Intelligent Design

Will the real Neutral Theory please stand up?

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What kinds of structural, functional and behavioral complexity can the neutral theory of evolution account for, and what kinds of complexity can’t it account for? According to Professor Larry Moran, to evince confusion on these vital questions is a sure sign of being an “IDiot.” But it is the “neutralists” themselves who are confused on these issues, as I intend to show in today’s post. (I have chosen to use the term “neutralist” to describe someone who adheres to the neutral theory of evolution, as Nature magazine uses that term, although Professor Moran evidently prefers the term “mutationist.”)

In a recent post titled, Sal Cordova tries, and fails, to understand evolution by Professor Larry Moran (April 22, 2014), Professor Larry Moran tears into Sal Cordova for asserting that “if most evolution had been non-Darwinian, one would rightly argue it would have been a random walk, and thus not much better than a tornado going trough a junkyard,” and for attributing to Professor Moran the view that “evolution is a random walk and we are obviously junkyards and you’re an IDiot if you think biological organisms are mostly functional.” These remarks prompted Moran to retort:

It’s very, very, difficult for me to believe that Cordova isn’t lying through his teeth. He can’t be that stupid, can he?

But the assertion that the neutral theory of evolution would be more appropriately described as “random-walk evolution” can be found in Ernst Mayr’s classic text, The Growth of Biological Thought: Diversity, Evolution, and Inheritance (Belknap Press, 1982, p. 593). And given that Professor Moran believes that “90% of the human genome consists of junk DNA,” I find it rather odd that Moran should take offense when Sal Cordova paraphrases this statement (in layperson’s language) as: “we are obviously junkyards.” Finally, the question of whether “biological organisms are mostly functional” obviously depends on the way in which you decide to look at them, but it should be clear that on Moran’s view, if you examine them at the genetic level, they will turn out to be mostly non-functional.

In a 2006 essay, Evolution by Accident, Professor Moran acknowledged the important role of natural selection in evolution, but he also argued that “evolution is fundamentally a random process, although this should not be interpreted to mean that all of evolution is entirely due to chance or accident.” Moran adds that “speciation — one of the most important events in evolution — is largely by accident,” which means that “the tape of life will never replay the same way.” He concludes his essay with the words: “I think the term ‘evolution by accident’ is an accurate description of how evolution occurs.”

If we look at the history of the neutral theory, however, we can discern an increasing trend on the part of its proponents to ascribe evolutionary changes at both the morphological and molecular levels – including the appearance of complex structures – to chance. Motoo Kimura (1924-1994), one of the founders of the neutral theory of evolution, was quite modest about what it could and couldn’t explain: he argued 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.

In a scientific paper titled, The neutral theory of evolution and the world-view of the neutralists (Genome, vol. 31, 1989, pp. 24-31), Kimura voiced his conviction that “The Darwinian theory of evolution by natural selection has served as a great unifying principle in biology,” adding that his 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.” The reason, he wrote, why “Darwinian evolution appears to be so prevalent at the phenotypic level” is that natural selection “eliminates phenotypically extreme individuals and preserves those that are near the population mean,” and thereby acts as a stabilizing factor.

Kimura expressed his views more plainly, in a 1985 article in New Scientist (pp. 41-46, cited here), titled “The neutral theory of molecular evolution”:

“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.”

Biologist Gert Korthof, in a review of Motoo Kimura’s ground-breaking book, The neutral theory of molecular evolution, comments:

This is an important admission. If evolution is defined at the morfological (sic) level, the evolution of adaptations such as eyes and brains, then natural selection is very important.

In his review, Korthof suggests 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. He also cautions his readers:

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.)

However, Motoo Kimura’s colleague, neutralist Masatoshi Nei, made much stronger claims for the explanatory power of the neutral theory, in a 2005 paper titled, Selectionism and Neutralism in Molecular Evolution (Molecular Biology and Evolution (December 2005), Volume 22, Issue 12, doi: 10.1093/molbev/msi242, pp. 2318-2342), in which he concluded: “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.”

More recently, neutralists PZ Myers and Larry Moran have spoken out even more boldly, 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. In a post entitled, Complexity is not usually the product of selection (11 December 2012), PZ Myers roundly criticized evolutionist John Wilkins for maintaining that “selection is the only process that results in complexity over any time,” refuting it with a detailed scenario for how new versions of a gene that codes for an enzyme might appear and spread through a population, even though “selection plays no role” (Myers’ italics). Commenting on the evolution of globin genes, Myers wrote: “The origin [of these genes – VJT] was not a selection event, but the refinement to specific roles probably was.” Myers also described the evolution of a biochemical pathway studied by Joe Thornton as having being “driven by an initial combination of chance mutation, drift, and subsequent selection” (italics mine – VJT). Myers was fully aware that the implications for the evolution of complexity during the history of life on Earth were very profound, and said as much:

I think if selection were always the rule, then we’d never have evolved beyond prokaryotes — all that fancy stuff eukaryotes added just gets in the way of the one true business of evolution, reproduction…

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.

Even in something as specific as the physiological function of a biochemical pathway, adaptation isn’t the complete answer, and evolution relies on neutral or nearly neutral precursor events to produce greater functional complexity.

Professor Larry Moran subsequently endorsed PZ Myers’ article, in a post of his own, entitled, On the Evolution of Complexity (11 December 2012), in which he wrote:

Can you go from some simple character to a more complex feature without invoking natural selection? Yes, you can. Complex features can evolve by nonadaptive means. Just think of our complex genome and read The Origins of Genome Architecture by Michael Lynch.

Want a more simple example? Read the latest post by PZ Myers: [αEP: Complexity is not usually the product of selection]1.

This is an important point. You can’t just assume, without question, that a complex trait must be an adaptation and must have arisen by natural selection. That applies to molecular complexes and also to complex behavior.

So I’d like to ask Professor Moran a few questions:

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?

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?

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?)

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?

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?

Five questions is enough for one day. In the meantime, I’d strongly recommend that readers of this post familiarize themselves with the articles below, as they raise a number of interesting issues that will be the topic of future posts of mine.

Recommended background reading

Evolution: A View from the 21st century by James Shapiro.

Shapiro and Intelligent Design

Non-supernatural ID?: University of Chicago microbiologist James Shapiro works with ID guys, dismisses Darwinism, offers third way by News at Uncommon Descent (July 4, 2011)

Is James Shapiro a Design Theorist? by Professor William A. Dembski (January 12, 2012)

“Is James Shapiro a Design Theorist?”: James Shapiro Replies by Professor James Shapiro (January 16, 2012)

Following the Evidence Where It Leads: Observations on Dembski’s Exchange with Shapiro by Dr. Ann Gauger (January 17, 2012)

Let Science Be the Arbiter: A Reply to James Shapiro by Dr. Douglas Axe (January 17, 2012)

A Response to Ann Gauger’s and Douglas Axe’s Comments by Professor James Shapiro (January 18, 2012)

Joining the Conversation: Perspectives on the Discussion with James Shapiro by Jonathan McClatchie

Doug Axe Knows His Work Better Than Steve Matheson by Anika Smith (June 10, 2012)

James Shapiro vs. Jerry Coyne

What Is the Key to a Realistic Theory of Evolution? by Professor James Shapiro (February 16, 2012)

Reply by James Shapiro (February 16, 2012), in a comment on Professor Jerry Coyne’s thread. Shapiro refers to “non-random (i.e., regulated, targeted, reproducible) changes to the genome.”

A colleague wrongfully disses modern evolutionary theory by Professor Jerry Coyne (February 18, 2012)

Jim Shapiro continues his misguided attack on neo-Darwinism by Professor Jerry Coyne (April 7, 2012)

Does Natural Selection Really Explain What Makes Evolution Succeed? by Professor James Shapiro (August 12, 2012)

Cell Mergers and the Evolution of New Life Forms: Symbiogenesis Rather Than Selection by Professor Jerry Coyne (August 21, 2012)

James Shapiro goes after natural selection again (twice) on HuffPo by Professor Jerry Coyne (August 22, 2012)

Larry Moran reviews Shapiro’s anti-Darwinian book; and another new anti-evolution book is about to appear by Professor Jerry Coyne (August 30, 2012)

Bob Dylan, ENCODE and Evolutionary Theory: The Times They Are A-Changin’ by Professor James Shapiro (September 12, 2012)

Why the ‘Gene’ Concept Holds Back Evolutionary Thinking by Professor James Shapiro (November 30, 2012)

James Shapiro gets evolution wrong again by Professor Jerry Coyne (December 2, 2012)

Inconvenient Truths: Why Are Self-Styled Defenders of Evolution so Resistant to Lessons From Molecular Genetics? by Professor James Shappiro (December 4, 2012)

James Shapiro, in his attempts to forge a new evolutionary paradigm, is reduced to going after my commenters by Professor Jerry Coyne (December 5, 2012)

James Shapiro vs. Larry Moran

Professor Larry Moran’s review of James Shapiro’s book, Evolution: A View from the 21st Century. In Report of the National Council for Science Education, Vol. 32, No. 3, May-June 2012.

Revisiting the Central Dogma in the 21st Century by Professor Larry Moran (August 26, 2012)

James Shapiro Claims Credit for Predicting That Junk DNA Is Actually Part of a “highly sophisticated information storage organelle” by Professor Larry Moran (September 13, 2012)

The meaning of “random”

What’s in a Word? “Randomness” in Darwinism and the Scientific Theory of Evolution by Dr. Jay Richards (April 2, 2012)

Seeking an Official Definition of “Randomness”: A Reply to Dr. Jay Richards by Professor Alvin Platinga (April 3, 2012)

So Where Does the Conflict (with Alvin Plantinga) Really Lie? by Dr. Jay Richards (April 5, 2012)

Where My Conflict with Jay Richards Really Lies by Professor Alvin Plantinga (April 6, 2012)

Evolutionary Theory and Theism (Reasonable Faith, #253 – Response by Professor William Lane Craig to a question from Andrew)

Who speaks for science? (Reasonable Faith, #269 – Response by Professor William Lane Craig to a question from Dr. Jay Richards)

Unguided or Not? How Do Darwinian Evolutionists Define Their Theory? by Casey Luskin (August 11, 2012)

Is “Unguided” Part of Modern Evolutionary Theory? by Professor Larry Moran (August 11, 2012)

Responding to Moran – Is “Unguided” Part of Modern Evolutionary Theory? by Jonathan Bartlett (August 12, 2012)

An Example of “Directed” Mutation and an Idiotic “Gotcha” by Professor Larry Moran (August 13, 2012)

Larry Moran Responds Regarding Directed Mutations by Jonathan Bartlett (August 16, 2012)

Statistical and Philosophical Notions of Randomness in Creation Biology by Jonathan Bartlett (director of the Blyth Institute)

22 Replies to “Will the real Neutral Theory please stand up?

  1. 1
    Acartia_bogart says:

    Natural selection, by definition, can only work at the phenotypic level. But “junk DNA” is outside natural selection and purely a statistical, probabilistic, process. I don’t see how ID can explain “junk DNA” but natural selection explains it quite convincingly (or, more importantly, explains why it is inevitable).

    Intelligent Design isn’t an explanation of anything, it is fall back position for lazy thought and reasoning.

  2. 2
    scordova says:

    Larry and PZ have done us a great favor by defending non-Darwinian evolution in molecular evolution.

    Kimura was sort of covering his tracks by saying his theory doesn’t apply above the molecular level. But Nei rightly argued, if most molecular evolution is free of selection, it stands to reason most other kinds of evolution should also be free of selection.

    Larry has opened a Pandoras box, and if we find a high proportion of DNA is functional and if there is a large amount of heritable epigenetic information that is functional, then the neutralists will be in a tough spot.

    Nevertheless neutral theory is helpful to ID because it shows most evolution cannot be Darwinian. There was the view in the 1950’s that now seems incredibly naïve that all features of biology were under selection!

    Finally, we might be able to test in the present day if molecular evolution is mostly non Darwinian and following a random walk of slow deterioration.

    If function is slowly being degraded and damaged as argued by Behe’s rule and Sanford’s genetic entropy, it demonstrates mindless nature cannot be a designer, which suggests the design of life comes from outside nature.

  3. 3
    Peter says:

    I saw the same benefit when reading Moran’s blog. Evolutionists have admitted defeat and have thrown out Darwinism. That is a major accomplishment. But like all the other good science which has contradicted Darwinism, they just invent another just so story and keep going. It is their religion after all. But well still have plenty to be thankful for. Darwinism is dead!!!

  4. 4
    scordova says:

    I think if selection were always the rule, then we’d never have evolved beyond prokaryotes — all that fancy stuff eukaryotes added just gets in the way of the one true business of evolution, reproduction…

    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.

    Amen PZ Myers.

    Thought I’d never find myself saying that!
    😯

    PZ is not alone:
    Selection has to fail for evolution to work

  5. 5
    Mung says:

    Then of course there’s this:

    Creatures of Accident

  6. 6
    Mung says:

    re: Creatures of Accident

    No mention of Kimura, or neutral theory, or neutral evolution or molecular evolution in the index.

    Apparently there is plenty enough of accident in Darwinian theory without any need for neutral theory.

    Go Figure.

  7. 7
    Mung says:

    Then there’s this:

    Randomness in Evolution

    No mention of Kimura, or neutral theory, or neutral evolution or molecular evolution in the index. So who needs it, really?

    Interestingly, chapter four is titled:

    The Evolution of the Decrease of Randomness

    “The main point of Bonner’s book is that the importance of randomness in evolution depends on size. What is new is the claim that small organisms are more likely to have selectively neutral morphological variation.”

    Shades of Lenski! All together now, let’s extrapolate!

  8. 8
    Mung says:

    re: Randomness in Evolution

    I work with microorganisms and I ask the question: Are they affected by natural selection the same way as large, complex ones? It is conventional to think that selection acts the same way on organisms of all sizes, and I make the case that it might not be so.

    – p xi

    One has to wonder if an in depth study of evolutionary theory itself would expose that it’s mostly random. May as well toss coins.

  9. 9
    Mung says:

    …randomness… is no great enlightening principle, and therefore it is often relegated to a background noise that really is not doing anything.

    Randomness in Evolution

    But at least it’s emerged now as a tool to beat IDiots over the head with. 🙂

  10. 10
    Mung says:

    And then there’s this:

    Mutation-Driven Evolution

    The purpose of this book is to present a new mechanistic theory of mutation-driven evolution based on recent advances in genomics and evolutionary developmental biology. The theory asserts, perhaps somewhat controversially, that the driving force behind evolution is mutation, with natural selection being of only secondary importance. … A brief history of the principal evolutionary theories (Darwinism, mutationism, neo-Darwinism, and neo-mutationism) that preceded the theory of mutation-driven evolution is also presented in the context of the last 150 years of research. … In contrast to neo-Darwinism, mutation-driven evolution is capable of explaining real examples of evolution … In this sense the theory proposed is more realistic than its predecessors, and gives a more logical explanation of various evolutionary events.

    Amazing what you can find these days on the internet.

    Larry Moran

    I can’t wait to get my hands on a copy of this book. Look for a review in a few months.

    Larry Moran

    That was not the last book I read but I’m not going to post a review.

    Pity.

  11. 11
    gpuccio says:

    Sal:

    I think if selection were always the rule, then we’d never have evolved beyond prokaryotes — all that fancy stuff eukaryotes added just gets in the way of the one true business of evolution, reproduction…

    Is that really a PZ quote? Amazing! I have defended many times, here, the simple concept that, if reproductive fitness is the driving force of evolution, evolution itself should have stopped with the prokaryotes, which are still the best reproductors we can fund in the world.

    It’s good to know I am not the only one believing that. 🙂

    In alternative, I have proposed the idea that the expression of new functions is really the driving force behind evolution, and that more complex being, while frailer and less successful in reproduction, come into existence because new functions need to be expressed through them.

  12. 12
    gpuccio says:

    Acartia_bogart:

    So, let’s come to a compromise:

    a) Non design theories of evolution (either based on NS or neutral evolution) cannot explain function, but they can explain junk DNA (if and in the measure that it really exists).

    b) ID can explain function in biological beings.

    That’s fine for me. 🙂

  13. 13
    gpuccio says:

    VJ:

    Recently, I posted the following:

    So, what has changed under the not so big tent of neo darwinism?

    Nothing. NS is still the only useful actor. An actor who cannot act, but an actor just the same. Neutral variation and genetic drift are there, as we have always known, but are irrelevant to the problem we debate here. I have said that simple thing for years, here.

    After all, Dawkins has no reasons to be unhappy.

    I really hate to be proved right.

    By the way, I am very proud to be an IDiot, and of my “confusion on these vital questions”. If vital questions are confused, I suppose it is fine to be confused about them.

    The real “confused” vital question, indeed, seems to be:

    What do “non design” theorists really believe?

    To be more clear:

    a) Do they believe that functional information is generated by neutral mutations and drift? (that would simply mean that it is the result of a random walk, I can see no alternatives, but maybe that’s just because I am an IDiot).

    b) Do they believe that functional information is generated by NS acting on RV? (that would simply mean that old good neo-darwinism is still the main theory, and that nothing has changed, but maybe I don’t understand because I am an IDiot)

    c) Do they believe that functional information simply does not exist and that it is stupid propaganda invented by IDiots? (I would bet for this option, but then why all the fuss about junk DNA being non functional, if everything is not functional? Again, maybe I am an only an IDiot, and all I can understand is the IDiot propaganda).

    So yes, I am confused. And proud of being confused.

    After all, I am even proud of being an IDiot.

  14. 14
    Andre says:

    A few years ago, Prof Moran argued with me about NS, I questioned it’s importance and he labelled me an IDiot that does not understand evolution, fast forward to 2014 and now he agrees with me? Does this mean he is also an IDiot now?

  15. 15
    gpuccio says:

    Andre:

    He is just an intelligent person committed to defend an impossible position.

  16. 16
    Mung says:

    For the more mathematically inclined:
    Chance in Biology: Using Probability to Explore Nature

    In a sexually reproducing organism, the frequencies of alleles “drift” from one generation to the next in a genetic analogue of diffusion; how long will it take before an allele is (by chance) lost from a population?

    By analogy, are molecules junk because they diffuse?

    What is the connection between neutral theory and genetic drift?

    Neutral Theory: The relative importance of drift and selection

    On the difference between Neutral Theory and random genetic drift

    I have this sense that people are confusing neutral theory with genetic drift. Am I wrong?

  17. 17
    Mung says:

    For example:

    But the neutral theory of molecular evolution suggests that most of the genetic variation in populations is the result of mutation and genetic drift and not selection.

    Does that need to be re-written?

    It seem to me the argumesnt being made are rather:

    But the neutral theory of molecular evolution suggests that most of the lack genetic variation in populations is the result of mutation and genetic drift and not selection.

    I’m just going to attempt some simple logic here, which doesn’t mean my conclusion is true, but:

    Selection would be more likely to bring about fixation of an allele than the absence of selection. Therefore, neutral theory is more about why more alleles are not fixed than it is about a means for fixation of alleles.

    How is it then that neutral theory says anything at all about what those alleles are for?

    help

    Larry Moran:

    Many people seem to equate Neutral Theory with random genetic drift. They think that random genetic drift is only important when the alleles are neutral (or nearly neutral). Then they use this false equivalency as a way of dismissing random genetic drift because it only deals with “background noise” while natural selection is the mechanism for all the interesting parts of evolution. I think we should work toward correcting this idea by separating the mechanisms of evolution (natural selection, random genetic drift, and others) from the quality of alleles being produced by mutation (beneficial, detrimental, neutral).

    I have to say, I think he has a point. He he heeded his own advice?

    Are we guilty of equating Neutral Theory with random genetic drift here at UD?

  18. 18
    Mung says:

    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?

    If I were an evolutionist, I would agree. Neutral theory is not about, and does not attempt to explain, adaptation. But I would also agree with Larry. “Strict Darwinism has lost.”

    And if I were arguing with an IDiot I’d switch back and forth as needed to make my theory unfalsifiable.

  19. 19
    Mung says:

    2. How do you respond to Dr. Gert Kothof’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?

    Gert Korthof is mistaken. IDiots commonly claim that Darwinian theory is not sufficient to explain complex life and adaptations. Does that mean Darwinism is not a theory of evolution?

  20. 20
    Paul Giem says:

    Mung (#17),

    You have hit the jackpot:

    And if I were arguing with an IDiot I’d switch back and forth as needed to make my theory unfalsifiable.

    If evolution is neutral, it can have no target, and according to Durrett and Schmidt, one, and in extremely rare instances two, mutations is all the farther large slow-breeding mammals such as humans or elephants can expect to walk randomly to create some kind of structure. But if evolution is dominated by natural selection, one should be able to find the pathway, or at least a pathway. But there are no demonstrated pathways, with the possible exception of the different kinds of cones, which differ by reportedly 3 amino acids (which are still too far for a random walk), so what we have is classic doublethink (and therefore doublespeak). As I said in a previous post, I’m glad I don’t have to argue that side. 🙂

  21. 21
    gpuccio says:

    Paul:

    A perfect summary of the problem. Brief, clear and, abobe all, true.

    How different from the ambuguity Moran’s false reasonings!

    As you said, it’s beautiful to argue on the right side of truth. 🙂

  22. 22
    tragic mishap says:

    he argued 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.

    And this is why ID people should not be overly enthusiastic about disconnecting phenotype from genotype.

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