Methodological naturalism

I’m a bit rusty at science. What exactly does ‘methodological naturalism’ mean? Does it mean that one should always presuppose a non-supernatural explanation? Am I right in thinking that this in no way proves that God cannot be shown scientifically, or that scientists cannot be believers?

It’s not rigorously defined, so there is no “exact” response.

That’s pretty close to how most people think about it, when/if they think about it at all. I wouldn’t use the word ‘presuppose’ and would probably opt for something like ‘proceed as if there will always be’, or maybe merely ‘prefer’ but I think you got it.

Yes, I think you’re right about those things, but a lot rests on what on earth it means to “show God” scientifically or otherwise.

Lots has been written about methodological naturalism, some of it by very, very good Christian scholars. Look for stuff by Del Ratzsch.

The problem with the expression “methodological naturalism” is that it means different things to different people, and as such it is very easily misunderstood.

From a scientific perspective, it simply means that under normal circumstances, the day-to-day behaviour of the world around us can be explained in terms of laws and equations, such as Newton’s laws of motion, Maxwell’s equations, and so on. The fact that this is so allows us to use these laws to make things, such as cars, cameras, or computers, or to find oil, or to come up with health and safety regulations.

However, there’s a widespread preception in Christian circles that it does mean ruling out (or at least, failing to consider the possibility of) miracles. This is especially the case in discussions around origins (creation/evolution and so on).

For this reason, I personally prefer to avoid using the term. Instead, I tend to focus on the more important issue of pressing for factual accuracy and technical rigour. When it comes to the possibility of miracles, I merely say that while they could be an alternative explanation for what we observe, the miracles that one is proposing should not be deceptive in nature, and they should not be merely a get-out clause for rejecting scientific findings that one does not like.

I explain my thinking in more detail here:


By its very definition, science deals with non-supernatural phenomena. A scientific explanation can’t include a phrase like, “and then God made it happen.” That does not mean science is atheistic. Science is absolutely silent on the subject of God. A good scientist can be religious or an atheist, just as a good scientist can follow any sport or listen to any kind of music. Anything a scientist does or thinks outside the field of science is completely irrelevant.

This is no different from other fields of human endeavor. A carpenter does not use inferior materials and then pray that the house will stand up. A mathematician does not say that 2+2 can equal 5 if God wills it.

Where science and religion can come into conflict is when scientists start to believe that the scientific method can apply to all areas of human experience, or that anything outside the realm of science is meaningless. Conflict also arises when religious people begin to restrain what scientists can study and what conclusions they can draw.

The reason why this concerns me is because I’ve seen New Atheists use the idea of MN to attack scientists (specifically Francis Collins) for believing in God. I’m personally on the fence as to whether or not the existence of God can be shown scientifically, though if this is correct it would go a huge way to proving a sentient higher power (which I think is the best way of defining God), certainly more so than any ‘fine tuning’ argument, which could conceivably be coincidence. I personally prefer philosophical/logical arguments

Usually it means the seeking of natural explanations for natural phenomena. It doesn’t involve the existence of God or any other supernatural explanations. Think of a doctor swabbing your sore, swollen throat, sending the sample to a medical lab. The lab technicians, whether or not they are believers, are going to try to identify bacteria or viruses. They aren’t doing their jobs if they blame an infection on God, Satan, karma, or whatever.

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I’ve enjoyed some thinking done by @Swamidass over on his blog on this topic and some of the challenges to changing/hijacking what is and is not science that’s been done by both extremes (New Atheists and Creationists):


Thanks @pevaquark. I’d also add that in my current thinking I do not think that Methodological Naturalism is correctly named. The name itself is anachronistic, because it does not arise from atheism, but from Christian theology (see Bacon’s Novum Organum). Though I still affirm it as the rule of science, the name itself might be creating some unnecessary conflict. Perhaps recovering the theological roots could be helpful.

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That’s a bit like attacking a baseball player because he also plays tennis on the side.

The scientific method is a set of rules and guidelines, just like baseball has a set of rules. Nothing in those rules says that you have to follow them for everything you do in your life, only that you follow those rules while doing science. In fact, the scientific method says nothing about God or the supernatural. There is no reason that Collins or anyone else is required to use the scientific method for all of their beliefs. All that people ask is that they declare which of their statements is science and which are not.

When people say that you can only use natural mechanisms within science they are actually saying that your hypotheses have to make predictions about the empirical results of an experiment. Most often, this requires a mechanism that can be manipulated and/or tested. Notice that I don’t have to use the words natural, supernatural, or God in order to describe the types of things that the scientific method requires or excludes. What you need are repeatable experiments that produce consistent and empirical observations and a proposed mechanism that can be further tested and manipulated.

For better or worse, predictable mechanisms that produce measurable effects within our universe are defined as “natural”. This is contrasted with the implied definition of supernatural which is “unpredictable and/or undetectable processes”. If God interacted with the world around us in a predictable and detectable manner, then God may very well be defined as natural, just as humans are defined as natural. All the kerfuffle about the scientific method (i.e. Methodological Naturalism) really comes down to the worldview that people bring to the table (IMHO), how they see the relationship between their religious beliefs and the world we can measure around us.



While that does make sense is many scientific discussions, it does not correct in all. It makes sense basically physical science, but not biological and human sciences, which are scientific also.

A big reason why the science of evolution is so difficult to discussion is because it is on the border of the physical and organic sciences. Evolution does not follow the laws of physics. It follows the rules of genetics and ecology.

Does MN really apply to biology?


That is incisive and correct. I’m going to use that one.

A question for you, @Reggie_O_Donoghue is why you would grant the presumption of logic to the New Atheists. They are are well known for twisting logic and facts to making emotive appeals. You just cannot trust much coming from them. They are not the best examples of atheists. I’d look instead to how atheists like @T_aquaticus handle these questions. He answers in the way of Eugenie Scott:

Because creationists explain natural phenomena by saying “God performed a miracle,” we tell them that they are not doing science. This is easy to understand. The flip side, though, is that if science is limited by methodological [naturalism] because of our inability to control an omnipotent power’s interference in nature, both “God did it” and “God didn’t do it” fail as scientific statements. Properly understood, the principle of methodological [naturalism] requires neutrality towards God; we cannot say, wearing our scientist hats, whether God does or does not act.

This is not to say MN has no problems.

The biggest problem is that there is no solid definition of “natural” and “supernatural”. This turns out to be an incoherent divide. This makes sense, however, if MN is an anachronistic attempt to explain a theological boundary in non theological language.

It seems the theological distinction that MN is trying to capture is Creator vs. creation. Not supernatural vs. natural. Understood this way, we immediately see this is about defining purpose of inquiry into nature to understand creation, but not to interrogate the Creator. That is why immaterial causes (non naturalistic) are regularly considered in science (including design!), but divine design is excluded. Science takes a hard pass on theological questions. That is not its purpose.

This view, it seems, solves the puzzle of MN in the first place. Its only a statement that makes sense when understood in within (or perhaps in opposition to) theology. This is not to say that atheists cannot do science. Its just a history that makes sense of why MN is part of science, even though we cannot define “natural.”

Actually, no, evolution does follow the laws of physics. It may not appear that way, but that’s only because you’re dealing with complex systems with many layers of abstraction on top of them. But ultimately, when you dig through the abstraction layers, you still find Maxwell’s equations, Heisenberg’s Uncertainty Principle, the laws of thermodynamics, the Standard Model of particle physics, chaos theory, and so on and so forth, at the bottom.

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I completely and emphatically agree. The scientific method didn’t appear in a vacuum, so it is burdened with the culture and cultural history that it emerged in. Early on (1700’s?), “natural” mechanisms were seen as dangerous and even heretical because they proposed mechanistic processes as the cause of the things we see around us instead of God acting directly on nature through mysterious means. I think that is where we might have inherited those burdensome definitions of natural and supernatural. Since then, theological outlooks have evolved to include concepts such as pantheism and God acting through nature instead of in opposition to it.

In my own view, it’s not as if science takes a pass on theological views. Rather, some of the questions posed by theology are simply not scientific (i.e. fail to meet the requirements for a hypothesis). This may be a case of Tomato v. Tomahto, but I think it is a subtle yet important difference. To use an analogy, it is like the Friday cut in a professional golf tournament. If your 36 hole score is too high then you don’t make it into the final two days of the tourney. It would be incorrect to then state that they won’t let you play because your height is under 5’10". It’s not as if science leaves a question alone simply because someone throws a theology sticker on it.

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Biology is an emergent property of physics, as are all of the physical sciences. Everything that occurs within biology conforms to the laws of physics. Biology wouldn’t work if it didn’t follow basic physical laws like thermodynamics.

Biology is a field of study, so it wouldn’t be correct to say that MN applies to biology. MN applies to hypotheses within the field of biology. Theories are collections of hypotheses, and theories are also used to form new hypotheses. For example, you can use the theory of evolution to create a hypothesis dealing with the distribution of endogenous retroviruses among primate species. You would predict that orthologous and non-orthologous ERVs should produce a phylogenetic signal which you can test for using various objective means (algorithms that test for tree-like structures in data). You can then run an experiment where you map ERV’s in various primate genomes, run them through those algorithms, and then see if the results match the predictions made in the hypothesis. That’s MN in a nutshell.

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In 1971, Dr. Blobel and a colleague, Dr. David D. Sabatini, who later headed cell biology studies at the New York University School of Medicine, proposed a bold idea known as the “signal hypothesis.” It suggested that each protein carries in its structure a sequence of signals comparable to address tags on airport luggage or ZIP codes on mail to ensure that it all arrives safely.

The signals, Dr. Blobel found, are chains of amino acids created by protein-making machines that read distinctive RNA codes and then fix them on each new batch.

Like transmitters, these signals order receptors in membranes to open up watery holes so that proteins can pass through. They then act as GPS devices to cross the crowded terrain of a cell or a human body and, like finding a mailbox across the universe, penetrate precisely the right worksite organelle for each protein’s assigned task.

Proteins have many tasks: rebuilding or replacing constantly dying cells, protecting against viruses and bacteria, regulating body chemistry, reading DNA to make new molecules, releasing hormones to signal and repair tissues and organs, carrying and binding atoms throughout the body, and many other functions.

From the New York Times obituary, 2/20/2018, for Gunter Blobel

The point this statement makes is that biology is different from physics. Proteins are molecules, but in organisms they act as if they can think, while inorganic molecules do not. This is how organic evolution is different from mechanistic physics.

Nowhere in that process is there something I would call “thinking”. The proteins aren’t deciding which RNA molecules to bind to. What I see is a lot of unnecessary and inaccurate anthropomorphizing. Proteins don’t use satellite signals to locate their target in cells. They bounce all around until they run into something that they bind to, and that binding is entirely described by physics (or more precisely chemistry). It’s like the north pole of one magnet sticking to the south pole of another magnet.



Roger, are you seriously going to advance this idea that in living creatures, proteins act intelligent, but non-organic molecules do not?

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I was terrifically impressed by energy of your writing in this essay !!! Especially here in this section:

"[Christian Evoutionists]. . . do not describe yourself as “opposing creationism” or “combating creationism” or “arguing against creationism.”

By expressing opposition to creationism itself you are giving yourself the appearance of being motivated by your own presuppositions again. You are also giving the impression that you would not take them seriously even if they did manage to come up with rock-solid, indisputable, watertight evidence to support their case.

It . . . makes me cringe when I hear Christians making this objection. This is an objection that is very easily misunderstood, and you can all too easily end up sounding like a non-Christian when you’re making it. It also opens you up to charges of “compromise” — a favourite YEC accusation. So be careful."


". . . the right way: demand that they get their facts straight. What you are to oppose, combat, and argue against, is sloppy thinking, falsehood, unjustified assertions, and resistance to critique. As such, your response to young-earth creationism needs to be simply a demand that YECs get their act together and start applying the same standards of rigour and quality control as everybody else."


Absolutely. That is my whole point.


I am not sure if I agree or not.

My main point is that they say that they are defending the Bible, when in truth they are destroying the Christian faith.

The problem is not bad science, but bad theology.

“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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