Why Science Uses Methodological Naturalism

Todays science is well described as “our best explanation of the world without considering God’s action.” The exclusion of God’s action is the rule of methodological naturalism (MN).

Today VJ Torley, our friendly ID proponent published an article on methodological naturalism in science.

Both @swamidass and @TedDavis responded in the comments. @swamidass also interviewed @TedDavis today about Boyle’s relationship to this question (this will hit the internet in the next couple weeks).

I’d be curious to hear the communities thoughts on this question. In particular, there will be an extended interaction about MN on my blog (http://peacefulscience.org) over the next several months. This hasn’t launched yet, but will shortly.

In particular, I do encourage readers to leave a kind comment to Torley on his blog if they feel so inclined. He has been a respectful dialogue partner to us and we want to reciprocate.


I read the OP on uncommondescent, and your and @TedDavis comments. There is a lot there. I am in basic agreement with your position. But as Ted says " The definition of what counts as science and what doesn’t changes over time, for reasons that are not always simple " Our friend @Jon_Garvey wrote a post recently on Hump, in which he pointed out that the definition of MN has changed as science changes. The most recent change, in physics, was forced by the advent of Quantum Theory and Relativity. But, (and this is my take, not Jon’s) although the concepts of time slowing down, and particles being entangled might have seemed to be outside of MN a hundred years earlier, they were counted as science because they fit the constant criteria of scientific investigation that has been passed down through several centuries. And that is a confirmation of prediction from theory, verified by consistent and reproducible experiment or observation.

So even if the observer effect in quantum mechanics seems mystical, it is demonstrably scientifically real, and therefore it is accepted science. And of course being so, means that scientists (and not all of them have even now 80 years later have gotten this point) need to “move the goalposts” of the definition of MN to include things that were not previously part of materialism in any sense.

So, who knows what’s next? Jon has suggested that we might be on the verge of a new expansion of what we accept into the tent of MN, and I hopefully agree, And perhaps, this may include some aspects of our world that have previously been in the province of the spiritual or philosophical. But I do not believe that this will ever include theological issues, or matters of divinity. This is not because I dont believe that God is real; I do. Its because I do not believe that God is part of this natural world, but is its creator.

God has never been, is not now, and never will be a subject for scientific study. I state this as a theological principle of faith. We may find in our research that there is room for God, or pointers to God, or consistency with a creative God hypothesis, but God cannot be a hypothesis that can be tested by any of the accepted methods of science, even with a greatly expanded definition of MN. We need other methods, those of the theologians, historians, philosophers, and others to explore the nature of God. We need prayer, discernment and spiritual methods for that.

Recently there was a brief kerfuffle in the scientific community about a paper published in PLOS One, that used the term Creator in the text of the paper. I wrote a blog post stating that I agreed that such a word should never be used in a scientific paper, to which Jon disagreed to some extent. My opinion was not based on my faith, but had the same source as the fact that I have never considered prayer to be a part of my lab work, but do as part of my life work.

If we allow the definition of MN to expand along with our expansion of scientific paths of enquiry, but firmly retain our agreement that we will limit science to our discovery and understanding of Gods natural laws that govern this universe in lawful ways, I believe we will be following the path we are meant to follow to find the great Truth behind everything and be witness to God’s majesty.


As Sy suggests, my own take on MN is that we should ditch the artificial and unbiblical Enlightenment division between the “natural” and the “supernatural”, because “natural” is such a fluid concept., and no longer easily definable now science has ditched the early-modern “mechanical philosophy” of inert matter and God-given laws.

Gravity had to be redefined as “natural” after Newton, though science had for a century or more rejected “occult” forces acting at a distance as definitionally supernatural. In our own age, the current paradigm deals very badly with concepts like “mind” (which many quantum theorists see as essential a component of natural reality as matter) and the linked concept of “information”, which is clearly immaterial, though equally clearly a part of nature, and especially of life.

Teleology, too, was originally excluded from science by Bacon as (a) supernatural if extrinsic and (b) dishonouring to God’s honour if intrinsic. But now it is increasingly clearly a real part of nature - so on what principle are final and formal causes still excluded from scientific methodology?

MN even reduces the concept of matter to a mystical duality, where “natural” simply seems to mean “expressible in mathematical equations”.

Theologically speaking, as we move away from Enlightenment deism, those in the science-faith dialogue have to reclaim a relationship between God’s daily providence (a core doctrine of truly Christian theism) and science: if God answers prayer for our daily bread, and governs history, then there ought to be at least for Christian scientists some concept of how that works, lest the familiar tendency of letting methodological naturalism encroach on our metaphysics and theology will always cause problems. I suggested one possibility here.

We also have to reclaim a proper theological understanding of randomness, given that under MN the proper scientific definition of “unpredictable” (cf Donald MacKay on this) is routinely extended to mean “causeless”, even by some ECs - that is done both by biologists opposing evolution to divine creation, and by physicists who say that quantum events are acausal. For the Christian whose metaphysics is theistic, the idea of God’s causing something that has no cause ought to be seen as no less incoherent than his creating a square circle.

Note that all this has nothing to do with miracles - the biblical picture of the natural creation is not of an autonomous nature being occasionally nudged by “interfering” miracles, but of a household constantly guided by God’s supervision and management. Yet miracles (exceptional events) do occur, now as in Jesus’s ministry. It is easy to neglect that, in the mathematical sense that they are negligibly rare, in the natural sciences, on the assumption (a theological assumption, rather than a scientific one) that nature has always been essentially a self-contained system.

But as I point out in a recent post, there are some scientific disciplines - notably medicine - where claims of the miraculous can only be sidelined by ignoring the data, or by insisting on interpreting it as if one were a metaphysical, rather than a methodological, naturalist. The believing scientist should not, surely, have to deny the remarkable works of God as if his professional methodology applied to the whole of life.

Incidentally - Sy, you’re spot on theologically in saying that God cannot be investigated scientifically, because he is above and beyond our universe.

But actually the question is more about the interaction of God with the physical world. to take the extreme case of the miraculous, at Cana real water was turned ito real wine; in Galilee 5 loaves and 2 fishes fed 5,000; and in doctors’ offices round the world, patients present with physical conditions healed after prayer.

If the Creationists are right about God’s direct action in any part of creation, such as the origin of life, or even if ECs are right to treat the Big Bang as creation ex nihilo, then in considering the supernatural one is not delving into God himself, but only his visible works, which were, after all, the subject matter of science from the start.

Yes, thanks for that clarification, Jon. I agree, and in fact meant to stress that it is the investigation of God’s creation (not God) that is the subject of science.

But the question remains (and we have talked about this before) how do we do that? What I was trying to say is that this question is actually a methodological one, not really metaphysical. For example, I fully agree that the issue of mind, or to go even further, the existence of souls, should not remain forever beyond scientific (using a newer not yet discovered form of MN) enquiry. But just as Newton and Einstein had to struggle with new methods to be able to achieve their breakthroughs, so do we.

I am glad you raised the issue of mathematical approaches. To me, this is a vital problem in modern science. Remember that Einstein’s theory of relativity was quite beautiful and mathematically convincing, but if it had not been confirmed by the observations of astronomers, it would have died. I had a professor who said (quoting somebody else, I believe) “a beautiful theory can be killed by a single ugly fact”. This is the terrible conundrum of modern physics, especially particle physics; some very elegant theories are not being confirmed by the linear accelerator experiments.

And its also why I become so easily annoyed by discussions of mathematical theories with no hope of empirical testing, like string theory and multiverses, and some of the more esoteric alternatives to the Big Bang as a singularity. Clearly if we accept pure math as part of a new definition of MN, then MN is meaningless, and is certainly no longer any kind of barrier against theism (whose ideas are much stronger, scientifically, than those mathematical flights of fancy).

So I think we have two choices as Christian scientists. We can simply abandon any concept of MN, and use math, logic, even theological reasoning to come to a fruitful understanding of all of creation, including miracles. That might be the right way, and if it is, I would be perfectly happy to pursue it. The only problem is that is would split the scientific community in half, because how we procede would then depend on radically different basic axioms. Those who believe that God does not and cannot exist (axiom 1) would get different results and conclusions from those who believe that God exists and is the creator (axiom 2).

We already see this happening. Neil Tyson hosted a panel discussion of atheist scientists who concluded that the universe is probably a simulation created by some alien teenager playing with his newest device. Christians would agree, except that we call the creator God, and attribute to Him a set of characteristics, generally lacking in most teenagers.

The alternative approach is to follow Newton, Einstein, and the other MN scientists of history, and find a way to empirically test the theories we create that will further stretch the boundaries of what we call the natural world. Of course the problem is, I have no idea how to do that, and I dont know anyone else who does either.

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That is a real issue… on the other hand, if a community actually has two radically different views of reality, it would be surprising if there weren’t some division.

However, maybe it’s not an insurmountable problem: take Donald Mackay, who described natural laws as “what God habitually does” (i think probably rather loosely - I don’t think he seriously embraced occasionalism or denied secondary causes). An atheist has some other view of laws as some kind of basic “given” of nature (though it’s actually a little difficult to justify metaphysically), but as far as science goes the investigations and the conclusions are the same: there’s a law, and how it got there is up to one’s personal convictions.

So I suspect that if we Christians found a way to describe, say, the providential actions of God in determining actual outcomes in nature, the atheist would be able to see the same things but describe them in some other (and to us, less correct) way. For example, in my earlier linked blog post, the category of “chance” is suggested to be, in fact, the mark of God’s free choices, and hence unpredictable to man. The atheist would see “chance” in an Epicurean way as chaos giving rise to order - philosophically incoherent, of course, as one hopes the philosophers would point out, but enabling the same categories to be used, but with fundamentally different understandings, by all scientists.

But it does need that degree of spelling out, so that Christians don’t find themselves tied into Enlightenment skepticism by their own methodology.

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I am provoked to speculate that the whole concept of MN, at least in regard to its need for a well-defined activity called science (so as to know where that fence is that it must not cross) may end up being illusory as a coherent concept. My reasoning is as follows.

You mention science as having frequently needed to move its goalposts, Sy. We can easily visualize this metaphor because a sports field is a very well defined thing. We see and evaluate it, but we also live outside of it and are very well aware of how its boundaries are marked, both as we may have the occasion to play on it (and not cross those well-marked boundaries!) as well as to observe it from a well-known world outside those boundaries. But when the subject becomes: “all of human knowledge” (which is what science in its widest philosophical sense has historically meant), we have no “outside” of that from which to discuss where fences or boundaries might be. So we are trying to erect an edifice (a wall), with access to only one side of that wall. May I suggest that it is a fool’s errand to think a wall can be demarcated when we only have access to one side of any such “demarcation”.

We may go on to think that God is the “exterior” presence that grounds our conception of this demarcation. So perhaps Revelation from God then shares with us some perspective that validates an “outside” which can then be distinguished from an “inside”. But the problem with this, even as Christians accept it on faith, is that God enters into our experience to communicate with us, accommodating to that which we can apprehend. In fact, this seems to be what much of the origins controversies and Biologos project is about: witnessing to the fact that God does not just foist on humanity some alleged ladder of “futurese” understandings that will allow us to intellectually and mechanically advance out of our created world and up into God’s world --at least not yet, and not under our own intellectual steam in any case. So if God does this, we still have no viable concept of an “out there” with regard to human knowledge. We only have faith that an “out there” must exist somehow because we know we don’t know everything. But the more “out there” we frantically annex, courtesy of all our efforts, scientific or otherwise, the more it seems evident to me that nobody can artificially erect a fence.

We know God will be forever beyond us --I totally agree, Sy. But MN may, at best become meaningless or at worst take on a foul odor to the religious, when it must artificially insist on demarcations that themselves have proven fluid and most probably meaningless in any case. And I speculate this as something of an MN enthusiast who has found his own views on that shifting over time because of the influence of various culprits here. Thanks a lot, Jon! :expressionless: Going and unsettling my happy-place views.

Pure math can never be part of the definition as the choice of any particular mathematical model is applied is a description or model, not the object under study. That is, an electron is not a number, it is an entity. That entity may behave in accord with a mathematical model but the model is not compelling the electron to behave that way.

There are any number of mathematical models that can accommodate any particular set of results. It is experiment and observation that allows us to assess which subsets of models better approximate the results.

For any two points, I can find unique parameters fitting an equation of ‘y=mx +b’, but I can fit any number of parameters through those same points with ‘y=ax^2 + bx + c’. So how does one assess which model applies? Generally speaking, there is no mathematically rigorous or foolproof method of determining this.

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Yes, that is exactly my point, but you made it in a much clearer and pointed way, so thanks

Indeed, Merv. Dr. Garvey has corrupted quite a few folks, including myself (at least to some extent). Your post goes quite a bit beyond mine, and I think your points are very well taken. In fact we cannot know what is “out there” until do. And I do think that the timing and method by which we get that knowledge is entirely in God’s hands.

Hi Eddie,
Let me start out by stating that I really like your approach to the intersection of science and faith, aiming to appreciate modern science while remaining committed to historical continuity concerning core Christian doctrines. I think that your posts are always written very thoughtfully and I have learned new things from them. Nonetheless, something has been nagging at me which I would like to point out.

Something which, I presume, has become tiresome for the regulars here (if I may be so bold to speak on behalf of others) is that a very large fraction of your posts center on rants criticizing the position of “some EC folks” or “some EC leaders”. Now, I ask, is that really a necessary and/or fruitful practice? Most of us have become very familiar with that point of yours. But no one seems to feel compelled to actually defend the views against which you are rearing yourself. Since this is a place of dialogue, wouldn’t it be better to discuss the positions which are actually being represented by people here right now? Without the participation of an actual representative of the critiqued position, you’re bound to end up combatting straw men.

In other words, I would suggest that it might be more constructive for the conversation overall if you were aiming your responses directly at the thoughts and beliefs expressed by people on the Forum, rather than criticizing the rather elusive category of “some ECs”. I want to repeat that I generally like your contributions, this is just something I had on my heart to say.

Your brother in Christ,


I remember back in school physics how we were able to prove pretty well any theory on the basis of a graph through one point and the origin!

I’m doing some modelling right now and I’m frustrated that the points seem to come out right in the middle of two possible scenarios.

Not long ago, when trying to determine the number of modification sites in a protein, experiments indicated 1.5 sites.

That was frustrating but expected. It aligns perfectly in with my proof of God via Ironic Design.

That is: It is highly improbable that a designer would leave ambiguous, non-objectively discernible marks on its creation. Similarly, it is improbable that a purely natural, designer-less universe would leave ambiguous marks behind. Considering the great difficulty in demonstrating the existence or non-existence of a designer throughout the ages, this leaves one to conclude: The universe was designed so as to make the certainty of a designer completely indeterminable.

Case in point: The mass of the Higgs boson. Theories suggested two likely mass ranges for the boson; a lower number, compatible with supersymmetry models, and a higher number, compatible with multi-universe theories. The European Large Hadron Collider experiments converged on a mass for the Higgs Boson almost perfectly in the middle, a mass where the field expects the universe to be unstable.

Ironic Design: Because the designer has a sense of humor.


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@Argon Your post is funny, but also, I believe profoundly true. It might be worth compiling a list of such examples. (BTW, I am finding the same thing with model gene regulatory networks, and always used to find it in my genetic experiments, where the answer could have so easily been unambiguous, and almost never was).

This is very close to Pascal’s position…

If it is a sign of weakness to prove God by nature, do not despise Scripture; if it is a sign of strength to have known these contradictions, esteem Scripture.


We know God only by Jesus Christ. Without this mediator, all communion with God is taken away; through Jesus Christ we know God. All those who have claimed to know God, and to prove Him without Jesus Christ, have had only weak proofs. But in proof of Jesus Christ we have the prophecies, which are solid and palpable proofs. And these prophecies, being accomplished and proved true by the event, mark the certainty of these truths and, therefore, the divinity of Christ. In Him, then, and through Him, we know God. Apart from Him, and without the Scripture, without original sin, without a necessary mediator promised and come, we cannot absolutely prove God, nor teach right doctrine and right morality. But through Jesus Christ, and in Jesus Christ, we prove God, and teach morality and doctrine. Jesus Christ is, then, the true God of men.

Bonhoeffer also writes…

A god who let us prove his existence would be an idol.

I think I am Pascalian. Maybe @argon is too?

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Methodological naturalism is generally understood as a methodological approach to the study of nature, and most often it is an outlook that excludes all but natural (and in practical terms) and material objects from study.

The techniques and maths involved are secondary to MN - the ultimate expression of MN is eliminative materialism.

The greatest objection to MN imo is the fact that we human beings can perform methodological studies on objects of nature, since we bring to our studies our beliefs and outlooks, while we are composed of the very substance that makes up the objects we study.

One more announcement. VJ Torley tells me he is planning on posting here when he gets a chance (hopefully tomorrow). I’m very glad to hear this. Please be respectful of him in this dialogue. He has been consistently a respectful dialogue partner, and I hope that we can reciprocate.

Also, @Jon_Garvey thanks for posting a kind comment on the Uncommon Descent article.

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I suspect you’ve just rediscoved my Important Scientific Law known as the Principle of the Conservation of Oddity, which I described in a Serious Medical Journal back in 1981. “Ironic Design” might be an equally good description.

More seriously, I’ve been musing in the last few days on what one might expect to see in providential design in nature, starting from the way that the traditional doctrine of diviene providence has always been seen to work out in human affairs and so on, rather than from human models of design.

The answer is, pretty much the “It’s design, Jim, but not as we know it” character of your protein outcome. Take a biblical example, like God’s clear intention to send Paul to Rome to witness to Caesar in Acts. In a simple Universe, Paul would have bought a ticket and gone, with the clear endorsement of the Church. In God’s economy, prophecies warned him not to go, arrest and imprisonment was the means by which he got his passage to Italy, and the ship was wrecked on the way (a shipwreck surrounded by signs of God’s providence and sovereignty).

In nature, it seems, the ends are obvious - natural theology has always seen beauty and wisdom in the things created. But the means - like the means of God’s Kingdom coming - are strangely convoluted. “Just as the (theological) theory predicted”, maybe?

But the point to note is that, in providence, God has never been thought to be trying to confuse people or hide his presence. Rather “his ways are higher than ours” - there were reasons for every event in Paul’s itinerary, as millions of sound sermons on those passages in Acts down the millennia demonstrate.

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