Why Science Uses Methodological Naturalism

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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“Regression to the mean” has often sent me off on investigations lasting weeks until I confirmed that the initial number were statistical flukes. And I was lucky. Many people publish papers before they find out. That’s one of the major sources of irreproducibility for papers.

Maybe it’s a corollary to the notion. See also, ‘jelly side down’.

I don’t know. Personally, I think Pascal was one of the first philosophers who could also write well. So many couldn’t get a simple point across to save their lives.

I also think this quote by James Tour (one of the ID heroes) is great…

I have been labeled as an Intelligent Design (ID) proponent. I am not. I do not know how to use science to prove intelligent design although some others might. I am sympathetic to the arguments on the matter and I find some of them intriguing, but the scientific proof is not there, in my opinion. So I prefer to be free of that ID label. Blaise Pascal (1623-1662, http://en.wikipedia.org/wiki/Blaise_Pascal), one of the finest scientists, mathematicians and inventors that the world has ever enjoyed, and also among the most well-respected and deepest thinking Christian apologists, wrote in his Pensees 463,

“It is a remarkable fact that no canonical [biblical] author has ever used nature to prove God. They all try to make people believe in him. David, Solomon, etc., never said: ‘There is no such thing as a vacuum, therefore God exists.’ They must have been cleverer than the cleverest of their successors, all of whom have used proofs from nature. This is very noteworthy.’”

As Kreeft (http://en.wikipedia.org/wiki/Peter_Kreeft) points out in his commentary on Pascal’s Pensees,

“If the Scripture does not use nature to prove God, it can’t be the best strategy. Notice that Pascal does not say that there are no good proofs of God or that none of them begin with data from nature. Elsewhere, he specifies merely that such proofs are psychologically weak, but he does not say they are logically weak. More important, they are salvifically weak, [meaning that] they will not save us. If nature proved God clearly, we would not have to search for him with all our hearts.”

Pascal further writes in his Pensees 429 ,

“This is what I see that troubles me: Nature has nothing to offer me that does not give rise to doubt and anxiety; if there is a God supporting nature, she should unequivocally proclaim him, and that, if the signs in nature are deceptive, they should be completely erased; that nature should say all or nothing so that I could see what course I ought to follow.”

Though 350 years since Pascal penned his dilemma, as a modern-day scientist, I do not know how to prove ID using my most sophisticated of analytical tools. I share Pascal’s frustration. Wouldn’t it have been wonderful if, when scientists had obtained the first molecular resolution images of human DNA, it had self-assembled (a thermodynamic process) into the Hebrew script to say, “The God of Heaven and Earth was here.”? But it did not, and I suppose that the wonder would have elicited no love from the skeptic anyway. Therefore, God seems to have set nature as a clue, not a solution, to keep us yearning for him.

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That just nails it. ID doesn’t even get out of the starting gate.

@Eddie[quote=“Jonathan_Burke, post:24, topic:5441”]
That just nails it. ID doesn’t even get out of the starting gate.

I agree. And I think I also agree with Tour that [quote=“Swamidass, post:23, topic:5441”]
I am sympathetic to the arguments on the matter and I find some of them intriguing

Perhaps this is the key issue with ID, and I would like to see Eddie’s thoughts on this. In some areas, like abiogenesis, ID might have a point (or not) and the general idea of design may not be wrong (although I think calling it intelligent is an insult to God, but thats another issue), and certainly some ID folks are not total evolution deniers, BUT, lets remember some history.

Whether intentional or not, ID sprang upon the scene as a SCIENTIFIC alternative to creation pseudoscience and evolutionary biology. And the rationale, at least as it seemed to me, and other biologists, was to allow the teaching of an alternative to Darwin in science classes. That is the failure of ID. It could be a wonderful philosophical idea, or even a theological one (although I personally dont think so) but it simply fails the test of what we call science based on our current usage of MN.

Could that change? Possibly, going back to the discussion of pushing the boundaries of MN and the definition of science. But that is the future, not now, and for now, my own view is that the DI should simply give up all the sciency sounding stuff and stick to the philosophical arguments for design. A modest proposal indeed.


Here’s another thought to consider. Science is not the only academic discipline to insist more or less firmly on methodological naturalism.

Sociology does, for example, so that investigation of the supernatural experiences of people (“supernatural” not the category I like, but the most comprehensible to make the point here) - such experiences must be interpreted naturalistically in the literature.

Likewise historians have a strong tradition of excluding the supernatural by methodological necessity as ahistorical. For history only studies the kind of events events that are known to occur in the common experience. This has significance because it applies not only to reports of miracles in Augustine or Bede, but par excellence in the field of biblical studies, which consider themselves to be guilds of specialised historians. Jesus’s miracles, or his resurrection, are not the stuff of academic history, and therefore not a subject for empirical study - hence all those distinctions between the “Jesus of history” and the “Jesus of faith.”

Accordingly, since the miracles are claimed as actual events, not simply as “beliefs”, then methodological naturalism also extends to theology: we cannot do theology on the basis that God actually acts in the world (because the historians, sociologists and scientists deal with the empirical world, and don’t do the supernatural. And theology depends on biblical studies, which are historical disciplines).

It seems, then, that not only physical sciences, but all empirical fields, have the same insistence on methodological naturalism in the Academy. So my question is, are these academic disciplines any less justified than the physical sciences in sharing their methodological naturalism. And if so, why, other than the assumed right of practitioners to decide their proper boundaries?

One can, of course, argue that it enables these disciplines to be pursued on an equal footing by those of all faiths and none. Theology shouldn’t, after all, be the domain only of the religious…

Sy, I don’t quite agree about the origins by I do concur with your assessment. I think ID sprang out of a response to ‘materialism’. At least that’s what many of the founders suggested. Even Philip Johnson noted that if ‘non-materialistic’ science (or ID) proved fruitful then questions like the age of the Earth would also come under review. Johnson repeatedly said that he took no position about the Earth’s age. See here.

There was no attempt made at distinguishing creationist pseudoscience. This was part of the ‘open tent’ strategy. One can see the approach in the testimony of many witnesses for ID who either refused to state their beliefs about the age of the Earth or demurred about having an opinion during Kitzmiller v. Dover Area School District trial.

Ted Davis outlined some of the problems with the ‘big tent’ approach previously. As I’ve mentioned elsewhere, ID must perform critical evaluations to discern which of its ideas are good and which should be discarded. All robust sciences do this. All robust sciences at their start have profound, passionate arguments about their subjects. However, at least until now, that work has been studiously avoided within ID. It refuses to draw lines within its sphere of support.

Science must be rational and relentlessly objective to remain science. It must follow the evidence wherever it leads regardless of its religious/philosophical implications. Christians have nothing to fear by true science taking this approach as it must to remain true science, because we know that the Author of nature is also the Author of true religion and truth itself, so any apparent conflicts between true science, religion and philosophy will ultimately be resolved; God is the Author of nature, true religion and correct philosophy.

Intelligence is a known reality. It can be a causal factor in a given phenomenon coming into being, just like other known realities. Sometimes this is undisputed, as in everyone accepting that technology only emerges through the activity of intelligent agents. This is because technology, by definition, is the application of knowledge for a purpose. Some phenomena can only arise via the application of knowledge. For example, it is beyond the capacity of the combination of chance and laws of physics to mindlessly and accidentally produce a fully programmed computer given only the limited probabilistic resources provided by a Universe that is only 13.8 billion years old and consisting of a finite amount of matter that could have only produced a finite number of events – nowhere near enough to mindlessly and accidentally generate something like Microsoft Windows running on an Intel-like box, or anything close to that.

The self-evident fact is that intelligent agency – whatever the nature of the agent, human or incorporeal – is necessary for technology to come about. Life is ultra-sophisticated, self-replicating, digital information-based nanotechnology that is light years beyond anything modern science knows how to build from scratch, and is far more unlikely to come about mindlessly and accidentally than is a computer. Mathematics, not Biblical belief, assures us of this.

ID is the last remaining instance of true science uncorrupted by methodological naturalism. Science perverted by methodological naturalism abandons the relentless objectivity true science requires. There just might be realities other than material realities. There is no evidence and can be no physical evidence that there are no non-material realities. There just might be incorporeal intelligent agents. Not wanting to accept that that is a possibility doesn’t prove it isn’t so.

ID remains true science, in accordance with those who created the modern scientific method. Methodological naturalism corrupts true science by its rejection of relentless objectivity in favor of a philosophical view. ID accepts the fact that technology only comes about via intelligent agency.

This is an excellent question.

In my opinion, any community of discourse (e.g. history, biology, arts, literature) is allowed to adopt Methodological Naturalism (MN) as a rule. Basically, any group can define itself however it likes. However, in adopting MN that community forfeits the right to make any pronouncements about God, God’s action, or God’s existence. To do otherwise would be to “beg the question” in obviously circular reasoning.

Case in point is the Jesus Seminar, that tried to understand Jesus starting from the assumption of no miracles or supernatural reality. Starting from that assumption, they necessarily conclude that Jesus was just a man and did not perform any miracles, and did not rise from the dead. This is their “best account of Jesus, assuming God was not involved.” The absurdity ensues when anyone tries to take their pronouncements as evidence that Jesus was not God incarnate. This is just absurd. By adopting MN, they cannot pronounce anything outside their discourse about God. Period.

So MN is never the real problem. The real problem is when communities of discourse adopt MN as a rule, but then hide it, so as to make authoritative pronouncements against God. In contrast, when MN is openly adopted, as it is in science today, it is useful and harmless.

Now regarding MN in history, this appears to be the rule according. In this, I stand in awe of NT Wrights deft rhetorical ability to operate in history to make the case for the Resurrection. http://ntwrightpage.com/Wright_Historical_Problem.htm Of course, He is wise enough not to insist his argument be included in public school history courses (which is what ID did with their arguments in science). If he did that, he might actually get kicked out of history, quite in the same way as did ID.


Wow, you nailed it. A great definition of scientism. Expect to be quoted.

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I think Wright was aware of sailing fairly close to the wind (and actually got some severe stick for mixing God and history from some scholars!). Of course, he should not have had to be so careful, were it not for a particular group of academics deciding they have the sole right to decide what “history” must be, when all of us participate in history all the time.

The question of group self-definition remains a rather strange one to me: you objected to ID calling itself a “science”, based on the fact that the rights of definition and methodology belong to the scientific community at large.

On that basis, what right does a Western Academic guild have to call itself “New Testament Studies” with a naturalistic methodology, when the New Testament, and its study, actually belongs to the Church of Christ, if not the whole world?

As for ID, I’m unaware that they (as a movement) ever wanted ID taught in school science courses. They argued against it at the Dover trial, having tried to discourage the school board from trying to push ID in class. But hey, contradictory “facts” fly around in these discussions.

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Teaching ID in schools is literally the entire rationale for the “genesis” of ID movement in the 1990s. Have you ever read Darwin on Trial by Phil Johnson? He lays it out very clearly in 1991. You would be very hard pressed to find any ID advocate that doesn’t think ID should be taught in the schools. Across the pond, this might be hard to see, but here in the US, to anyone paying attention, this is as clear as day.

ID can certainly try to claim the label “Science”, but in doing so they open themselves to the charge of being a “pseudoscience”. Any one that claims the label “science” while the entire scientific community rejects them, is by most people’s definitions “anti-science” and “pseudoscience”.

That would just save themselves the headache by focusing on doing “science-engaged philosophy.” We would welcome that. Of course, because they really want to alter public school curriculums, this is not really an option for them. So the culture war continues…

I, too, am a card-carrying Pascalian! Interestingly, the proofs of God from nature that Pascal mocks are the 17-century equivalent of ID – arguments for the existence of a creator from the evidence of design in nature. The more things change …

Hmmm. Yes and no. The social sciences began to adopt the methods of the physical sciences in response to the great advances being made in those fields. You must admit that many advances in knowledge in the “soft” sciences would not have been made if researchers in those fields had not begun using techniques borrowed from the “hard” sciences. We would be fumbling around in ignorance along many fronts if some Christian apologists had their way and could turn back the clock to erase the Enlightenment from the pages of history.

What would you have them do? Christians throw out lines like this all the time, but I’m not sure we really think about what it would mean to do otherwise. Perhaps this is because we assume that our Christian “supernatural” explanation is the only one that is discriminated against. Should we accept Homer’s version of the Trojan War as a completely historical record of events? Should we accept Plutarch’s account of the prophecies surrounding Alexander the Great’s birth? Do we accept Josephus’ descriptions of signs in the sky that foretold the destruction of Jerusalem? Is it only the signs and wonders accompanying Christianity that we want historians to treat with respect, or do we include the supernatural explanations of other faith traditions as “factual events” in world history textbooks? When do we get the American History textbook that includes Jesus’ trip to North America, as related by Joseph Smith? We can’t make a special rule that exempts only our Christian explanations from the historian’s bias against the supernatural.

Personally, I have no problem with the social sciences adopting techniques from the scientific method. In the arena of historical inquiry, I think it is entirely appropriate for the researcher to look for natural (as opposed to supernatural) explanations as the first option. And when the researcher’s methodology causes him/her to run aground, such as trying to draw unsupported distinctions between the Jesus of faith and the Jesus of history, the defenders of the faith used the historian’s own techniques to critique their conclusions. (For example, see the works of NT Wright, Craig Blomberg, Craig Evans, Ben Witherington, etc.)

I also should like to point out that Christianity, on the whole, has benefited from challenges to it. We know far, far more about the Bible than we would if it had never been questioned. The liberal theologians and textual critics of the 19th and 20th centuries pushed us to better understanding of the texts, better understanding of the historical context in which they were written, better understanding of Hebrew and Koine Greek, better understanding of Biblical theology, of the already-not yet eschatology of the kingdom of God, etc.

As for me, I am more than happy to have Christianity compete openly and freely in the realm of ideas. Our faith did not spread by the force of arms; it spread by the force of spirit and truth. Methodological Naturalism is not the enemy. Our enemy is untruth. And that is why, friends, I find it so deeply disturbing that those who say they are defending the gospel against the “lie” of evolution are, far too often, found to be distorting facts, misrepresenting conclusions, ignoring relevant data, etc. Far more damage is caused to Christianity by such lies than by any confrontation with competing ideas, evolutionary or not.


Hi everyone. Thank you very much for patiently waiting for me to post here. I haven’t had much sleep during the past few nights: it’s been a pretty busy week, which is why I’ve been so late in coming over here.

I’d just like to make a few quick comments. Re my list of 31 great scientists who flouted methodological naturalism: of course I would agree with Professor Ted Davis that it’s up to scientists to define what counts as science. My aim was to show that until relatively recently, they didn’t define it in a way that rigorously excluded God-talk from science books; in fact, many of them made arguments for God in science books. Should science go back to that? At the very least, I would like to see it return to a phase where God-talk would no longer be considered taboo in science texts and in scientific papers. The current climate of self-censorship is intellectually stifling.

Re the quote from James Tour: it’s true that he doesn’t call himself an Intelligent Design proponent. But his reason for doing so is simply that he doesn’t think science can prove Intelligent Design. I’d agree with him on that. I’d also agree that for all we know, science might disprove the case for ID tomorrow.

Nevertheless, Professor Tour does make a strong case in his talk, “The Origin of Life: An Inside Story,” that foresight would have been required in order to produce life. I provide the relevant quotes here:

Professor Tour regards the origin of life as a profound mystery, but he acknowledges that future scientific advances might demystify the origin of life. Fair enough. But in forming one’s worldview, one should be guided by what we now know. We cannot second-guess the future.

Some people would argue that science has a long history of eliminating gaps in our knowledge. That’s true, but it also has a history of creating new ones. The origin of life would have been no mystery to Aristotle or Aquinas: they envisioned it as an ordinary process. Science, as I see it, creates as many new mysteries as it solves.

Finally, I think it would be theologically very dangerous for someone to hang their faith in God on the nail of Intelligent Design, which doesn’t even claim to be able to prove the existence of a Designer, let alone God. All ID proponents claim to do is provide very good evidence for a Designer. I’ve previously warned against the dangers of putting all one’s theological eggs in one basket, as far as proofs for God go. So I can sympathize with Blaise Pascal’s caution. But at the same time, I would say that ID can buttress the philosophical arguments for a necessary First Cause and an Intelligence behind Nature - especially for modern-day people, who are wary of relying exclusively on metaphysical arguments when making theological commitments. My two cents.

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Joshua, I would greatly appreciate your opinion on how I, in maintaining my Christian Faith, have approached the ‘rule of methodological naturalism’. Find it on the link: http://www.albertleo.com/scireligion.pdf

Sorry it is so long, but you can skim it.
Al Leo

Hey @aleo, you only have a couple references there. You say:

Procedural atheism (or methodological naturalism),
which is a valid attempt by science to explain natural phenomena without resort to
supernatural forces

In principle, I see where you are coming from. I would emphasize that coining the new term “procedural atheism” as a synonym for MN is not helpful at all. I would avoid that term, and instead draw the contrast between “methodological naturalism” vs. “philosophical or scientific atheism.”

And then you write.

Nevertheless, the past success that science has had using procedural atheism does
not rule out there being ‘gaps’ that remain unclosed in the future. In this presentation I
suggest that there are two such gaps that likely will remain unclosed: the beginning of
Life, and the beginning of Humankind.

Many scientists would think that these are not intractable gaps. I’m inclined to agree, but am not certain. Still, your claim is true in principle, though even if there are no gaps, that does not really have any bearing on our faith. If God uses natural means to accomplish his purposes, who are we to complain? We look to Jesus, not to science, for confident faith.

@vjtorley thank you for joining us here. I want to start by pointing out all the places where I see agreement with you.

Well this is a major point of agreement. This, I think, is the big question.

My response would be: it’s fine by me if scientists define their enterprise. Why shouldn’t they? But if scientists get to define it, then they can also redefine it, in a way that dispenses with the principle of methodological naturalism, if they so choose.

We agree here too. I did not know you thought this way. Honestly, this makes you an outlier in the ID movement, doesn’t it? I thought most think that ID philosophers get to decide what science is.

Once again we agree here too. I’d say that this is a great unknown. We do not know yet what happened, and even if it happened by natural means, we do not know if science can figure it out.

That is absolutely correct.

Once again I really agree with you here too.

So where do we disagree? Well, more than disagreement, I’m hoping for some clarification…

This seems like such a minor change, but it is consequential.

In science, we are allowed to talk about God in our personal reflections all the time. In our scientific work, the rule in place for good reason I think, and we all benefit from it. I’m glad that I can read scientific papers without regularly encountering Odes to Vishnu, Buddha, or unnamed Middle Eastern religions. I’m happy to leave Jesus out of my scientific papers as a common courtesy to other. Why, exactly, is this rule stifling? For you in particular, as a philosopher, how is this rule stifling? Can’t you publish in philosophy journals referencing God whenever you like?

Also, the 31 examples you give in the paper, only a fraction of them are actually violating MN. Most of them are just commenting personally about their scientific work. This is allowed now days already. If that is all you want to see more of, why not just encourage more Christians to enter the sciences? If they have peaceful ways of engaging science (like BioLogos instead of ID), they will be embraced and can declare God in science too. MN makes this vision possible by protecting the peace in science, so we can hold our religious beliefs without having to fight professionally about them.

I’m not trying to be difficult here. I’m just trying to understand you…what do you think?

We have talked about this in the past. I agree that science is a strong epistemological challenge to our faith. How do we know it is true? To this, I look to the Resurrection, as you do also, and my true experience with the Risen Lord. Encountering Him, why do I need more? I suppose more evidence would be helpful, but what if ID arguments are not strong in science’s current rules. How useful are they really?

IMO, this part of the disagreement is really beside the point, and can be saved for later if you like. I’m more interested about why you think MN is stifling in science.

Also, I hope that @Kathryn_Applegate chimes in. I know she was wanting to comment on MN…

“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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