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Professor Larry Moran has graciously responded to my five questions on the neutral theory of evolution in a recent blog post at Sandwalk, titled, Answering creationist questions about Neutral Theory (6 May 2014). I’ve highlighted Professor Moran’s responses below.
1. Do you agree or disagree with the view expressed by Motoo Kimura that natural selection is necessary to explain evolution occurring at the morphological level?
Professor Moran:
Some evolution at the morphological level can be attributed to natural selection and some is due to random genetic drift. The latter category includes neutral morphological changes and a small percentage of detrimental morphological changes.I was influenced in this view by Masatoshi Nei’s book Molecular Evolutionary Genetics (1987). [Professor Moran then proceeds to quote a passage from Nei’s book, in which he acknowledges that “there is no question about the importance of natural selection in the formation of intricate morphological characters,” but then goes on to add that “in some morphological characters a substantial part of genetic variation is nonadaptive.”]
So, the answer to your question is “yes;” natural selection and random genetic drift are both necessary to explain evolution at the morphological level.
2. How do you respond to Dr. Gert Kothof’s Korthof’s claim that the neutral theory “is not a theory of evolution,” because it “is not sufficient to explain complex life and adaptations”? If not, why not?
Professor Moran:
I respond by saying that Gert Korthof – whoever that is — doesn’t understand the definition of evolution [What Is Evolution?]. Neutral Theory and random genetic drift are integral parts of evolutionary theory. They are not very good at explaining most adaptations but there’s a lot more to evolution than adaptations.
In a footnote to his post, Professor Moran seems to have taken back his criticisms of Dr. Korthof, implying instead that I had “quote mined” Korthof. I’ll say more about that below.
3. Can you point to any complex structures, functions or behaviors which you believe could not have arisen in the absence of natural selection? (You’ve already nominated the change occurring in the human brain over the past few million years as an event in which natural selection played an indispensable role; what else would you put on your list?)
Professor Moran:
The vast majority of complex structures seem to be adaptations of one sort of another. I suspect there are many “functions” and “behaviors” that are neutral, or even detrimental, but it’s difficult to rule out any adaptive component.
4. In which of the following events do you see natural selection as having played a decisive role: the origin of eukaryotes, the origin of multicellularity, the 20-million-year Cambrian explosion, the origin of land animals, the origin of the amniote egg, the origin of angiosperms, and the radiation of mammals immediately after the extinction of the dinosaurs?
Professor Moran:
I think that natural selection played an important role in all of those events.
5. Or is it simply your contention that natural selection, while not playing an important role in the origin of complex structures and novel morphological features, exerts a refining and purifying effect subsequent to their appearance, weeding out non-viable life-forms?
Professor Moran:
No. I have always contended that natural selection plays an important role in the origin of most complex structures and novel adaptive morphological features. There are likely to many “novel morphological features” that are non-adaptive.It’s also true that negative natural selection acts as a break on evolution by preventing detrimental changes and “weeding out non-vaible life forms.”
My verdict: An embarrassing climb-down for Professor Moran
Reading Professor Moran’s post, I was struck by its muted tone. Moran believes that “some evolution at the morphological level can be attributed to … random genetic drift,” including “neutral morphological changes and a small percentage of detrimental morphological changes.” He admits that “Neutral Theory and random genetic drift … are not very good at explaining most adaptations,” adding that “the vast majority of complex structures seem to be adaptations of one sort of another.” He then tentatively proposes that “there are many ‘functions’ and ‘behaviors’ that are neutral,” but concedes that “it’s difficult to rule out any adaptive component.” He finally acknowledges that “natural selection plays an important role in the origin of most complex structures and novel adaptive morphological features,” but goes on to suggest that “there are likely to [be] many ‘novel morphological features’ that are non-adaptive.” However, since Professor Moran has already conceded that “the vast majority of complex structures seem to be adaptations of one sort of another,” it is difficult to know what to make of his last suggestion.
In short: Professor Moran’s endorsement of the neutral theory is hedged with so many qualifications that his post might as well have been written by Professor Jerry Coyne, who articulated his views with the utmost clarity, in a post dated December 5, 2012:
Regardless of the source of genetic variation, if new variants are to become “fixed” (i.e. ubiquitous) in natural populations after they arise, and to become part of complex adaptations, there is no credible alternative to natural selection for the process causing that fixation.
Too hot to handle: the book that Professor Moran refuses to review!
One of the commenters on Professor Moran’s blog post, Claudiu Bandea, posed a question about a book by the accalaimed molecular evolutionary biologist, Professor Masatoshi Nei (pictured above, courtesy of Wikipedia), which Professor Moran had previously praised to the skies, hinting that it was about time for him to honor his promise to review the book:
About a year or so ago, our host Lary (sic) Moran wrote a post entitled “Mutation-Driven Evolution” (http://sandwalk.blogspot.com/2013/06/mutation-driven-evolution.html). The post was a preview of a new book by Masatoshi Nei entitled “Mutation-Driven Evolution.” Larry ended his post saying: “I can’t wait to get my hands on a copy of this book. Look for a review in a few months.”
I don’t know if Lary (sic) kept his promise or not, but in the outline of his book Masatoshi Nei writes that, unlike Motoo Kimura and Jack King, who believed that phenotypic evolution (in contrast to molecular evolution) is caused primarily by natural selection, he believes that both molecular and phenotypic evolution are primarily caused by mutation.
John Harshman’s reaction was: “Larry, this seems to conflict seriously with your (and my) preferred definition of evolution”.
For whatever reason, Larry chose to be silent on this difficult and inconvenient issue about the Neutral Theory because, I presume, he wanted to read the book first. It would be enlightening, if Larry and John would be willing to discuss the significance of Neutral Theory and the Mutation Theory in explaining evolution. (Emphases mine – VJT.)
Professor Moran replied:
@Claudiu Bandea,
Sorry to disappoint you but I’m not going to write a review of Nei’s latest book.
You’re going to have to read it yourself.
Claudiu Bandea persisted with his question, asking Professor Moran:
The relevant issue here is science, not the book: do you agree with Nei’s proposition that Kimura and King’s perspective was wrong and that the molecular and phenotypic evolution are primarily caused by mutation?
To date, there has been no reply from Professor Moran.
Masatoshi Nei: A new kind of mutation is required to account for functional complexity!
I found out why Professor Moran hadn’t reviewed Professor Masatoshi Nei’s latest book when I had a look at what Professor Nei had to say on the origin of functional complexity. (Parts of his new book are accessible via Google books.) I was tipped off by a hint provided by biologist Kenneth M. Weiss in his Amazon review of Professor Nei’s book:
… Nei challenges the often automatic assumption that such traits are due to ‘selection’ rather than mutation. The prevailing idea has been that there’s always enough standing variation for selection to screen to enable new adaptations to occur. But Nei explains his challenge to that idea, that new adaptations for complex traits must await ‘constraint breaking’ mutations that enable new pathways out of entrenched developmental systems.
“Hmm,” I thought. “Sounds interesting.” And I wasn’t wrong. Professor Nei is no friend of Intelligent Design; he explicitly states in the last sentence of his book (p. 199) that in his view of evolution, “there is no need of considering teleological elements.” But what he has to say about constraint breaking mutations in the General Summary and Conclusion of his book (pp. 196-199) makes for fascinating reading:
The conclusions we have reached may be summarized as follows. (1) Mutation is the source of all genetic variation upon which any form of evolution is dependent. Mutation is the change of genomic structure and includes nucleotide substitution, insertion/deletion, segmental gene duplication, genomic duplication, changes in gene regulatory systems, transpositions of genes, horizontal gene transfer, etc. (2) Natural selection is for saving advantageous mutations and eliminating harmful mutations. Selective advantage of a mutation is determined by the type of DNA change, and therefore natural selection is an evolutionary process initiated by mutation. It does not have any creative power in contrast to the statements made by some authors. However, selective advantage of a mutation is also dependent on the set of other genes and the environmental conditions, the latter varying from generation to generation. (3) Evolution is a process of increase or decrease of organismal complexity and enhancement of phenotypic diversity among different species. It may or may not be associated with the increase of fitnesses (number of offspring per individual), and therefore evolution can occur by neutral genetic processes such as gene duplication and gene co-option as well as by natural selection. (4) A gene is not a random collection of nucleotides but a very specific arrangement of nucleotides that encodes a biochemically functional protein or RNA molecule. Because of this functional constraint, most mutations occurring in a gene are deleterious and eliminated by purifying selection. (5) For a gene to have a new function, constraint-breaking mutations caused by new combinations of harmonious genes and gene sequences are necessary. These mutations occur with a low frequency at functionally important sites. A gene cannot have any function without having interaction with other genes. Therefore, constraint-breaking mutation may be controlled by many gene loci. (6) A genome is an integrated and conserved set of genes that is capable of producing healthy organisms. The innovational change of phenotypic characters is generated when constraint-breaking mutations occur at the genomic level. There is a considerable degree of flexibility in genomic constraint so that diploid individuals with two different genomes can survive without trouble within a species. However, if two different populations are isolated for a long evolutionary time, interpopulational hybrids become inviable of sterile because of genomic incompatibility. This hybrid weakness occurs because the genomes of two populations evolve independently and therefore the compatibility of genes between different populations gradually declines. No positive selection is necessary for the establishment of hybrid sterility. (7) Although any organism lives under ecological constraints, such constraints are usually not very strong. Therefore, most organisms can live in a range of ecological niches, which can be called the ecological survival range. For this reason, a species may flourish easily in a new territory to which it was transferred. (8) Evolution occurs primarily as a result of constraint-breaking mutations rather than as a result of the struggle for existence. If a species moves to a new habitat (e.g. marine habitat to land), a radiational speciation may occur because of relaxation of purifying selection and some advantageous mutations for different new territories…
Neomutationism or the theory of mutation-driven evolution is also different from the classical mutationism, because it covers not only genic mutations but all kinds of genomic change including genome duplication. In neomutationism, the molecular study of mutational change as well as the selective advantage of new mutations are emphasized. Therefore the cause of mutation is no longer treated as a black box. For these reasons, neomutationism or the theory of mutation-driven evolution is applicable for much wider biological situations than classical mutationism and at the same time demands a more sophisticated molecular approach…
At the present time we have little idea about the evolution of the human brain or even less complicated characters such as parental care in some mammals. However, the evolution of these characters will eventually be clarified at the molecular level…
In the study of phenotypic evolution it is important to realize that there are two evolutionary forces operating at the genomic level. One is the genome conservation force that maintains the developmental integrity of genes within individuals and the reproductive unity of individuals within species or populations…
The other evolutionary force is the genomic diversification of different species. This occurs because many constraint-breaking mutations are species-specific and these mutations contribute to the diversification of different species.
From the foregoing passage, it should be apparent that Professor Nei envisages his neomutational theory of evolution as a comprehensive theory of evolutionary change, which can ultimately explain even the evolution of the human brain at the molecular level. This is radically different from the more conservative position defended by Professor Moran in his replies to my five questions.
Why, then, is Professor Moran glossing over these differences between his theory and Professor Nei’s?
Professor Nei’s remarks on constraint-breaking mutations are also interesting. The critical question that needs to be asked is: can he demonstrate mathematically that the constraint-breaking mutations he envisages are capable of generating the kinds of structural, behavioral and molecular complexity that we observe in the world of living things?
Professor Masatoshi Nei’s explosive interview with Discover magazine
Still curious about why Professor Moran hadn’t reviewed Masatoshi Nei’s book, I did some research, and came across a very revealing interview which Professor Nei gave to Gemma Tarlach, in Discover magazine (“Mutation, Not Natural Selection, Drives Evolution,” March 16, 2014):
Charles Darwin said evolution occurs by natural selection in the presence of continuous variation, but he never proved the occurrence of natural selection in nature. He argued that, but he didn’t present strong evidence.
But among the people working on evolution, most of them still believe natural selection is the driving force.
If you say evolution occurs by natural selection, it looks scientific compared with saying God created everything. Now they say natural selection created everything, but they don’t explain how. If it’s science, you have to explain every step. That’s why I was unhappy. Just a replacement of God with natural selection doesn’t change very much. You have to explain how.…
Mutation means a change in DNA through, for example, substitution or insertion [of nucleotides]. First you have to have change, and then natural selection may operate or may not operate. I say mutation is the most important, driving force of evolution. Natural selection occurs sometimes, of course, because some types of variations are better than others, but mutation created the different types. Natural selection is secondary…
Kimura believed morphology [appearance] evolves through natural selection. He applied neutral theory only on a molecular level. I say it can determine morphological characteristics as well because DNA determines everything, but to prove this has not been so easy. [Laughs.] Forty or 50 years later, I am still trying to prove it…
… Darwin is a god in evolution, so you can’t criticize Darwin. If you do, you’re branded as arrogant.
But any time a scientific theory is treated like dogma, you have to question it. The dogma of natural selection has existed a long time. Most people have not questioned it. Most textbooks still state this is so. Most students are educated with these books.
You have to question dogma. Use common sense. You have to think for yourself, without preconceptions. That is what’s important in science.
“Question dogma.” I have to say that I like Professor Nei’s iconoclastic attitude, and I hope we see more of it among evolutionary biologists, in the years to come.
Professor Moran suggests that I may have quote mined Dr. Gert Korthof
In my post, Will the real Neutral Theory please stand up?, in which I posed the above five questions, I quoted a passage from a review by Dr. Gert Korthof of Motoo Kimura’s book, The neutral theory of molecular evolution. Dr. Korthof seemed to be implying in his review that Kimura’s willingness to cede a dominant role to natural selection when accounting for the origin of morphological complexity was the decisive factor that rendered his theory acceptable to his Darwinist contemporaries. I then quoted the following remark by Dr. Korthof, in which he expressed his own opinion on the neutral theory of evolution:
Please note that ‘the neutral theory of evolution’ is not sufficient to explain complex life and adaptations. In that sense it is not a theory of evolution. (Emphasis mine – VJT.)
In a footnote to his recent blog post, Professor Moran, in response to a complaint by Dr. Korthof, proceeds to give what he calls “the full quote”:
‘Please note that ‘the neutral theory of evolution’ is not sufficient to explain complex life and adaptations. In that sense it is not a theory of evolution. However it is accepted that the neutral theory explains a lot of differences in DNA. Kimura:
‘Of course, Darwinian change is necessary to explain change at the phenotypic level – fish becoming man – but in terms of molecules, the vast majority of them are not like that. (7)’
Professor Moran then comments:
Looks like Vincent Torley might have quote mined a scientist. Isn’t that amazing?
A few of the commenters on Professor Moran’s blog post were more direct. One wrote: “Gert strongly opposes creationists on his blog, so it is funny to see Vincent Torley quote him in defense.” Another accused me of quote mining Korthof, while yet another commenter added that I have “the (sic) tendency to quote mine everybody in very interesting ways.”
Dr. Korthof himself claimed that the quote in my post “was wrong and out of context,” and in another comment, referred to it as a “misquote.”
What quote mining is – and isn’t
It seems that evolutionists need a basic lesson on what quote mining is. Here’s how RationalWiki defines quote mining:
Quote mining is the deceitful tactic of taking quotes out of context in order to make them seemingly agree with the quote miner’s viewpoint or to make the comments of an opponent seem more extreme or hold positions they don’t in order to make their positions easier to refute or demonize.
Let’s break this down into very simple steps.
1. In my post, I provided a direct link to Dr. Korthof’s review of Motoo Kimura’s book, enabling readers to check the accuracy of my quote at the touch of a button. Had my intention been to deceive, I obviously would not have done that. Since RationalWiki defines quote mining as a “deceitful tactic of taking quotes out of context” (italics mine), it follows that I cannot be guilty of quote mining.
2. Nowhere in my post did I imply or state that Dr. Korthof agreed with my views on evolution. The commenter who wrote, “Gert strongly opposes creationists on his blog, so it is funny to see Vincent Torley quote him in defense,” was therefore completely missing the point I was making.
3. The reason why I quoted Dr. Korthof was very simple: to illustrate the point that I was making – namely, that a theory which “is not sufficient to explain complex life and adaptations” cannot be properly described as “a theory of evolution.” Evolution is by definition an all-encompassing theory of biology, as atomic theory is to chemistry. Any biological theory (such as the neutral theory) which does not even attempt to account for key aspects of our biology – such as “the vast majority of complex structures” (to quote Professor Moran’s own words) cannot be accurately called “a theory of evolution.” At best, one might call it “a theory of molecular evolution.”
4. Dr. Gert Korthof apparently thinks that I should have appended the following sentence from his review to my original quote: “However it is accepted that the neutral theory explains a lot of differences in DNA.” The reason why I didn’t quote that sentence is that it’s fairly non-controversial, and obvious to nearly everyone. I myself would agree with it, as would Professor Moran. Why belabor the obvious?
5. Dr. Korthof also chides me for omitting the following quote from Motoo Kimura:
Of course, Darwinian change is necessary to explain change at the phenotypic level – fish becoming man – but in terms of molecules, the vast majority of them are not like that. (7)
But if Dr. Korthof had bothered to read my post, he would have seen that I did quote this passage, in an earlier paragraph. I even provided a link to Dr. Korthof’s review for a citation of this passage, for the benefit of those readers who don’t own back issues of New Scientist magazine, where the quote originally appeared!
In other words, my original post correctly quoted the substance of Dr. Korthof’s views, as well as quoting Motoo Kimura in context.
6. For the benefit of commenters over at the Sandwalk blog who have trouble appreciating what a quote mine is, here’s an example. Suppose that in my original post, I had simply quoted Dr. Korthof as stating that “‘the neutral theory of evolution’ … is not a theory of evolution.” Now that would have been quote mining, as it fails to supply the proper context. The following quote supplies the relevant context, and is therefore a legitimate quote:
Please note that ‘the neutral theory of evolution’ is not sufficient to explain complex life and adaptations. In that sense it is not a theory of evolution. (Italics mine – VJT.)
7. The whole point of my quoting from Dr. Korthof was to put forward an embarrassing criticism of the neutral theory of evolution, from someone who is clearly in a position to understand it – namely, a Dutch biologist who has read hundreds of books relating to evolution, and who vocally supports evolution in his blog posts. Quoting highly credible people who hold views very different to your own, but who nevertheless agree with you on a vital point that you wish to argue for, is not quote mining. It’s simply smart tactics.
Dr. Nick Matzke’s amusing rant
The first person to comment on Professor Moran’s blog post was Dr. Nick Matzke, who wrote what he himself described as a “rant.” This one’s a beauty:
Creationists seem unable to hold in their heads the idea that multiple natural processes can be in operation, and that some of those processes can explain one class of observations, and other processes can explain other classes of observations.
Earth to creationists/Sal/vjtorley: natural selection is the main explanation of complex adaptations (e.g., eyes). Neutral processes are the main explanation of non-adaptive changes (e.g., sequence change in junk DNA). The fact that most molecular evolution is neutral makes sense because most of the genome of humans (and other large-genomed organisms) is junk. This statement does NOT mean ALL genomic change is neutral, and basically any evolutionist would agree that selection plays an important role when it comes to adaptive changes in functional DNA such as genes. Also, most molecular evolution being neutral says nothing in particular about the evolution of morphology, which is controlled by non-junk DNA.
There is more that could be said (as always; see in particular Michael Lynch), but that’s a good first approximation. This should have been obvious to you guys from the beginning, if you had bothered to think and read about it for 5 minutes, rather than trumpeting your ignorance in blogposts. Don’t you ever get embarrassed about getting such fundamental basics wrong? Don’t you see why this level of ignorance, when coupled with accusations that it is the evolutionists who are wrong / evil / misleading the world, is totally infuriating to professional biologists and guarantees that you will be seen as nothing but malicious, intellectually lazy cranks?
(end rant)
Here’s a piece of advice for Dr. Matzke: you really need to take a long, cold shower.
And here’s a question for Dr. Matzke: how do you reconcile your statement that “most molecular evolution being neutral says nothing in particular about the evolution of morphology” with Professor Masatoshi Nei’s claim in his paper, Selectionism and Neutralism in Molecular Evolution (Molecular Biology and Evolution, December 2005, Volume 22, Issue 12, doi: 10.1093/molbev/msi242, pp. 2318-2342): “It appears that mutation (including gene duplication and other DNA changes) is the driving force of evolution at both the genic and the phenotypic levels” (italics mine)? In his latest book, Mutation-Driven Evolution (Oxford University Press, 2013), Professor Nei is even more direct:
…[M]any evolutionists including Motoo Kimura and Jack King believe that
mutationphenotypic evolution is caused primarily by natural selection. By contrast, Nei (1975, 1987, 2007) proposed that since phenotypic evolution is ultimately controlled by DNA and RNA molecules, both molecular and phenotypic evolution must be primarily caused by mutation. (p. 9)
For that matter, Dr. Matzke, how do you reconcile your position with that of Professor PZ Myers, who in a post titled, Complexity is not usually the product of selection (11 December 2012), wrote:
The bottom line is that you cannot easily explain most increases in complexity with adaptationist rationales. You have to consider chance as far more important, and far more likely to produced elaborations.
Here’s a final question for Dr. Matzke. You refer to me, Sal Cordova and unspecified “creationists” as getting the “fundamental basics” wrong. Very well, then: what “fundamental basics” did I get wrong in my post? I took great pains to accurately characterize the views of Motoo Kimura: I quoted him as saying that “The Darwinian theory of evolution by natural selection has served as a great unifying principle in biology,” and that his own neutral theory “does not deny the role of natural selection in determining the course of adaptive evolution, but it assumes that only a minute fraction of DNA (or RNA) changes are adaptive.” I also described Kimura as claiming that “molecular evolution was dominated by neutral evolution, but at the phenotypic level, natural selection probably accounted for most changes in characteristics, rather than genetic drift.” I quoted the exact words of Motoo Kimura’s colleague, Professor Masatoshi Nei, and I also took great care not to put words into the mouths of Professors PZ Myers and Larry Moran: I described them as arguing that “most of the complexity that we see in the biological world could be largely the result of chance, although they do not wish to rule out a role for natural selection.” Given that I took such pains to accurately represent the views of the key protagonists in the current debate on what the neutral theory of evolution can and cannot explain, why do you continue to accuse me of being wrong in my facts? Is it not you who are wrong in yours, Dr. Matzke?