranted conclusion that this required the direct intervention and intelligence of God somehow. The exact mechanism of this appears to be a mystery, except to say that God appears to have used largely (though not-necessarily exclusively) law-like means, and a process of descent and diversification from common ancestors.

This appears to be the dominant BioLogos position.

A common response of this to explain, “Than BioLogos is promoting design! This seems totally incoherent with MN and their opposition to ID.” There are several big differences:

  1. In contrast with ID, we think that valid design inferences are not science. So we do not even think that good arguments for design (like that from Scripture in Genesis or morality) are science. This puts us at odds with the ID movement that really wants to be called science, for no reason that I can affirm. The arguments here are very contorted.

  2. In contrast with ID, we are much more willing to walk away from a bad design argument. We are not aiming to prove design using science or to debunk evolution. Many of us (look at me and @DennisVenema) have history with ID and found that the arguments relied on ignorance of modern evolutionary theory and biology. They were not sustainable as we learned more about Biology. With that experience, we do not have much trust in ID arguments in general. None of them that I know are flat out wrong have ever been retracted.

  3. In contrast with ID, because we are willing to play by the rules of the scientific discourse, we are considered part of mainstream science. Scientists do not care if you believe in God. They only care if you falsely claim that science says God exists.

  4. I am maintaining two ways of thinking about most question, (1) from a purely scientific view, and (2) as a Christian that takes the whole picture into account. On one hand, what “science says” or what “I think science says.” On the other hand, “what I personally affirm and think on my own.” I can have different views by each perspective, and I am comfortable with this because I do not look to science as my ultimate authority.

On this last point, I’m often accused of being duplicitous for this, but this is common to many contexts. For example, an employee for a company might say, “The company does not endorse any specific religion, but I personally am a Christian and go to church every Sunday.” That is a perfectly reasonable separation to make.

In contrast, an employee would get into a lot of trouble by consistently fighting and suing the company to officially endorse Christianity over other views, and saying “The company itself endorses belief in God” when the company itself does not. That is the reason ID has so much difficulty in science. They are often claiming authority that is not theirs, and constantly agitating redirect the scientific enterprise to questions about God that it has no interest in redefining itself to address.

There is no inconsistency here. Yes, there are some very superficial similarities. There are more differences.

  1. Alien intelligence is not divine intelligence. Methodological naturalism is more about excluding the Christian God from human inquiry (because that would blasphemous), not excluding the immaterial of intelligence.
  2. SETI does not have a pattern of political activism against established scientific theories.
  3. SETI has only proposed a few specific signals of alien intelligence in its long history, and abandoned them when evidence showed otherwise; ID does not generally abandon bad arguments (in fact many would argue they essentially do not have bad arguments).
  4. SETI hopefully looks for signals of alien intelligence but does not actually know if they will ultimately find it; the ID movement knew the only acceptable answer before the started.
  5. SETI is not preoccupied by defining their effort as science or not science. They are just focused on figuring out if there is evidence of alien intelligence.
  6. SETI looks for the aliens behind the signals the detect, instead of insisting that it is possible to detect design without characterizing a designer as doe ID.
  7. The math and procedure behind SETI signal detection bears no similarity to ID arguments. SETI seeks to disprove all its signals, not to insist they are all real without testing them.

That is quite a lot of differences. Anyone of them alone is enough for ID and SETI to be considered distinct concepts and treated differently.

The only valid point that can be drawn is that at a high level, in just one of its steps,l SETI (like ID claims to do) looks for deviations from natural laws as preliminary evidence for intelligence. Even here, ID"s efforts are not comparable, because they use strawman models of natural laws that are obviously inconsistent with what we know of biology from the start. Regardless, at best this is just a preliminary filter. SETI then works to look for natural laws that could explain the signal, and look for alternate and independent evidence of finite beings (as opposed to God) as a confirmation. They have never confirmed a signal.

If anything, the key lesson from SETI is that there are lot of “false positives” that arise from just looking for deviations from known natural laws. They have been smart not to bank anything on any of these errors. ID on the other hand thinks all the noise is real signal.

I hope that helps. The problem is not the subject of study (design), but the manner of study and the track record of the people doing it. Moreover there is a strong distinction between Divine Intelligence and any other created intelligence. That should be self evident. It seems like anti-christian position to argue that these are comparable things.

I believe we can study creaturely intelligence with Science (which is not material), but I do not think it is possible or advisable to study the Creator’s intelligence with science. Any analogy we draw between the two cannot be trusted. This is some of the theological justification for why MN was part of the science’s founding 400 years ago, and should properly be understood as consequence of Christian-revelation-based-theism, not naturalism. It’s too bad we call it MN.



This is a key point. At best one can conclude that something else was at work. Science cannot prove that ‘something’ was God. Scientifically, one wouldn’t presume that intelligent beings found elsewhere in the cosmos are God.

Personally, I don’t think the problem with ID is about ‘detecting intelligent agency’. Rather, it’s how such detection is performed and the validity of the reasoning.


Sir, again, thank you for your thoughtful, thorough, and kind response. However, regarding the differences you noted between ID and SETI, I respectfully think the differences you noted to be “superficial”, at least in relation to my core question about whether the endeavor itself - using science to discover evidence of intelligent agency - is or is not rightly considered science. I recognize (and to some extent share) your critiques against the current state of ID methodology, but my question at core is as to whether the search for intelligent design in biology (perhaps SIDB?) - in itself -can rightly called “science”, not the question of how well the current ID movement lives up to ideal scientific methods.

So specifically:

The observation of something as being the result of intelligence should not - philosophically - turn on the assumptions some make about the identity of said intelligence.

If an archaeologist examined an ancient stone, and discovered part of the Ten Commandments written on them, he can safely (scientifically) conclude this was the result of an intelligent agent, no?. The question as to whether this was a copy carved by a man, or the original inscribed by God himself, seems irrelevant to the basic question of whether or not he is seeing the result of an intelligent agent.

[quote=“Swamidass, post:5, topic:36197”]

SETI does not have a pattern of political activism against established scientific theories.[/quote]

Sure, but if this pattern of political activism were absent from current ID politcal goals, would the approach become thereby recognized as “scientific” just like SETI?

(Besides, does this make Galileo’s methods unscientific since he found himself in significant political conflict with established scientific theories?)

[quote=“Swamidass, post:5, topic:36197”]SETI has only proposed a few specific signals of alien intelligence in its long history, and abandoned them when evidence showed otherwise; ID does not generally abandon bad arguments (in fact many would argue they essentially do not have bad arguments).
[/quote]. I to some extent concur with your critique of current ID methodology, from the little I have observed. but again, this does not speak to the core question of whether or not the pursuit itself is or is not “science”.

(For instance, do I recall that some scientists some time ago were charged with fabricating data in a global warming study? If so, we could conclude only that they were bad scientists, or were doing their research very badly. This would not condemn the entire endeavor - the study of earth’s global temperatures - as unscientific).

I would sssume they must be different, that seems self-evident: DNA code is a totally different medium than electromagnetic radiation. But again, this is methodological, not to my core question of the propriety of calling the endeavor itself to detect intelligent agency in biology…

But in my limited understanding, at least some of this is done in ID circles. Behe for instance seems to believe in large amounts of biological development and change through the natural forces of evolution alone (I.e., “disproving” signals that may at first appear designed)… though he seems to view some of the biological data, though, as significant enough to demand intelligent agency.

Let me make a comparison to wrap up my perspective: I cheerfully grant that current ID proponents may be doing science very badly. but for comparison: I have heard many people make similar critiques about global warming activists: they are politically motivated, they start with a foregone conclusion, their science is bad, they don’t retract bad data, etc., etc., now even if every critique against them were true, it would only prove that they were bad scientists, not that the endeavor itself (to catalog and determine cause of earth’s changing temperatures) was itself, inherently, “unscientific.”

You have carefully laid out for me, here and and elsewhere, various reasons why you find the ID movement and its proponents to be doing bad science - and I don’t significantly disagree. But it also sounds like you are arguing that the endeavor itself - of trying to detect intelligent agency in biological systems - is itself - inherently an “unscientific” (or non-scientific) pursuit. This simply doesn’t follow from a critique of their methods. And that is my core contention with the BioLogos perspective that I am trying to better grasp and understand.

They’re both within the realm of science.

In principle, detecting intelligent agency of finite non-godlike beings is within the domain of science. Detecting the intelligent agency of godlike beings (i.e. anything resembling the Christian God) is not.

Absolutely this can be science. We already look for evidence of design like this in biology (GMO detection, the impact of sexual selection, cultural selection). That is not a problem and is totally accepted.

Science is certainly allowed to study the action/intelligence of finite non-godlike beings doing the designing in any domain, including DNA.

Here we make a model of known processes (H1) and of the design process (definable because it involves a specific mechanism based on the action of a finite being) (H2). Then we test if H1 or H2 fits the data more (in some cases this comparison is implicit, but it always requires H2). If H2 fits better, we take this as some evidence that the design process we specified gave rise to the biological system. Using formal models, can quantify the strength of this inference too.

These methods work NOTHING like ID, which is trying to prove detection of design without ever considering the designer (which is impossible in science). ID argues that H2 is impossible for the type of designer they are thinking of (who is it if it’s not God?), so they will not try. Or rather that they have invented new ways of detecting design that do not need to use H2 (even though everyone else does). Instead they look for a gap between H1 and the data. That gap could be (1) a new process we have not discovered, (2) noise or experimental error, or (3) a signature of intelligence. Without ruling out #1 and #2 (which is provably impossible in Information Theory), they just assume that any gap is #3, a signature of intelligence. They stop there. Of course there is “noise” every where, even in systems we perfectly understand. So, of course the method fires off positive all the time.

The only way to resolve this is to get plausible way of creating H2 for God’s process of design. There are a few attempts that failed (e.g. the Biotic Message of Walter ReMine). However, these models do not have any basis for their assumptions and end up not matching the data as well as common descent. If the Designer is the Christian God though, we expect there will never be a way of doing this, and many early Christian scientists would call attempts at this a type of blasphemy (see Bacon’s Idols).

Which is why things like ID are disallowed in science.

Almost but not quite. I have no problem with detecting design and intelligence of finite non-godlike beings in biology. That is within science’s domain.

For theological reasons, this cannot be extended to the intelligence and design of the Christian God. If you believe the Christian God, than ID does not make sense theologically. We mostly believe:

  1. God’s thoughts, plans and intentions are largely inscrutable outside revelation. We cannot expect to understand how
  2. God is more powerful than we can imagine and can do things beyond our comprehension.
  3. God regularly acts in this world in ways that we most often cannot give any account (e.g. how would anyone prove that God caused the state of Israel to be reformed without reference to revelation?),
  4. We are commanded not to subject God to the “test,” which parallels pagan notions that they should not “test” the gods in nature.

To be clear, this is not a special rule for biology. It applies everywhere. We cannot be certain or clear of God’s action anywhere unless He tells us in Revelation. The belief that creation was separate from the Creator, and therefore could be subjected to tests in science is cited as one reason early science made sense in a Christian context.

This also explains why attempts to prove God from nature never gave rise to science, and why many early Christian scientists (and BioLogos) resist using science for natural theology. To them (and to me) it may be possible, but it runs counter the purpose of science, and very quickly starts to seem like idolatry. That is why I oppose ID, and why I think MN is misnamed. The rule is right, but the reason is not well explained.

You should really read this too:


Sir, your thoughts and time are very much appreciated. This helps very much clarify for me, and I especially appreciate the acknowledgement that one can scientifically recognize intlligent agency in biological systems (GMO, etc.)

I’m afraid,though, this cements in my mind my skepticism of the BioLogos position. It creates an arbitrary division where one can recognize any intelligent agency in a biological system unless one - subjectively - believes the intelligent agent in question to be God or God-like? Thus If a scientist sincerely believed that biological complexity on earth was the result of non-God-like, alien intelligence, then he could scientifically recognize and detect intelligent agency, but if a Christian scientist does the exact same procedure his conclusion is deemed unscientific? This is by definition arbitrary, and seems clearly an a priori commitment to avoid certain conclusions based on previous assumptions, rather than following the evidence wherever it leads.

Hence my thought experiment : an archaeologist publishes a paper proving, by rigorous scientific methods, that the weathered scratches on an ancient rock correspond so closely to the letters of the 10’commandments in ancient Hebrew that these scratches are the intentional work of an intelligent agent, not the result of random natural forces.

But then, by some means, he comes to believe this is in fact a fragment of the original tablet of the Commandments, carved by God himself… what does he do? Does he retract his research, claiming that his methods, while sufficient for detecting human intelligence, are now erroneous since he believes these letters to have been carved by God? It strikes me as absurd. He should be able to recognize that those letters are the result of purposeful intelligence regardless of whether he thinks them carved by a man, a “God-like” being, or whatever.

I do very much appreciate your kind conversation, and I have read your pascal page and Find much in common (I am a pascalian at heart myself, very antagonistic to the idea of trying to scientifically prove God.) But when examining the question of darwinistic evolution, especially whether natural forces are sufficient in themselves to explain biological complexity, I have great difficulty trusting the conclusions of any who have ruled out certain conclusions - for whatever noble or ignoble reason - from the outset. When one starts with a method that will only consider naturalistic mechanisms, I know in advance what results they will find.

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He explains the means by which he arrived at that conclusion and explains why he didn’t teach that conclusion through the scientific method.

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People with a complete commitment to the supernatural will find the same results.

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I think it is of paramount importance to understand the limits methodological naturalism. Most of us here believe that there is truth and reality beyond what we can detect with physical methods. And it is critical to understand

  1. what does


  1. what does NOT

fall into the realm of the current scientific disciplines.

Finite non-godlike beings fall into category 1, while God himself, creator of the universe and transcendent from it, falls into category 2.



You have written a great many words… and yet you have skirted exactly the issue that plagues I.D. thinkers. Why is that?

Legitimate scientists who might seek intelligence behind the creation of of Earth’s life would do something very simple:

They embrace the full scope of all the sciences - - and thus they would hypothesize that the Intelligence was active in Earth’s deep past … not 6000 years ago.

Find us an I.D. scientist willing to do this and you will have made the necessary adjustment to I.D. as a scientific effort!

@Daniel_Fisher you have been a kind dialogue partner, and I hope I am not trying your patients.

You are missing what I said. It is impossible to determine if something is “designed” without modeling the process of design, at least implicitly. We cannot do this for a truly god-like being. It is possible we can do this for aliens. In fact, one would have to in order to detect the design of aliens. If you look at how GMOs are detected, it is because we know a priori what sequences were inserted to make the GMO, so we look for those.

What are the specific sequences function this way to determine God’s design? We have none. So the two researchers would most definitely NOT have the same procedure.

To be clear though (you seem to miss this), we do believe that God designed us all. We just doubt the ability of human effort (i.e. science) to bring us to God. That is an orthodox Christian position.

That only works in this case because it looks like the things that humans design. And in science the carving of a god-like being would not be considered. As a Christian, he might take Scripture into account, and believe God carved it, but that science cannot tell that God carved it.I In this case, the reasoning to intelligence would be based on a H2, a model of hebrew text.

The thing about biology is that it is almost nothing like human design. So this type of reasoning doesn’t work. We have no way of making a H2 of God-designed vs. a H1 non-God-designed biology. This is not too complex to follow. In practice, there is just no way to distinguish between (1) noise, (2) undiscovered law, and (3) design, without a clear model of design. We do not have this for God’s design of biology. Period.

Well this is not the claim of science. Science does not conclude this but assumes this. As I have already said, it is entirely possible that God’s action was required. We do not know this from science though.

Moreover, darwinistic (i.e. atheistic) evolution is not what I affirm. I affirm evolutionary creation.

All this means is that you should doubt atheists when they say they have disproven God with science. You also should not be surprised that science does not officially declare evidence of creation. That is just not what will ever do, so just stop caring what it says about this. Rather, it is here to tell us about creation. Not the Creator, just creation.

As for me, I have not ruled out God’s action in evolution, nor have I denied design. Rather I say that God created and designed us by a process of common descent. On the other hand, science has ruled these conclusions. Outside science, I’m willing to consider other conclusions. Why is that so hard to follow?


No disagreement, but to me that isn’t the real dilemma. Of course God himself falls into category 2. But what God does within our material universe by whatever means falls into category 1. The people ate manna that was in category 1, the miraculous loaves and fish were in category 1, resurrected bodies would be in category 1, the original inscribed tablet of the Commandments would be in category 1…

And, had he in fact intervened directly in some manner distinct from regular natural processes to design and initiate biological life, that handiwork would also be in category 1 for us to examine, no?

These are all great reasons to doubt science gives us a complete account of the world, even in category 1. As Christians we should doubt any human effort, including science, could give us a complete view of the world because of this. The fact that we can so easily produce failure cases for science is a wonderfully good thing. It helps us delimit what science can and cannot do.

If you want to ask questions about God in nature, we cannot get this from science alone. Instead we have to look at both science and theology, and do some thoughtful work. We need to look to theologies of nature. When it comes to Truth, Christians should trust theologies of nature more than science.

No dilemma here at all. We just do not trust science as our final authority, especially if we have good reason to think God has acted in our world.

Concur with all, thanks.

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I don’t understand your agenda… my words have had nothing to do with age of the cosmos because that is not my area of disagreement with BioLogos that I am wanting to explore.

But moreover, since you asked:

That would be pretty much every scientist at the discovery institute, at least. Certainly that describes Stephen Meyer or Michael Behe who clearly articulate their position as hypothesizing that the designing activity was taking place millions of years ago.

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The problem with Meyer is he doesn’t support Speciation, yes?

And I believe that is true about Behe as well. I know that Behe supports the term de-evolution which is bogus science from the get-go.

So, as I was saying … I.D. folks almost always reject some integral part of science:
A) the geology of Old earth; and/or…
B) the molecular chemistry of speciation; and/or …
C) [the more rare issue of ]the non-logic of de-evolution.