The Neutral Theory of Evolution

I reviewed Koonin 2009 back in 2011, so am reasonaly familiar with his overview. Koonin also says that over evolutionary history there is no tendency to increased complexity:

There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation.

But complexity isn’t the issue - making complicated things is easy. Making complicated things that work beautifully is not. It seems not to have got any easier since we began to see that most phenotypic traits are related to most genes, and that that is complicated by epigenetics and sophisticated mechanisms like alternative splicing (large differences between similar species like chimps and humans, or perhaps hobbies and peregrines).

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That I agree with. There is no good account of beauty in evolution. I fall back on CS Lews and Is Theology Poetry? Have you read this yet?

Though variations on a theme very beautiful. As a musician you should know…

I wonder why that is?

Nope, but I will. Thanks for the link.

That, of course, is one of those “functions” that all theories of evolution leave out. I was tempted in the previous comment to say that the hobby’s red trousers help ornithologists both in identification and appreciation, but it would go beyond my point. Yet what else is the entomologist’s appreciation of a trayful of near-identical mosquiotes, but a finely-honed sense of the beauty of minor variation?

But to answer the Lutheran, I think he sets up a false dichotomy between art and engineering. One of the things I like about music is that it’s a technical and mathematical as well as an aesthetic challenge, perspiration as well as inspiration. Not to mention the emotional, spiritual, communicative and so on.

So to play a spoken piece in 5/4 time is as much a process of calculation and physical training as (one hopes) an aesthetic experience for the hearer. And of course the George Lowden’s design for the guitar is art and technique too.

The beauty of a peregrine is, to a large extent, that it is such a superbly efficient killing machine. I certainly agree that impressing research funders is not on God’s agenda, but that was not what motivated Ettore Bugatti, R J Mitchell or Leo Fender, either.

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Shouldn’t we be calling solar power theory and applications “Teslaism?” : )


Last paragraph is a classic. It is fundamental to my point of view on these things.

Ha, yes, well, there is that. Still, it can be helpful in providing context for the quotes from extended synthesis folks to explain that they at least think they are advocating for a different model – or that the same model has evolved enough to warrant a new name. (And so the species problem comes to evolutionary biology at yet another level.) At the same time, it can also be helpful to bring up the point you are making; after all, the whole reason there is an ongoing conversation from which to pull such quotes is that some folks don’t see different models.

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(The above is quote of @swamidass quoting Larry Moran, but I haven’t mastered the forum formatting sufficiently to make that clear. Thus this text, so we all know the actual source of the statements.)

This reminds me of something similar that Stuart Kauffman talks about with regard to autocatalytic sets. An autocatalytic set is a set of molecules (or more generically, entities) that collectively catalyzes the production of its members. These sets tend to be larger rather than smaller, which might seem surprising at first because you might expect it to be easier to make a few molecules than a lot. But basically, as you add molecules (or entities) to a set, the number of things you need to make grows linearly, but the number of interactions that can produce those things grows exponentially. Thus we would expect such autocatalytic sets to be relatively complex.

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7 posts were split to a new topic: Is Quantom Randomness Ontological?

Yes indeed Joshua - another excellent piece by Lewis. One wishes more scientists - even Christian scientists would read it. It would be interesting to have heard the conversation at the Socratic club afterwards - no doubt there were Wellsians amongst their number, since logical positivism was much in vogue. But it seems Lewis’s thought outlived that of Ayers.

For myself, I’m reminded of a stanza from the poem extemporized by Mr Toad, which I didn’t quote in my “Indegenous Theologian” piece on the Hump, out of modesty…

The clever men at Oxford
Know all there is to be knowed
But they none of them know one half as much
As intelligent Mr Toad.

I learned that at age 10, of course, for my role. Maybe that’s the subconscious reason I didn’t apply for Oxford…

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A post was split to a new topic: Quoting Primer and Suggestions

Update on neutral theory and its prevalence (in discourse, more than in biology).

A rather poor BBC series of three “live” programmes on the world heritage Jurassic Coast was aired this week here. Only of interest because (a) it dealt with fossils and (b) it was filmed on our doorstep. It’s hard to think of anything less suited to live broadcast than looking for fossils on a beach, and it showed: “Nope, that’s not a dinosaur tooth, but an American rifle round from military exercises.”

Nevertheless, it was interesting in bringing palaeontologists at all levels to bear on some of the specimens - one of the presenters was a geologist (and shouted too much), there were several “professional” local collectors and conservators, there were palaeontologists from both regional and national museums. And one of the world’s top paleo-artists.

What was intriguing was that at all these levels, adaptive explanations were assumed for every interesting feature pointed out (usual with the admission that experts disagreed on the adaptive purpose). Spines on ammonites, horns on scelidosaurs, proto-feathers on psittacosaurus, long necks on (some) plesiosaurs, etc, etc. Nobody even hinted that neutral change was a possibility as an explanation - nothing in the whole three days was out of step with adaptationist Neodarwinism.

However, regarding the trademark features of my two closely-related falcons, above, Josh wrote:

So it seems that for British palaeontologists, at least, either:
(a) News of neutral theory hasn’t trickled through, or
(b) There is a degree of disconnect between the versions of evolution favoured by population geneticists and palaeontologists, or
© Paleontologists slip habitually into adaptationist mode for public consumption, for reasons unknown.

I’m reminded of a blog post I found by a working biologist back in 2011:

“I personally don’t give a flying f*** about modern synthesis, extended or shrunk. There is no single theory of evolution, and your perception of the dominant evolutionary principles changes drastically depending on your field. As a molecular/cell biologist, I can hardly maintain a discussion with an evolutionary ecologist - our take on the subject are [sic] worlds apart. As someone immersed in the microbial world, I am extremely skeptical of the mostly-zoocentric central dogmas - what works for lions may not necessarily work for microbes. To me, obviously the microbial models are vastly more representative of the fundamental evolutionary processes, but that’s because I’m a protistologist. I doubt a fish ecologist would agree with me there. Instead of maintaining an irreconcilable discipline-wide bitchfest attempting to form some Unified Grand Theory of biology, why don’t we accept there is no such thing?"

Nobody here doubts the diversity of evolutionary theory - but there also seems to be significant interdisciplinary diversity as well, which is worth remembering.

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I finally got around to reading this post. Thanks @swamidass.
One fundamental question that comes to mind is how does neutral theory account for design/functionality in life? With Natural selection, we could visualise small changes being selected for according to adaptive significance and the these changes adding up due to natural selection leading to big changes over time.N natural selection mimicked teleology.
However, how can a non-teleological phenomenon such as random neutral mutations create complex systems? There is no reason the changes should add up to achieve a goal such as Improved function.In fact if it’s truly neitral, the net result should be loss of function.Shouldn’t neutral mutations stay neutral over time instead of turning out to be useful and adding function?

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The abstract in Koonin’s paper:

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.

Ultimately, is there a difference between the purging of deleterious sequences and the adaptative selection of positive ones? To be clear about what I’m saying, this sounds important for how biologists think about evolution, but I’m not seeing the relevance to how I might think about evolution as a purely natural process or one guided by a designer.

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You are missing that most changes are neutral, neither negative or positive.

It is extremely important. It means any signal for a designer would be drowned out by a sea of neutral mutations. Given that so much of the data is explained by neutral evolution,

  1. we just have no way to know if God ever tinkered.

  2. we also have a clear way to test for common descent, that is independent of design.

Therefore, from evidence, we do not know from science if it was purely natural process or one guided by a designer. We can also say with high confidence that humans and apes appear to have common ancestors.

But we didn’t have that to begin with. And that didn’t stop some people from believing that God was the guiding hand behind evolution.

  1. we also have a clear way to test for common descent, that is independent of design.

Hmmm, I’ll have to read more here and see if I can grasp this.

Therefore, from evidence, we do not know from science if it was purely natural process or one guided by a designer. We can also say with high confidence that humans and apes appear to have common ancestors.

Again, I’m not sure what’s changed here. I will look at it all more closely!

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You can pick up the story here: Common Descent: Humans and Chimps / Mice and Rats.

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How would you respond to the below paper claiming that neutral theory was false? They claim the following :

In this perspective, we argue that with modern data in hand, each of the original lines of evidence for the neutral theory are now falsified, and that genomes are shaped in prominent ways by the direct and indirect consequences of natural selection.

The link has a connection to the pdf of the entire paper.

Yet on Koonin’s overview, @John_Dalton is right that selection’s main role is purifying selection of deleterious sequences.

If most changes are near-neutral (and I understand that more are classed as “mildly deleterious” than “mildly beneficial”), and most of the already rare beneficial mutations act by loss of function (apparently quite dramatically sometimes), there does seem to be some problem of a “loss of capital” over the course of time, in terms of the ability to create new functions and well-adapted forms.

It still appears that the only really creative mechanism available is the indeterminately downgraded adaptive selection. And if that’s the case, it would still be qualitatively the most important factor in the tree of life. If, though, Koonin is right that it is a bit part player, the only naturalistic option seems to be to deny that evolution is a design-substitute at all, and treat the axiomatic “endless forms most beautiful” as an illusion.

That seems often to be done by those who say evolution is a bodger, life isn’t really well-adapted at all, and the genome is a jerry-built mess. To anyone who actually knows the natural world, that’s a cognitive disconnect. Maybe that’s why it’s adaptationism, and not neutral theory, that rules wildlife documentaries - there’s a problem when good science doesn’t begin to explain the world of experience, however well it copes with genetic data.


Thank you all for an excellent discussion. @jongarvey sees to the heart, as usual, and it is, at least provisionally, the randomness of neutral evolution. But how, he says, does it account for beauty, or for marvelous form that matches function, such as the falcon. To say the form came first as a few unique but random traits and the function then fitted itself to the form is expecting too much of neutral evolution. A hodgepodge of traits might just as well produce crippled birds, failed experiments, not optimal design like the peregrine or the hobby. Here is a space for the designer to act, by guiding mutational choices. If you are going to preserve neutral theory, and natural selection isn’t strong enough to provide direction, then how does anything work, let alone be beautiful?

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If a population randomly evolves a genetic constellation that is particularly suited to defending against a disease vector like plague… is it not STILL information even if the population is EVER exposed to the plague?

Doesn’t the answer have to be Yes?

It is only because of our limited awareness of the molecular basis for disease resistance that we don’t realize the value of a genetic drift that enables half or even one third SURVIVE the first appearance of the plague.