Friday, December 06, 2013

Die, selfish gene, die!

"Die, selfish gene, die!" is the provocative title of an article by science writer David Dobbs [Die, selfish gene die!].

Dobbs begins with ....
The article attracted the attention of Jerry Coyne who effectively dismantles the strange ideas promoted by Dobbs. Read all about it at: David Dobbs mucks up evolution, part I and David Dobbs mucks up evolution, part II.

As it turns out, this is just another example of a science writer who has been mesmerized by the latest effort to overthrow modern evolutionary theory by some scientist promoting their own work. In this case it's Mary Jane West-Eberhard.

But there's a more serious issue here and I'm not sure that Jerry Coyne recognizes it. The selfish gene metaphor can be interpreted in several different ways. Here's how Richard Dawkins describes it in the preface to the 1989 edition of The Selfish Gene.
Lot's of people misunderstand the selfish gene metaphor. They think it means that organisms behave selfishly but that's not what Dawkins meant at all.

Jerry Coyne explains this in his book Why Evolution Is True (p. 226) ....
As Dawkins shows clearly, the "selfish" gene is a metaphor for how natural selection works. Genes act as if they're selfish molecules: those that produce better adaptations act as if they're elbowing out other genes in the battle for future existence. And, to be sure, selfish genes can produce selfish behaviors. But there is also a huge scientific literature on how evolution can favor genes that lead to cooperation, altruism, and even morality.
There are two main criticisms of the selfish gene metaphor and both of them are quite valid. It's the reason why Dawkin's view hasn't caught on the the evolutionary biology textbooks. It usually merits nothing more than a footnote.

The most damning criticism comes from evolutionary biologists who point out that the primary unit of selection is the individual and not the gene. Stephen Jay Gould and Richard Lewontin are prominent opponents of what they see as an unnecessary reductionism in Dawkins' writing. Clearly, hierarchical theory (Gould) is inconsistent with the selfish gene metaphor because evolution can also operate at the level of groups and species (according to Gould and others). There are plenty of other evolutionary biologists who object to selfish genes for these reasons.

The second objection comes from the focus on natural selection and "Darwinism" (or neo-Darwinism). Many evolutionary biologists have a pluralistic view of modern evolutionary theory. That view includes random genetic drift where the appropriate metaphor might be "lucky gene" or "accidental gene." The problem with the Dawkins' metaphor, according to these critiques, is not that "selfish genes" don't exist, it's that the metaphor is not appropriate for evolution in general.

While I admire Jerry's take-down of Dobbs, I'm not sure that he (Jerry Coyne) fully appreciates these other criticisms of the selfish gene. Here's what Coyne wrote ...


I’m not sure why the hype continues, but perhaps it has to do with the fact that the main paradigm of evolution—the neo-Darwinian synthesis—is largely consolidated, and is correct. Sure, there are surprises to come, and interesting new phenomena, but there’s no “quantum mechanics” of evolution on the horizon. Some theories don’t need to be overthrown because they’re generally right. Perhaps people don’t like working in a field where there’s no new “paradigm” to forge, and Kuhn has ruined us all!

The "neo-Darwinism is dead" trend may have to do with ambition, or perhaps with boredom. I don’t know. What I do know is that the many recent challenges to neo-Darwinism have all failed to hold water, but people keep pouring liquid into that sieve.
The problem here is that Jerry doesn't really say what he means by "neo-Darwinism." Most of his writing suggests that he's talking about natural selection, albeit updated by a knowledge of genetics. He does mention, from time to time, random genetic drift and other aspects of modern evolutionary theory but I'm not sure if he appreciates the fact that some legitimate evolutionary biologists really do think that neo-Darwinism is dead.

Here's the Wikipedia description of neo-Darwinism. It illustrates the problem.
Neo-Darwinism is the 'modern synthesis' of Darwinian evolution through natural selection with Mendelian genetics, the latter being a set of primary tenets specifying that evolution involves the transmission of characteristics from parent to child through the mechanism of genetic transfer, rather than the 'blending process' of pre-Mendelian evolutionary science. Neo-Darwinism can also designate Darwin's ideas of natural selection separated from his hypothesis of Pangenesis as a Lamarckian source of variation involving blending inheritance.
I think we should refer to modern evolutionary theory as "modern evolutionary theory" in order to make sure we're not talking about "Darwinism," "neo-Darwinism," or the hardened version of the "Modern Synthesis." Modern evolutionary theory includes an important role for random genetic drift, Neutral Theory, and population genetics.

We could clarify a lot of discussion if we stopped talking about extending "Darwinism" or extending the Modern Synthesis or proclaiming once again that the selfish gene has died. In fact, the selfish gene has died, it died almost thirty years ago but most people don't know that. RIP.


  1. Larry,

    Nice post. I don't want to derail you from your main point here, which is well-turned and a helpful addition to this whole dust-up: clearer than either I or Coyne.

    But I do want to say that while I find West-Eberhard's work interesting, my inclusion of it in this story did not originate nor was in any way driven by her promoting her work to me, at all. I came across her work, read some of it (along with other material in this area), contacted her after a bit of effort (she wasn't terribly easy to run down), finally caught up with her on the phone; it took a while. She agreed to talk, but was hardly a self-promotional type.

    Much obliged if you could change that paragraph to avoid impugning her in that way. She simply shared and tried to explain her work to me, not to push it.


    David Dobbs

  2. I don't know about textbooks, but the gene as a useful way to look at selection seems to be quite alive. And not just the strawman "beanbag genetics". Sure, only individuals are selected in any single generation, but it's useful to consider unlinked genes to be selectable in a population over many generations. Individuals may be selected but except in clonal organisms phenotypes aren't inherited. Genes are inherited.

    I find Jerry's critique of David Dobbs to be spot on. Did you find anything wrong with it? The main point seems to be Dobbs' failure to understand that phenotypic plasticity is itself based on genetic features that have been evolved under selection, that gene regulation also has a genetic basis, and that the important differences among species are also genetic. I doubt you find any of that surprising. But Dobbs seems not to be responding to any of those points.

    1. I agree with you that Jerry's critique of Dobbs is accurate.

    2. Natural selection seems to have a lot of brains and foreknowledge. How did it come about by evolutionary standards? Natural selection seems to be more intelligent than the people like Jerry Coyne who claim they have figured it out .

    3. You are being unusually dim lately. And that's an accomplishment.

    4. LouiseG very succinctly demonstrates why she/he should not be commenting on matters concerning evolution.

  3. I find Coyne's assertion that regulatory genes are selfish replicators rather dubious, myself. Actually, outside of transposons and similar elements, I'm not sure there are many genes that act that way.

    1. Would you mind explaining your opinion here? I see you have much more experience than I do (I'm an undergraduate), and so when I read things like this I end up rather confused. Cis-regulatory elements are functional and conserved across species. Perhaps convergent evolution is sometimes the case but surely they are subject to positive selection. Same with trans-regulatory elements (i.e., protein transcription factors) or functional RNA such as miRNA which are involved in gene expression regulation. Why would they have to behave like transposons? The "selfish replicator" metaphor isn't about moving within the genome.

    2. They might well be under positive selection in the sense that mutations in them get fixed under selection. But that's not the same thing as being a selfish replicator. And transposons don't just move -- they leave copies behind as a selfish replicator would be expected to. Some genomes are practically overrun by transposons which become a large fraction of their genomes. While some regulatory elements may have arisen from others by duplication, I don't think there's much evidence to suggest that regulatory elements are in any danger of overrunning a genome.

    3. Isn't the point that they behave like protein-coding genes in that they are selected for and rise in frequency? Again, I don't understand why the characteristics of transposons are being invoked here. They're not essential to the metaphor.

    4. The metaphor is about chunks of DNA that successfully replicate themselves without any "concern" for the organism they are in -- that's what makes them "selfish" and "replicators". Transposons do exactly that and we can see it. Simply claiming that alleles that increase their frequency in a population are acting as "selfish replicators" is stretching the metaphor to the point of being meaningless. The metaphor adds nothing of value.

    5. That isn't at all what the "selfish gene" metaphor is about. Have you ever read anything by Dawkins? The idea is that genes want (metaphorically) to make more copies of themselves. Usually, this requires making more copies of the organisms in which they are embedded, which is how selfishness generates "concern" for the organism. And often, this requires cooperation (metaphorically, again) with other genes. But there's conflict too. Really, the whole selfish gene metaphor is just about the gene as a unit (not the unit) of selection.

    6. Yes, I've read "The Extended Phenotype", Dawkins' one and only book that rises to slightly more than pop science where he goes into his replicator model. And I know that in recent years he likes to stress the cooperative nature of genes, which is a clever strategy as it rather co-opts the arguments of many of his critics. But if you weaken the model to not actually be about selfish replicators, it may be more like reality, but what's the point? What does it *get* you? Does it actually make any testable predictions that can't be explained without it?

    7. Why would you consider cooperation a contradiction of selfishness?

    8. Because that destroys the initial simplicity of the model which made it attractive to start with. The original idea was that genes working selfishly to replicate themselves resulted, as a side effect, in organisms that prospered. Basically the same model of classical unfettered capitalism with companies working selfishly resulting in a prosperous society as a side effect. But it came clear in both cases that this didn't really capture the reality of the situation which was far more complicated. When pressured, both arch-capitalists and arch-selectionists accept this, but they keep trying to imply that the tweaks required to make their models work are minor -- it's not clear what could falsify their models in their minds. While the rest of us are left to wonder why models with so many tweaks are useful at all.

    9. Selfish cooperation is a perfectly reasonable idea. A common form is known as "byproduct mutualism". It doesn't make the "selfish gene" perspective any less simple.

      The "it's more complicated than that" critique misses the point of building simple models. Of course, there's more to life than selfish genes. Selfish genes are a metaphor to help visualize adaptation. That's how they are billed - not as some kind of complete model of living systems.

  4. As before I believe that you overestimate the problem of biologists not taking drift into account. It is the null hypothesis against which adaptation is always tested. The thing is, adaptation generally makes the stories that most people are interested in, and that is why we hear and read so much more about about it than about drift.

    As for the selfish gene, the major weakness of this concept appears to be that it does not explicitly say "selfish pieces of functional DNA, including e.g. regulatory elements". But at least to me the inclusion of pieces of DNA that are not protein-coding is a no-brainer.

    What I find very useful about the concept is that it can be used to clarify why natural selection does not necessarily lead to selfish individuals: a selfish gene can make an altruistic individual. In that sense I would disagree with one thing you wrote above: Selection may happen at the level of individuals and groups in the sense that individuals and sometimes entire groups die, but evolution is ultimately about the frequency of alleles in populations.

    1. Do you find the selfish gene metaphor helpful in understanding junk DNA? How about phylogenetic trees based on sequences? Does the selfish gene metaphor give you insight into the huge amount of variation you see in populations?

      The problem with selfish gene as a metaphor for evolution is that it isn't a metaphor for evolution. It's a metaphor for natural selection and even then it fails to convey the idea that most beneficial alleles are lost before they are fixed.


      I agree with this although I'm somewhat sympathetic to species sorting. The unit of evolution there is the species. It may not be true but it is still part of evolutionary theory.

    2. "evolution is ultimately about the frequency of alleles in populations".

      No -- evolution can be *modelled* by the frequency of alleles in populations but that isn't the only thing going on. For example, I'm interested in the evolution of the Actinobacteria, which, with few exceptions have very high GC content in their genomes. It's not clear why. It may be selected for, or it may be just an accident of history, but clearly their high GC content is something that evolved. And which can't be captured in the pre-genomic population genetics models of evolution involving alleles.

    3. You make it sound as if you only accept a metaphor if it captures absolutely everything that is going on. If you set the bar that high you will be disappointed all the time.

    4. @Alex SL,

      Your comment is unfair. The sole purpose of a metaphor is to simplify understanding of a rather complex topic. Since a huge part of evolution is due to random genetic drift, the "selfish gene" metaphor represents an incorrect view of evolution. It may serve as a metaphor for natural selection but that's not how it was advertised.

      Your bar is way too low. The metaphor of the "lucky gene" would be a far more accurate one to describe evolution. Would you accept it? Why not?

    5. Okay, right, then it is a metaphor for the selection part of evolution. I do not really need to defend Dawkins here or anything.

      But people also have very different ideas of what is meant with evolution, from "descent with modification" over "change of allele frequencies" and "common descent" to a complex body of theories encompassing everything that is needed to understand the existence of contemporary biodiversity.

      Quite a few people would not quite agree that evolution as they understand it is mostly 'about' drift. If you took a bacterium and let it evolve for three billion years ago under drift but no selection (however that would be possible), would you get something like vertebrates, land plants and insects? I'd say probably not because if everything can survive by luck the DNA would just mutate into random directions, which is mostly gibberish. If you took the same bacterium and let it evolve for three billion years under selection but no drift (however that would be possible), things would look very differently.

      So if you ask people what the theory of evolution is 'about', many would probably lean towards 'explaining the illusion of design', and that does not come from drift. Again, does not mean that drift is unimportant or anything. But when we ask ourselves what astronomy is about the answer isn't 'empty space' either although most of the cosmos is just that.


      Of course they would. You might think that's a good thing. I don't. Almost all of those people are arguing from ignorance.

      Are you trying to make the case that evolution by random genetic is unimportant therefore it's okay to use an adaptationist metaphor to describe evolution?


      Not a good analogy because it compares an important mechanism like random genetic drift to "empty space." What if you were to say that astronomy is all about supernova, black holes, and beautiful nebulae without mentioning gravity, dark matter, or background radiation?

    7. Sorry but I don't know how else I can phrase that to bring across my point. When nobody knew how genetics work there was already a theory of evolution, and if we had never figured DNA out there would still be the same theory of evolution to explain the diversity of life and the illusion of design. So how can it make sense that everybody who thinks that drift is not what the theory of evolution is about be ignorant? (Unless you mean 'ignorant of drift', but I understand you to mean 'ignorant of what evolution is about'.)

      Personally, I deal with proponents of paraphyletic taxa who have fallen in love with the definition "evolution is descent with modification" because they somehow believe that that definition shows phylogenetic systematics to be un-evolutionary. I don't get their 'reasoning', nor do I find their particular definition very good at capturing what evolution is about. But they appear to think that it is the truest to Darwin, and I have to deal with them.

    8. I really don't care what people thought about evolution in previous centuries. This is 2013 and anyone who denies that evolution is mostly about drift is ignorant of evolution. Even Richard Dawkins admits that fixation of neutral alleles is the dominant form of evolution. (He's a bit confused about the difference between Neutral Theory and random genetic drift.)

      Dawkins just doesn't think that fixation of neutral alles is very interesting. His specialty was animal behavior and he preferred adapationist explanations.

      I don't have a problem with that perspective as long as people don't mistakenly equate natural selection with evolution and don't claim that the "selfish gene" is a metaphor for EVOLUTION as opposed to a metaphor for NATURAL SELECTION.

      They should not refer to modern evolutionary theory as "Darwinism" or even "neo-Darwinism" if they truly understand the importance of Neutral Theory and random genetic drift. Those are anti-Darwinian concepts.

    9. Larry,

      You have been saying it ever since I have joined your blog few months ago in one form or another:



      I don't know Joe's F view on the issue-maybe I missed it-but Harsh-man, Coyne and it seems Dawkins they all disagree with you. I'm not an evolutionist, but I try to learn as much as I can from people like you and the above, but I don't know if RGD is very popular among evolutionary experts... I, however, respect your own view and the courage to oppose the above mentioned scientists...Larry, don't misunderstand me! Just because you seem to be alone, it doesn't necessary mean you are wrong....I know something about that...That's why I will be retiring soon, coz my company is being "absorbed" by another much, much richer company, just because I stuck to my guns....:) So, Larry, if you believe it, stick to it! Just make sure you are I was...

    10. Idiot. Genetic drift is dominant if by that you mean that most fixations in most genomes are due to drift, not selection. It isn't dominant if by that you mean that most adaptive evolution is a result of drift. Larry's major disagreement, if you can call it that, is that many biologists tend to pay less attention to non-adaptive evolution than to adaptive evolution. Not because they don't think it happens, and not because they think it doesn't happen a lot, but just because they find adaptation more interesting and tend to forget to mention drift. (Which is also not to deny that drift can at times be a factor in adaptation too.)

      And I'm pretty sure anyone reading you finds your fantasy life uninteresting.

  5. All I have to say is that nobody really know how evolution is supposed happen. Larry likes the genetic drift and Coyne likes the natural selection. When I asked my biology professor how evolution accomplished all the diversity, he told me to never expect a true explanation from experts who claim to know something, who really know nothing.

    How true this turned out to be.

    1. Yes, that is so true, in all fields. Like, I ask one person how a car works and they say that the wheels turn to move it across the ground, and I ask another and they start talking about engines. Clearly nobody really knows how cars are supposed to work.

    2. Ahh, the age old "there is debate - therefore noone is right and the truth can't be known, believe whatever you want".


    3. And then IDiots like LouiseG come along and tell you that it's chipmunks under the hood that make the car go and you just know they've never bothered, and never will, to open the damn thing up and take a look for themselves.


    Not really: modern theories of multi-level selection are equivalent to kin selection (in the sense that both methods of accounting for genetic change in populations make the same set of predictions). Kin selection was championed in Dawkins (1976) and has always been perfectly compatible with the idea of the selfish gene.

    1. Do tell me more about this weird theory of yours.

      Explain how species sorting is just another version of Hamilton's equation.

      You do realize, don't you, that Dawkins has always been firmly opposed to both group selection and species sorting? ... No, you probably don't realize that.

    2. Er, it's not a "weird theory of mine" it's the modern consensus on the topic.

      For my references see the article "Group selection and kin selection: formally equivalent".

      Multi-level selection models are mostly concerned with how selection between groups promotes cooperation within groups. Species sorting is an extreme case of this - where the groups are not necessarily very closely related and the resulting "cooperation within groups" is negligible. It's not a sensible place to start when trying to understand the topic. It's more the place a critic might start if looking for obscure corner cases to use as counter examples. If you don't know about the equivalence, I advise not starting to learn about the topic in that way.

    3. The modern consensus is that multi-level selection doesn't exist. Group selection is dismissed for a variety of reasons, mostly becsuse there's no evidence. It's true that there are some scientists who are willing to concede evidence for group selection but they explain it by some verion of kin selection. Naturally, these scientists have a myopic view of life since their theories usually apply only to animals. I don't know how they might account for group selection in bacteria, protozoa, or algae.

      When we're talking about multi-level selection we're talking about a lot more than just selection at the level of groups. You said that "modern theories of multi-level selection are equivalent to kin selection." Now you say that you were only talking about group selection and it was not sensible of me to assume that you included species selection in your "theory of multi-level selection."

      I don't think we can have a productive discussion if you continue to say things you don't mean. This isn't the first time I've noticed this problem.

    4. Practically nobody thinks that multi-level selection "doesn't exist". Rather there are debates about its significance in producing group-level adaptations - and its usefulness (compared to the rival kin selection

      You have previously explained that you don't see how kin selection applies to non-animals (in the article "squirrels, Dawkins, and Evolution"). My reply is in the article "Kin selection without brains". Its references include cases of kin selection in bacteria and amoebae and other microorganisms. I'm not clear what problem you are having here - but surely looking at the literature on kin selection in such creatures will clear things up.

      No, I was *not* saying that I didn't include species sorting! That is a misreading or a misinterpretation of what I wrote. You "challenge" was analogous to asking a kin selection enthusiast to explain how kin selection applies to interactions between a bat and a bird. Well, that's just the case where relatedness is negligible (r=>0). Kin selection boils down to ordinary natural selection in such cases. The same applies to species sorting within multi-level selection frameworks. Such cases aren't counter examples that invalidate the theory - they are just cases which don't fully exercise it.

  7. Coyne:



    "Epigenetics" drives phenotype?

    1. Just for the record. I completely agree with Jerry Coyne. Epigenetics, per se, is not a significant factor in evolution.

      We've known about restriction/modification for over thirty-five years and nobody has ever shown that it represents a new way of evolution.

      Restriction, Modification, and Epigenetics
      Nobel Laureates: Arber, Nathans, and Smith

    2. Thanks for the links Larry....

      As usual the links, for me personally, create more questions than answers I got....I will get back to you that...

      BTW: I'm not quite sure I understand your statement though...I hope you don't mind me asking further....?

      "I completely agree with Jerry Coyne. Epigenetics, per se, is not a significant factor in evolution."

      As you may remember Larry, English is not my first language (apparently once someone learns more than 3-4 pretty well, they can't tell which one is which-that's me-(if it is true)....). So I'm puzzled... a bit...

      If "epigenetics, per se"-what's that mean to you?

      ....", is not a significant factor in evolution."-So, it does play a role.... to some degree. Right? I'm just trying to get the facts straight.... It's my Aspergers Larry...

  8. Mr Coyne says ambition and boredom is the secret motivation behind wrong criticisms.
    Well then what are selling here!?
    Creationists do, can, will continue to say secret motivations are behind evolutionary biology error or any opposition to the fingerprints of God in nature.
    If he believes ernest scientists are under false motivations disturbing their scientific investigations then this can also nullify the concept thrrown at ID/YEC that its WRONG to question scientists on their conclusions in these matters.
    Sure we can question because its not just pure investigationg. People are under influences in their thinking.
    Mr Coyne said so about his group.!
    Where am I wrong here?

  9. Resurrect! Unselfish Gene, Resurrect Yourself!!!

    "Lazarus Microbe's Immortality Secret Revealed"

    I have never thought I would live long enough to see this...

  10. Hi,

    Is there a layman-understandable way to explain the difference between Neutral Theory and random genetic drift?

    I suppose neutral theory is much more general than drift, and random genetic drift can have an effect on any genes, not just neutral ones.
    Is that in the right direction?

    1. Drift in the general case relates to the operation of 'random' factors upon population frequency changes. It can be understood as the distortion of frequencies in any sample compared to the wider collection from which it is drawn. The population makeup of any generation is a sample of the previous, and so this effect is inevitable in any finite population, proportional to the population and 'sample' sizes. In successive generations, the distortions compound and lead to fixation by random process alone.

      Selection is a consistent bias in the sampling, such that variants with a consistently greater net output are more likely to increase. But this can still be opposed by sampling error; it's a skew in the probability distribution, not a certainty.

      Neutral theory relates to the case where there is no selection at all - there's no bias, the only factor is that sample error. If one imagines a tiltable plane, the Neutral position is when the plane is level. The population wanders around that plane with no restraint. Adding various degrees of selective differential 'tilts' the plane - there remains an element of 'wandering', but at steeper and steeper angles, the random effect (drift) diminishes as the selective effect strengthens, and except at the extremes it's never an either-or situation.


      Allan Miller did an excellent job of explaining the difference but let me just add a few points.

      You are correct that random genetic drift is the more general phenomenon. It affects all alleles. It can lead to the fixation of deleterious alleles (in small populations) and it can prevent fixation of beneficial alleles. (These are two sides of the same coin.) Most people don't realize that the vast majority of beneficial alleles are lost before they become fixed in real populations.

      Neutral Theory only deals with neutral alleles. Nearly-Neutral Theory incorporates the fixation of slightly deleterious alleles. But it's still random genetic drift that serves as the other main mechanism of evolution.

    3. In other words, drift is much more general than neutral theory.

  11. How does selfish gene concept reconcile with monoallelic expression or genomic imprinting? What is in those for the selfish gene?

  12. Most of the discussion begs the question, which hinges on Dawkin's inept use of language and the current attempt to rationalize it all as a metaphor.

    Dawkins was unambiguous when he stated that humans were mere robots operating at the behest of their genes.


    There is no metaphor in that perspective.

    He even ended TSG with the following statement:
    "We, that is our brains, are separate and independent enough from our genes to rebel against them."

    Since when is it necessary to rebel against a metaphor? More importantly, I would be truly interested in how our brains are separate from our genes.

    Regardless of evolution and natural selection, this is an extremely poor choice of words, it is a meaningless metaphor, and it has done nothing except increase the level of confusion. Even Coyne's quote above aggravates the problem when he states that "genes act as if" ... Genes don't act. There is no "as if". There is no metaphor.