The Neutral Theory of Evolution


This is the most important and misunderstood theory of evolution. It is this insight that ultimately falsified Darwinism back in the 1960s. Neutral theory vs. pan-adaptionalism.

The study of any biological features, including genomic sequences, typically revolves around the question: what is this for? However, population genetic theory, combined with the data of comparative genomics, clearly indicates that such a “pan-adaptationist” approach is a fallacy. The proper question is: how has this sequence evolved? And the proper null hypothesis posits that it is a result of neutral evolution: that is, it survives by sheer chance provided that it is not deleterious enough to be efficiently purged by purifying selection. To claim adaptation, the neutral null has to be falsified. The adaptationist fallacy can be costly, inducing biologists to relentlessly seek function where there is none.

If you care about understanding the science of evolution, this is a must read paper. Over at Sandwalk, they are saying the same thing:

I’m happy to answer any questions that arise.

The Explanatory Power of Darwinism
Which Irreducible Complexity Argument?
Four Christian Views of Evolution
What is the Extended Evolutionary Synthesis?
The Dissent from Darwinism

Now here’s a conundrum, then. Koonin describes the futile adaptationist quest for function, and that neutral theory predicts how what is essentially a random walk permits survival regardless of function. Presumably lip service is paid to adaptation by natural selection as a bit-player, but nobody seems very keen to quantify that.

And that overturns the major presupposition of the original Darwinism, that variation under natural selection ensures that all surviving changes are for the benefit of the organism - ie, they are “for function”. Neutral theory says that many or most features of living things are not “for function,” but for nothing.

But (BIG but) since the dawn of history, the recognition of design in nature - exemplified by the formal natural theology of the historical Christian tradition from the Fathers to ID - has not been about function alone, but about the evident beauty, utility, interdependance, moral instruction and a thousand other things, all pointing to the wisdom and skill of God manifest in his orderly creation of this biological part of his cosmos.

This may not (as per threads here on ID etc) be proveable, but neither is it a vain intuition, being shared by me, Joshua, Kathryn Applegate at BioLogos, the Discovery Institute, the Catholic curia, RTB, AOG and even Richard Dawkins or Francis Crick (staunchly resisting its compulsion), not to mention Muslims, Hindus, Aristotle and Plato.

But nobody I’m aware of has seriously suggested how the random walk of neutral evolution could possibly result in pervasive “beauty, utility, interdependance, moral instruction and a thousand other things.” Such mechanisms have no wisdom to manifest, and no surrogate for design, meaning that necessarily all such perceived qualities must be mere pareidolia.

So once we pitch adaptationism, as our sole quasi-design mechanism, into outer darkness, and remind ourselves that “biological function” was the reductionist view of design demanded only by that theory’s insistence on survival of the fittest individual, it seems to me the conclusion is obvious. Neutral theory explains molecular changes, but has little to say about biological form, taking “form” in the wide sense of the evident wisdom and purpose in the biosphere, visible as soon as one looks out of any window, or at the dog under your desk, or at the hands with which you type.

In other words, neutral theory does not demonstrate that there is no design in life (including, but not restricted to, “biological function”), but only that neutral theory is not remotely adequate as an explanation for what is most interesting about life, including its evolution.

In so thoroughly refuting adaptationism, neutral theory may not have quite cut of the branch naturalism was sitting on, but it’s sawn most of the way through it.


@jongarvey , I have to, no, MUST keep telling myself that the evident design and eloquence in your prose IS NOT REALLY THERE, but only a manifestatiom of an evident struggle to survive, on your part. : )


No - that would be an adaptationist error. No struggle - just luck, and my writing not yet being weeded out by purifying selection.:smile:


Such metaphysical dogma parading itself as neutral wisdom will not be tolerated.


Neutral theory does not refute adaptation and natural selection, to be clear. It just refutes the notion that these are the dominant mechanisms of change.


What kind of percentage of the morphological features of, say the peregrine falcons I saw over the house again today are the result of adaptive genetic natural selection, would you say? Compared with, say, its relative, the smaller hobby I saw trying to take out a swallow a week or so ago, whose lifestyle and equipment are very different? And what features are the result of dominant neutral evolution?


I would think that the time period which you look at would determine which is dominant. Over short time intervals adaptive generic natural selection would matter most especially with varying climate and changing environments. Over long time periods, neutral evolution would dominate. Dr. Swamidass, is this a proper understanding of the processes involved? Also thank you for providing this dialogue. I learned a lot about modern evolutionary theory by reading the material attacked. It is truly remarkable about what has been learned in the past ten years or so. Evolutionary theory is even more dynamic than the theory of gravitation where a lot of new discoveries and confirmations of General Relativity are taking place.


Great question. This question is a great prism for the failings of the public debates. For 50 years, there has been one right “flavor” of answer to this, though you wouldn’t know it from reading the “popularizers” (which I mean in derogatory sense here, so I won’t name them). The right answer is: "most their differences, if not all of them, are neutral, and have nothing to do with positive selection."

But first, what is a peregrine falcon and a hobby falcon? They are two very similar birds. There is much internet discussion on how to distinguish between the two of them:, as they are very very similar. They arise just about 10 mya in the fossil record, and are different species in the same genus (like Sapiens and Neanderthals. They have slightly different hunting habits, slightly different sizes, and slightly different colouration. (See photos at top of post).

So the null hypothesis, the most likely explanation, for these differences is neutral drift. This is especially true for animals with minds that can adapt their behavior to their form, and its even true for plants. For example, it is likely more valid to (1) explain the distribution of plants as a consequence of neutral variation of their traits, than to (2) explain the variation of their traits as a consequence of selective pressures. Same is true of many traits. This does not deny positive selection, but it is certainly not the first explanation we should invoke. It is not the null hypothesis.

Any adaptationalist story is highly suspect, and most likely wrong. It is probably a nice and convenient “just-so” story to make the us feel better at night. Most these differences likely do not contribute much at all to selection. Of course, maybe one or two traits were strongly selected for in their evolution. That is a hypothesis worth testing, but that is not our default null hypothesis.

Going a little deeper, @patrick has the right instinct to think that traits might be classified somehow to figure out which ones are most likely to be neutral, or to be positively selected. I’m not sure the time scale is the right one to be looking at.

Rather, the more fine-grained the trait, the more likely it is to be neutral. For example, at one end of the scale, a point mutation difference between the two of them is very unlikely to be anything but neutral. However, the difference in coloration (or perhaps body weight) is perhaps the most likely thing to be positively selected. Even that, however, is dubious in an apex flying predator like falcons. Look at bald eagles; there is no adaptive explanation for their baldness. :eagle:

For any adaptive trait, however, such as their ability to fly with feathered wings, the majority of changes required to evolve wings will arise by neutral drift, not by positive selection. So even though wings as a whole are positively selected, many of their internal details are fixed by random drift and common ancestry.

That explains why, for example, bats seem to fly just fine without feathers, and use sonar to locate prey. Birds, on the other hand, are reliant on their eyes, and use wings with feathers. We can certainly imagine a world full of featherless birds (see pterodactyls). There are many ways to solve the same problem, and the precise way a given organism ends up solving it depends on drift and common descent much more than our intuition would have us believe. The ability to fly certainly came with strong positive selection, but the internal details of how to fly were not in the same way we might think.

The linked article too mentions exaptation, which is a critical concept. The key materials for feathered flight, feathers, pre-exist winged birds. That is because they had other uses. Feathers end up being co-opted for a new purpose. Incidentally, the evolution of feathered flight is really remarkable, and goes through an unexpected intermediate, four-winged birds.

Any how, coming back to the main point, the null hypothesis is neutral evolution. There needs to be evidence to make us think there is anything else at play. This becomes a stronger heuristic the more detailed we look at biological systems. The more fine grained our analysis, the more we expect neutrality to dominate.

That is why neo-Darwinism ends up being false. It has nothing to do with naturalism. It is just a false theory of origins. Neutral theory is the real revolution of evolution, and it took place 50 years go.


@jongarvey you should also read this paper from 1979 with great relish, thinking about questions of teleology and such,

Read that linked paper, on Panglossian and the Spandrels. That is a modern classic, from Gould. Then review the public debate on natural selection and evolution. Try no to be too appalled by how much they missed the boat, on all sides. Neo-Darwinism has been dead for a long long time.


@swamidass How do you navigate the fuzzy use of labels when discussing different evolutionary biology models? You are clearly using neo-Darwinism to refer to the early 20th century understanding which did not include neutral theory. Others like Mayr prefer to have neo-Darwinism refer to the current collective understanding of evolutionary biology, whatever that might be (presuming it descends from Darwin’s theory in some fashion, I imagine). Moran seems to go the other way, using neo-Darwinism for the outmoded view that was challenged not by neutral theory but earlier by the modern synthesis, while using Modern Synthesis for a more expansive understanding that (at least partially) accommodates more recent developments including neutral theory. (


Very good question.

I lean towards with Larry Moran, because I think he has the history and the science most correct.

That is how Moran uses it, and I think that is correct. If you go back and look at the literature in the 1950’s and 1960’s they all defined themselves in opposition to neo-Darwinism, not as an extension of it.

That is a confusing anachronism. I strongly resist this. Such use fo the terminology contributes to a great deal of misunderstanding. I have yet to meet a knowledgeable scientist that considers themselves a neo-Darwnists. This would be like finding a Newtonian physicist.

I’m resistant to the term modern synthesis (which technically predates neo-Darwinism I think). This is one point on which I deviate from Moran. I’ve gone through several options on the right term to use, especially when engaging the public.

Ultimately, I’ve settled on “evolutionary science.” This is the most overarching and neutral term that causes the least confusion. It does not force readers to make a choice in the “modern synthesis vs. EES” internecine war, and it doesn’t invoke the controversy of Darwin’s name, and it doesn’t direct people falsely to positive selection driven change. For all those virtues, when engaging the public, “evolutionary science” is the best term I’ve found.

When asked to clarify, I lean heavily on “common descent” and more specifically on “the common descent of man.” The mechanisms of change are really beside the point for the public. Science is silent on God’s action, and certainly could have inspired mutations. The evidence for common descent, however, is overwhelming and with the most theological consequences in the “common descent of man.” That is where action is. The rest is all really beside the point.


How do you navigate them?


Similar to you, I prefer “evolutionary biology” when possible. Perhaps “science” would be even more appropriate; maybe I still cling to some bias towards my preferred sciences.

I try to avoid all variations on Darwinism when possible, because as you note that invokes all sorts of associations with the person of Charles Darwin. Relatedly, given how often he is referenced, I think some folks think the sum total of science around evolution was done by Darwin and nothing else has been added in 160 years.

I’ll sometimes contrast the modern synthesis and the extended synthesis in the context of conversations around quotes from extended synthesis advocates. And then only in an attempt to explain how those scientists seem to be saying or writing things that sound critical of evolution, but are really critiquing one specific model while simultaneously advocating for another model that is still very much evolutionary biology with common descent.


Your welcome @patrick. I felt the same way when I first learned of all this. It was pretty stunning how much of this is missed by “experts” debating this in public. They are just talking past the current understanding of evolution, not ever really engaging.

Same here. That is one thing that keeps me hook. Ironically, BioLogos was never really that engaged with the scientific side. On the other hand, interlocutors from ID (e.g. @pnelson and @Agauger and @vjtorley) have been informative, even when I have disagreed with them. There has been more than one time I’ve received an email from @pnelson with something in the literature I would never have found without him. I first got to know @Agauger and @vjtorley in a exchange about the evolution of placentals and pseudogenes for egg yolks. That was an immensely informative exchange, where I learned a lot. Evolutionary science is just really interesting, and ironically I’ve learned a lot by engaging its critics.


Except, they are actually advocating for the same model, with just a different name. :smile:

Evolutionary biology is just fine by me.


@jongarvey there is more to this than you’ve seen so far. Larry Moran echos a good point from Koonin:

Koonin also makes an interesting point about species with historically small population sizes. These species accumulate a lot of junk in their genomes because natural selection is powerless to remove it. This junk DNA provides a pool of potential exaptations that usually lead to an increase in complexity (constructive neutral evolution). Thus, paradoxically, a weakening of natural selection often leads to more complexity.

So that junk DNA has a purpose, so is it junk? :smile: Purpose is in the eye of the beholder. There is no such thing as junk, but that is not what we might think it means.



I chose those two species because they’re so closely related but, as soon as you get to observe them, completely distinguishable. Ask any falconer! I could have added a member of the third falcon group, the kestrels, whose form and lifestyle are equally unique.

Anatomically, there are diferences such as the specialised nostrils of the peregrine enabling it to stoop at 200mph while breathing (and emulated by jet fighters). You can just see the lack of those in your hobby photo (though it’s the Australian rather than the British model).

Comparably, the wing geometry of the two is different, and it’s no surprise that the more swift-like wings of the hobby are employed in a flying style that is very similar to swifts and swallows - which are its prey.

The behaviour, as a package, is entirely distinct: most characteristically the peregrines will appear as a pair once in a few weeks - ranging a mile or so from home, at which distance their unique vision can spot prey - soaring high and, if they attack, coordinating their stoops from a great height to make a killing blow. If the tiercel misses, the falcon has a go, because they’re too fast to turn quickly. The hobbies, on the other hand, one encounters singly, typically finding them flying at head height in front of your car the way and following the corners the way swallows do - they take out dragonflies and swallows in level flight. Hobbies fly for fun - peregrines save their energy for the hunt.

The flight of the Hobby is unique. When hunting it will
fly along at a fair height, gliding and winnowing alternately.
If it sees a prospective quarry it hurls itself after it, following
the turns and twists of its prey with rare skill and great

Nothing like a peregrine at all.

Nesting (including brooding, feather and feeding development), calls, flight, diet, flocking are all different, but the overall impression is that you are seeing two different specialists - to the extent that after awhile, a mere glimpse is enough to distinguish them. I’m reminded of Arthur Jones who, doing his PhD work on Cichlid fish, was able to spot a species he’d not seen before in an aquarium out of the corner of his eye, from the way it behaved.

These are just the gross differences - ornithologists will note very many differences in character and behaviour that make up their unique roles in the world.

Now, one way of viewing this would be to say that, finding itself lumbered with unique nostrils, wing-shape, habits etc by neutral evolution, the peregrine soon found out it would starve trying to chase swallows, and elbowed itself the vacant niche of fastest bird in the world. Net result - superb adaptation of the entire lifestyle to a mainly accidental body plan. And such lucky accidents all within 10m years! Owing to a series of manufacturing errors, the Ford factory ends up with an F1 instead of a people-carrier and decides, consequently, to race, the company being equipped with “minds that can adapt their behavior to their form.”

Likewise for the hobby which, suffocating if it tried to stoop at high speed, was lucky enough to find itself with more manoeuvrable wings and body (remarkably similar to the most aerial birds in the world, the swifts, which touch ground only to breed); and with a convenient supply of swallows and swifts now within grasp. It took to nesting in trees rather than on cliffs (because it found itself with a compulsion to co-opt old nests instead of preferring laying on bare ledges).

All this, according to neutral theory, occurs because of the overload of adaptive selection in small populations, and a lot of weeding out of rubbish by purifying selection… fortunately the random changes keep the birds’ mental agility intact so they have the wit to turn the outrageous blows of cruel fortune into what - to all appearances - resembles supreme design for a special role.

And that’s how the elephant got his trunk.

Is Quantom Randomness Random to God?

I believe you!

I’m not saying its only neutral theory. Of course there is selection at play here. Though many of the distinctions you point our are behavioral too, and it is unclear how much of this is independent of the changes in form. Some of the behavioral differences might be them making the best use of the body plan they have.

I never said that natural selection wasn’t part of it. I’m sure it was.

I also never said that design wasn’t part of it. I would also agree, that this…

All these things can be true at the same time. However, the more granular the details, the more likely it is to be neutral. Even most OEC and YEC would agree the two share a common ancestor. That does not deny natural selection or design. It is just that most of the differences are likely to be neutral.


Well, one needs to cash out that first sentence philosophically and theologically: is a process of truly neutral change (in evolutionary terms every bit as undirected as any other mutations, only also undirected by selection) also capable of being designed? We still have the problem of arrival of the fittest that plagued Neodarwinism.

It’s the old problem of ontological randomness being seen as a cause. What does “neutral” mean if the total result is a peregrine falcon? That the changes were random? But that’s a naturalist metaphysic that lacks any coherence anyway: it means we don’t know what caused them. That the changes were not directed to the organism’s benefit, and not made so by selection? But here’s the peregrine, the bird flown only by princes because it is so special, and here’s the hobby keeping up with swifts. Don’t tell me most of the F1 car is due to mildly deleterious accidents when it’s just won the world championships.

In the two falcons, I’ve chosen examples in which virtually all the identifiable differences contribute to their specialist roles and excite the admiration of naturalists and engineers. In that context, to attribute the majority of features to neutral change… and to limit natural selection or design to some unspecified role, raises more questions that it answers.

I’ll happily grant that the hobby’s red trousers (absent from its Australian cousin) might be of no adaptive significance: with over 700 genes known to contribute even to human height, a few spandrels are almost bound to occur if you’re talking about the hobby genome. No doubt hobbies have learned to love red trousers as somehow crucial to their chosen ecological niche.

Now that might give a lead. We put the falcons to one side, and home in on the molecules, and lo and behold, most of the change appears neutral. But equally, if you forget me as a thinking human being and home in on my cell fluids, it will look to be mostly Brownian motion going on at the granular level. But zoom out again, and Brownian motion has not explained the man at all. And that takes me back to my original point at the top of the thread: when one’s evolutionary theory is driven by uncorrected accidents, the existence of “forms most beautiful” likely has a better explanation waiting to be discovered.