David Dobbs mucks up evolution, part I

Although I haven’t read much by David Dobbs, I’m told he’s a good science writer. But you couldn’t prove that from his latest effort in Aeon magazine: “Die, selfish gene, die” (the subtitle is “The selfish gene is one of the most successful science metaphors ever invented. Unfortunately, it’s wrong.”) I was going to write a critique in a single post, but I see that it would be too long, so I’ll divide it into two parts.

When I read Dobb’s title and subtitle, I thought “Whoa!” I keep up with evolutionary biology, and I wasn’t aware of any serious objections to the selfish gene metaphor. (Granted, there are misguided folks like Mary Midgley who don’t understand the metaphor, but they don’t count.) After all, the metaphor simply means that, during the process of natural selection, genes “act” as if they were selfish.  And that means that those genes that replicate faster than others—those that make their “vehicles” leave more copies of those genes—spread through the gene pool, out-competing other gene copies. It’s a metaphorical and, to me, enlightening description of natural selection, for it helps one see more clearly how evolution works. For example, “meiotically-driven” genes, which don’t really improve the “adaptations” of their carrier but act by simply killing off the other gene copy in the gonads (each gene is present in two copies), are “selfish” but not conventionally “adaptive.” And they spread exactly as if they were selfish. This shows one difference between natural selection and adaptation.

At any rate, Dobb’s goal is several fold. First, he wants to claim that the metaphor of the selfish gene is wrong.  Second, he wants to show that it’s wrong because new understanding of gene regulation—how genes turn on and off during development—render the selfish gene metaphor passé.  Finally, he claims that a new theory, that of “genetic accommodation,” relegates much of conventional evolutionary theory to the dustbin, for the new theory deposes the centrality of the gene in favor of the centrality of the environment and its non-genetic effects on development. I’ll deal with the first two issues today, and the third tomorrow.

All three of these claims are wrong. However good Dobbs’s other writing may have been, this is a dire piece: one that is loaded with misinformation, wrong information, misleading information, and unsupported speculation. None of it even comes close to deposing the value of the “selfish gene” metaphor, and I’m not saying that just because I’m friends with Richard Dawkins.  Indeed, it’s with a heavy heart that I set out to write this post, because I’ll have to devote at least 4 hours over two days to pointing out what’s wrong with Dobb’s article, and most people won’t read this anyway.  I’m writing this only to set the record straight, to give my response to the several readers who sent me this article while praising it, as well as to those who have touted it on the internet as a wonderful and informative piece, and, finally, in hope that those interested in evolution might learn how to distinguish the wheat from the chaff in popular science writing. Sadly, even some science writers have praised it:

Picture 1

Dobbs begins with a gratuitous slur (disguised as praise) about Richard Dawkins:

These days, Dawkins makes the news so often for buffoonery that some might wonder how he ever became so celebrated. The Selfish Gene is how.

That comment is completely out of line in a serious popular article. Everyone who knows about evolution knows how Dawkins became celebrated: by writing and talking first about evolution, and then, more recently, about atheism. He succeeded brilliantly at both.  But Dobbs can’t refrain from making fun of what, I suppose, are Dawkins’s statements on Twitter.

And then, after that faint praise, Dobbs tries to demolish the gene-centric view of the selfish genes. I’ll put in bold Dobb’s claims that I contest (indented quotes are from his piece):

New discoveries in gene regulation make the gene-centric view outmoded.  Dobbs seems to conflate two issues and, on top of that, makes an error about the evolution of gene regulation.  He begins with an example of what we call “polyphenism”: the change in an organism’s form over its life cycle. Dobbs’s example is that of grasshoppers turning into locusts (they’re the same species): when certain species of grasshoppers are crowded, they undergo striking changes in form and color, turning into the migratory insect that wreaks so much damage on crops. Other, uncrowded populations remain grasshopper-like.

Another example of polyphenism are castes of hymenopterans (mentioned by Dobbs). All female bees in a nest share similar genomes, but those fed royal jelly as larvae (an environmental effect) turn into queens, for that feeding activates different genes.  The different cases of worker ants in some species, with some being soldiers and others trash-disposers, are a further example.

Similar striking changes in form occur also occur during the development of many species: male deer grow antlers, and, more dramatically, some species experience huge changes in form during their life cycle, as when a caterpillar undergoes metamorphosis into a butterfly.

Now these are all clearly examples of changes in gene expression: when a caterpillar turns into a butterfly, or a deer grows antlers when it ages, that must be due to differential gene expression—some genes are turned on and others off.  The same holds when crowded grasshoppers become locusts or bee larvae become queens. This must be the case, for an individual has the same set of genes over its life, and so if it has programmed changes in behavior, morphology, or physiology during its lifetime, those changes must be due to the differential expression of the set of genes it inherits as a zygote. (The development of different cells and organs in the body reflects the same thing: they all have the same genome, but a liver cell differs from a heart or brain cell because it’s expressing a different set of genes.)

The changes above are all adaptive ones—grasshoppers are better off migrating when they’re crowded because they’ll run out of food if they stay put, and it’s obviously good, as the Tin Man found, to have a heart as well as a brain. Ergo, the changes in gene regulation that cause changes in form over one’s lifetime are evolved changes, created by the process of natural selection. In other words. the bits of DNA determining whether genes turn off and on (the so called “regulatory genes” or “regulatory elements”) have evolved. And they’ve evolved as selfish replicators.  Bits of DNA that produce adaptive responses to environmental changes, like those that turn sedentary grasshoppers into migratory locusts, will be favored by natural selection and sweep through the species. They are no different from any other “selfish” gene that promotes the reproduction of itself or its carrier.

Note that this kind of evolution is precisely that outlined by Dawkins in The Selfish Gene. The difference between migratory grasshoppers and species that never transform is an evolved difference, and presumably an adaptive one. There are no principles here different from that those outlined by Dawkins.  Adaptive differences between species that depend on differences in gene expression rather than differences in DNA sequences of structural genes (e.g., the hemoglobin gene) are both based on evolved differences in the DNA. The only difference is that the DNA changes reside in regulatory elements rather than full genes that code for proteins.

But Dobbs implies that somehow evolved differences in gene regulation do not involve “selfish-gene-ology” (the wrong or speculative parts are bolded):

Transforming the hopper is gene expression — a change in how the hopper’s genes are ‘expressed’, or read out. Gene expression is what makes a gene meaningful, and it’s vital for distinguishing one species from another. We humans, for instance, share more than half our genomes with flatworms; about 60 per cent with fruit flies and chickens; 80 per cent with cows; and 99 per cent with chimps. Those genetic distinctions aren’t enough to create all our differences from those animals — what biologists call our particular phenotype, which is essentially the recognisable thing a genotype builds. This means that we are human, rather than wormlike, flylike, chickenlike, feline, bovine, or excessively simian, less because we carry different genes from those other species than because our cells read differently our remarkably similar genomes as we develop from zygote to adult. The writing varies — but hardly as much as the reading.

This raises a question: if merely reading a genome differently can change organisms so wildly, why bother rewriting the genome to evolve? How vital, really, are actual changes in the genetic code? Do we even need DNA changes to adapt to new environments? Is the importance of the gene as the driver of evolution being overplayed?

Sorry, but he’s wrong here.  First. he implies that, within a species, adaptive changes that evolve by natural selection don’t involve “genetic distinctions”: changes in DNA sequence. That’s wrong; in fact, it ‘s not even wrong! Even if species differences rest on changes in how genes are “read,” those differences in “reading” must themselves reside in the DNA, and thus must evolve as all selfish replicators evolve.  Our differences from cows and cats do indeed reside in differences in the genome between species, but those differences can involve both the DNA sequences coding for proteins as well as in the sequences of “regulatory elements”. All heritable differences between species, in fact, must reside in the DNA; we know of no cases in which they don’t. Where else could they be?

Second, Dobbs conflates changes within an individual’s lifetime—changes that must be due to differential expression of genes carried by a single individual—with differences among species. The former must involve evolved differences in gene expression, while the latter can involve changes in both the sequences of proteins (“structural changes”) or gene expression (“regulatory changes”).  There is an active controversy in the field—a controversy in which I’ve been involved—over the proportion of adaptive differences between species that involve changes in gene regulation  versus those involving changes in the sequence of genes that make proteins (and hence the sequence of proteins). We know examples of both types of evolutionary change: genes that differentiate marine versus freshwater forms of stickleback fish, for example, seem to involve changes in gene expression, while the production of “antifreeze proteins” in Antarctic fish, differences between hemoglobins of birds that fly at high vs. low altitude, or insecticide resistance in insects, involve changes in protein sequences. But in all cases the evolutionary changes came from natural selection acting on selfish replicators. So we need not throw out the notion of “selfish genes” here, so long as we keep in mind that some genes, or bits of DNA, control the expression of others.

Differences between humans and other species cannot reside in differences in their DNA sequences. Dobbs makes another mistake: he argues that humans’ 20% DNA difference from cows is not enough to explain our profound morphological and behavioral differences.  But it must!  What other explanation is there? In fact, a 20% difference in DNA sequence adds up to a lot of genetic differences when you consider that the human genome contains 3 billion base pairs. A 20% difference is 600 million differences! Now many of the nucleotides reside in junk DNA, but if you consider that the human genome still has 21,000 genes, and assume (I’m just floating reasonable estimates) that genes have an average size of 800 DNA base pairs, then the average number of nucleotide differences between the genomes of humans and cows is 3,360,000 (21,000 X 800 X 0.2). Even the oft-cited 1% difference between humans and chimps works out to 168,000 differences in the genes.  As I noted, some of these differences reside in non-coding parts of genes (like junk DNA or third positions of triplet “codons”), but there are also other bits of DNA, not in these 21,000 genes, that can affect gene expression.  So even between humans and chimps there are thousands of genetic differences, and between humans and cows there are millions! How can Dobbs confidently conclude that our 20% DNA difference from cows isn’t enough to explain why we don’t eat grass or walk on four legs? He can’t. He’s just trying to flummox us with misleading “similarity indices.”

So when Dobbs says “you are 80 percent cow,” don’t be misled.

When you consider that adaptive changes within a lineage, or adaptive differences between species, must involve natural selection acting on DNA, whether that DNA involves making proteins or regulating whether protein-coding genes are turned on or off, you have to ask where the new paradigm really is.  Is there a there there? Dobbs quotes my colleague Greg Wray, who answers “yes”:

Gregory Wray, a biologist at Duke University in North Carolina who studies fruit flies, sees this flexibility of genomic interpretation as a short path to adaptive flexibility. When one game plan written in the book can’t provide enough flexibility, fast changes in gene expression — a change in the book’s reading — can provide another plan that better matches the prevailing environment.

‘Different groups of animals succeed for different reasons,’ says Wray. ‘Primates, including humans, have succeeded because they’re especially flexible. You could even say flexibility is the essence of being a primate.’

According to Wray, [Mary Jane] West-Eberhard and many others, this recognition of gene expression’s power requires that we rethink how we view genes and evolution. For a century, the primary account of evolution has emphasised the gene’s role as architect: a gene creates a trait that either proves advantageous or not, and is thus selected for, changing a species for the better, or not. Thus, a genetic blueprint creates traits and drives evolution.

This gene-centric view, as it is known, is the one you learnt in high school. It’s the one you hear or read of in almost every popular account of how genes create traits and drive evolution. It comes from Gregor Mendel and the work he did with peas in the 1860s. Since then, and especially over the past 50 years, this notion has assumed the weight, solidity, and rootedness of an immovable object.

But a number of biologists argue that we need to replace this gene-centric view with one that more heavily emphasises the role of gene expression — that we need to see the gene less as an architect and more as a member of a collaborative remodelling and maintenance crew. . .Wray, West-Eberhard and company want to depose genes likewise. They want to cast genes not as the instigators of change, but as agents that institutionalise change rising from more dispersed and fluid forces.

Do these people not realize that gene expression is itself caused by differences in DNA sequence, and that those regulatory bits of DNA evolve precisely like “structural” genes themselves? And why on earth must “flexibility” reside more on changes in gene expression than on the structure of proteins themselves? We have no idea whether changes in gene regulation evolve more rapidly than changes in gene structure. Finally, Dawkins himself emphasizes the interactive nature of genes in The Selfish Gene, using another metaphor that of genes as individuals rowing in a crew boat (the organism). They all have to stroke in harmony to make the boat move, but you can still make it move faster by substituting a stronger oarsman for a weaker one. Selection often proceeds by that route: replacing one gene form with another in a way that keeps the vehicle—the organism—moving forward.

Further, there’s no sharp distinction between “regulatory” and “structural” genetic elements. If you know anything about genetics, you’ll know that some bits of DNA that regulate others themselves produce proteins: the so-called “transcription factors”.  And a change in a gene making a transcription-factor protein (the famous Hox genes are one example) can cause changes in how other genes are regulated. A mutated “regulatory” protein, for example, can change how it interacts with the genes it regulates, so that a structural gene has regulatory effects.

It is still an unsolved question what proportion of adaptive differences between species reside in the DNA that makes proteins versus in the non-protein-coding “regulatory elements” of DNA that turn structural genes on and off. (Those elements are often adjacent to the genes they regulate, but need not be, so finding how and where a gene is regulated is often a complicated issue.) But that doesn’t matter, for in every case bits of DNA that are responsible for adaptations evolve “selfishly”: bits that improve an individual’s reproductive output become overrepresented in the next generation.

Nor does it matter that polyphemism, like the production of locusts from crowded grasshoppers, rests—as it must—on differential gene expression.  For the ability of a genome to respond adaptively to environmental change by changing the expression of its constituent genes is itself an evolved phenomenon. (Another example is how Daphnia grow fish-deterring spines when placed in ponds that contain fish.) And the only way that adaptive evolution can occur is through the “selfish” behavior of genes.

An historical error.  Maybe this is nit-picking, but it shows the level of Dobbs’s scholarship about the history of genetics. Dobbs claims that the idea of “kin selection,” or “inclusive fitness” came from the three founders of mathematical population genetics: Ronald Fisher, J.B.S. Haldane, and Sewall Wright:

Fisher, Haldane and Wright, working the complicated maths of how multiple genes interacted through time in a large population, showed that significant evolutionary change revealed itself as many small changes yielded a large effect, just as a series of small nested equations within a long algebra equation could.

The second kink was tougher. If organisms prospered by out-competing others, why did humans and some other animals help one another? This might seem a non-mathy problem. Yet Fisher, Haldane and Wright solved it too with maths, devising formulas quantifying precisely how altruism could be selected for. Some animals act generously, they explained, because doing so can aid others, such as their children, parents, siblings, cousins, grandchildren, or tribal mates, who share or might share some of their genes. The closer the kin, the kinder the behaviour. Thus, as Haldane once said, ‘I would lay down my life for two brothers or eight cousins.’

The first part is right: those three men did reconcile Mendelian genetics with Darwinian evolution.  But they did not solve the problem of altruism or kin selection with maths. True, Haldane’s quote, whose authenticity is dubious since it was reportedly uttered in a pub, suggested offhand that he knew relatedness was the key to the problem. (But even this is at issue: see the discussion on pp. 174-178 in Ullica Segerstrale’s new biography of Bill Hamilton, Nature’s Oracle.) But that is all Haldane supposedly said about the issues of altruism and kin selection. There were no “formulas quantifying how altruism could be selected for.”

The problem of altruism and selection through kin was not in fact solved until the 1960s, largely by Bill Hamilton, whom Dobbs mistakenly and snarkily describes as a “funny statistician with a shaggy haircut.” (Hamilton was not a statistician but both an accomplished naturalist and a theoretical biologist. He didn’t work on statistics itself, but, like all biologists, used them.)  Others like John Maynard Smith also made contributions to the problem of animal cooperation.  Anybody who has studied the history of evolutionary biology knows this, and I wish Dobbs had let someone who knew that history vet his piece. (Dobbs also gets the modern method of assessing gene expression wrong: we have moved beyond microarrays.)

***

Tomorrow I’ll deal with the other main point of Dobb’s article: that there is a new paradigm—the notion of “genetic accommodation”—that completely revises how we should view evolution. A preview: he’s wrong here, too, and on two counts. Dobbs mischaracterizes how “genetic accommodation” works, and he doesn’t mention that we have no credible examples of that process producing any adaptations. Genetic accommodation is a complicated and unparsimonious idea in search of data.

In contrast, we have plenty of examples of “regular” Darwinian evolution acting on standing genetic variation.

But that’s for tomorrow, as Professor Ceiling Cat has work to do.

_______

UPDATE: Dobbs has, in the comments below, referred us to his website, where he clarifies what he really meant in this piece. I am not going to read that site until I finish critiquing the Aeon piece tomorrow, for I want to analyze the piece as it was published, without being influenced by Dobb’s clarifications.

171 Comments

  1. francis
    Posted December 5, 2013 at 7:10 am | Permalink

    //

  2. Posted December 5, 2013 at 7:29 am | Permalink

    This is an extremely clear and well-written post.

  3. Posted December 5, 2013 at 7:31 am | Permalink

    I won’t engage this point by point at this stage. I ackowledge I may have muddled some things in my article, but feel that Coyne here overstates and engages in something close to willful misreading.

    To try to clarify some of this, I’ve a post at my blog: http://j.mp/TLDRdie

    • Posted December 5, 2013 at 7:40 am | Permalink

      It’s more than muddling, it’s wrong in places. For example, it’s simply, flatly, palpably wrong to give Fisher, Haldane, and Wright credit for devising the genetic theory of altruism and kin selection.

      And I stand by what I said.

      • galois
        Posted December 5, 2013 at 10:16 am | Permalink

        shit. scientist putting his foot down.
        *takes picture due to rarity*

      • Posted December 5, 2013 at 9:08 pm | Permalink

        While Dobbs’ stature may not comparable to Stephen Jay Gould, this kind of mistakes based mostly on personal emotions (remember punc-eq?) should not be left muddled the real science for too long. Combination of promise-of-popularity, near-miss-theories, and shoot-the-king mentality is major waste of time.

        The fact that genes are not just the structural genes, but including all and everything, mislead the Dawkins’ critics like Dobbs here.

        All the regulatory, the on-off and environmental-effectee-genes are there! Junks they may not be, but all are there! All written in the same code, and live by the code.

        We don’t know exact details yet, but it is clear that everything’s “there” (the real debate actually is on lamarckian version, but it was long time ago). And careful reading of Dawkins’ books, it is clearly and repeatedly stated.

        Jerry’s article is clear, timely and important, and he has the stature to set these things right.

        Hail to the followers of ceiling-cat!

        (as non-believer I do not use capital letters)

      • What. The. Hell.
        Posted December 9, 2013 at 11:33 am | Permalink

        Thanks for breaking this down. I have had a few friends ask me about this article because I study evolution, and I started to explain it, but it’s easier to just point people here. :P Seriously – this article doesn’t change anything from my perspective. Perhaps this is earth-shattering for laymen who have a superficial grasp on evolution, but people doing research are fully aware of this. That’s why we do RNAseq and other mRNA analyses to figure out what genes are involved in different processes – because this is old news.

    • Peter Beattie
      Posted December 5, 2013 at 8:33 am | Permalink

      I ackowledge I may have muddled some things in my article, but feel that Coyne here overstates and engages in something close to willful misreading.

      If you make that kind of accusation, you should at least be able to point to one instance that you think represents that willful misreading. From where I’m sitting, Jerry seems to be spot-on.

      And your TL;DR version simply repeats your central mistaken assertion: that Dawkins, in The Selfish Gene, was “arguing for the primacy of an individual gene that creates a trait that either survives or doesn’t”. Instead of simply saying, ‘Nope, he doesn’t say that’, maybe I should ask you to quote a passage from TSG to support your point. (In your TL;DR version, you rather suspiciously pretend that “please note book’s title” is doing that job. It isn’t.)

      Also, Dawkins seems to have pointed you to the fact that the fixing of regulatory genes is done by exactly the same process as in structural genes—which you neither explained nor even mentioned in your article. Jerry’s point about a lack of proper vetting seems to be just as apt in this instance.

      And one bit of honestly well-meaning advice from a fellow journalist: Your apologies notwithstanding, if you mention more than once how many people “loved” your article, the odds are that you are lacking in critical attitude towards your work. Ten people telling you how brilliant your work is aren’t as useful as one person bluntly telling you that a particular bit in your text is distracting, pretentious, or just crap.

      • Jeff
        Posted December 5, 2013 at 11:59 am | Permalink

        Wait, so should I not find his incessant re-tweeting of laudatory support for the article from random people compelling evidence that his premise is correct?

        • Peter Beattie
          Posted December 6, 2013 at 6:38 am | Permalink

          I can see the point of that in a fledgling writer who needs more exposure. But if you already write for really big outlets, that looks much more like a really bad need for confirmation. And Dobbs, who says he’s all about learning, should know better—because you only learn from criticism.

    • Marta
      Posted December 5, 2013 at 8:43 am | Permalink

      I’m wondering, Mr. Dobbs, how you reconcile saying:

      “These days, Dawkins makes the news so often for buffoonery that some might wonder how he ever became so celebrated.”

      with saying this:

      “Many have liked  “Die, Selfish Gene, Die,” my Aeon piece challenging Richard Dawkins “Selfish Gene” meme. Quite a few readers have objected to and disagreed with the story, sometimes sharply. Some readers have both liked it and objected to it. I want to thank everyone who’s read it, and to acknowledge right here at the top (as well as later, at bottom) the extra energy and goodwill extended by those who objected in constructive spirit. The hardest but most necessary sort of reading is to read charitably, and with a sincere, sustained effort to understand, something that sharply challenges you.”

      Aren’t you asking your readers for the charity you were unwilling to extend to Dawkins?

    • darrelle
      Posted December 5, 2013 at 9:32 am | Permalink

      Willful misreading? That is inaccurate, and low. It seems to be an effort at damage control rather than a reasonable response to criticism.

      The choices are limited. Either your article was really bad at communicating your ideas, or you are mistaken both on many specific points and about your general thesis. Which Jerry clearly and specifically described.

      Being wrong does not, by itself, reflect badly on a person. How a person behaves when their mistakes are pointed out is usually much more telling.

      Here you have another experts attention. For a journalist I would expect that to be seen as a great opportunity to ask some questions and vet your ideas, and what your other experts have told you. Jerry’s post here alone is a gold mine of information.

      Unless your agenda is somthing other than an accurate portryal of the current best understanding of the science you are writing about.

      • Peter Beattie
        Posted December 6, 2013 at 6:31 am | Permalink

        Being wrong does not, by itself, reflect badly on a person. How a person behaves when their mistakes are pointed out is usually much more telling.

        +1

      • Posted December 6, 2013 at 9:48 am | Permalink

        I’ll second Peter’s +1.

        Complete honesty, especially including the willingness to unconditionally acknowledge when you’re wrong, is one of the most respectable traits a person can have.

    • CJ
      Posted December 5, 2013 at 10:30 am | Permalink

      The selfish gene is about replicating information. It’s a fundamental error to think in terms of only protein coding genes. The book is so well written that it amazes me how misunderstood it is.

      • CJ
        Posted December 5, 2013 at 10:31 am | Permalink

        …biologically replicating information that is.

      • gbjames
        Posted December 5, 2013 at 10:35 am | Permalink

        Yes.

        (But not just biological information, as mentioned in your follow-up note. His last chapter did point out that this process can happen for non-biological systems, too. He invented the word “meme” for cultural variants of this process.)

      • Posted December 5, 2013 at 10:11 pm | Permalink

        Yes, I got the feeling that most of the critics do not actually read the book. Like Dobbs here I am not sure he actually read Dawkins’ book (!).

    • Posted December 5, 2013 at 4:22 pm | Permalink

      It’s kind of a shame that you have to write a blog post clarifying your article when a solid proofread (or a sub-editor) could’ve done that in the first instance. You’d think a little more attention to clarity would be warranted by a piece that purports to as important as this one.

    • Hoss
      Posted December 6, 2013 at 8:32 am | Permalink

      What structure would cause a geneotype to change in response to the environment, without any testing? If species just changed gene expression to fit their environment, the dinosaurs would be still with us.

      And by the way: If you want your clarification article to be taken seriously, using ¨f***¨” isn’t a good idea

    • Gary Sisco
      Posted December 9, 2013 at 11:54 am | Permalink

      A writer who must write again to “clarify” what he has previously written has not written it very well. All a reader has to go on, necessarily, is what the writer has written on the page.

      *Factual* errors, however, never mind when fundamental to the subject itself, are not matters of “clarification.”

      In this latter light, Dobbs doesn’t seem to understand that his factual errors render his attack on “the selfish gene” entirely wrong.

  4. Posted December 5, 2013 at 7:32 am | Permalink

    Your work is not in vain, I read it, that’s one person. What’s more, I also read the Dobbs article and, I’m young and unused to thinking critically about things, originally liked the article. The only hiccup I had was the bit about Hamilton so it was quite a shock to read your article and thinking ‘how did I not see this?’ for many of the problems you point out with the article.

  5. NinetyEight
    Posted December 5, 2013 at 7:42 am | Permalink

    Thank you for this. Only PZ’s recommendation had me repeatedly re-read that muddle of an article looking for a hidden point. I can stop now.

  6. Michael Fisher
    Posted December 5, 2013 at 7:44 am | Permalink

    THIS has just been put up on David Dobbs’s NEURON CULTURE site in response to some of the criticisms he’s received:-

    “…I apparently did not make clear that “Die, Selfish Gene, Die” is a story less about how genetics and evolution work than about the stories we tell about how genetics and evolution work — and, most crucially, about how those stories about nature percolate out beyond academia and into the minds of the lay public. I could write for pages to try to clarify all this. Possibly I may. But I do want to give here a tl,dr attempt to clarify…”

    See the link I’ve provided for more information. I’ve yet to read it myself.

    • Michael Fisher
      Posted December 5, 2013 at 7:45 am | Permalink

      I see Dobbs has beat me to it by 13 minutes :)

    • David Galiel
      Posted December 5, 2013 at 8:17 am | Permalink

      ““Die, Selfish Gene, Die” is a story less about how genetics and evolution work than about the stories we tell about how genetics and evolution work — and, most crucially, about how those stories about nature percolate out beyond academia and into the minds of the lay public.”

      Utterly disingenuous; as I’ve pointed out, the piece does not go into this at all. It is an attack on the science, not a discussion of pop meda “stories”. And, it is of a piece with other recent articles by Dobbs as well as his upcoming book.

      • darrelle
        Posted December 5, 2013 at 9:40 am | Permalink

        Yeah. That sounds just like Reza Aslan talking about a sophisticated understanding of religion. Complete horseshit, not sophisticated. Diversionary, not illuminating.

        That is the comment that caused me to, provisionally, place Dobbs in the “not worth much more than an eye roll” category.

  7. Posted December 5, 2013 at 7:53 am | Permalink

    “…for the new theory deposes the centrality of the gene in favor of the centrality of the environment and its nongenetic effects on development.”

    Sound familiar?

  8. NewEnglandBob
    Posted December 5, 2013 at 8:07 am | Permalink

    “and most people won’t read this anyway”

    I think you underestimate the followers of your web site.

    Also, having read Dobbs sort-of-response link above, Both Coyne and Dobbs agree that the original article was misleading to some degree.

    I anticipate the forthcoming back-and-forth and hope that few arrows go zipping around and the topic shines more clearly.

    • Posted December 5, 2013 at 10:31 am | Permalink

      Although I have the highest regard for most readers of this website, I seriously doubt that we constitute “most people.”

  9. peltonrandy
    Posted December 5, 2013 at 8:32 am | Permalink

    sub

  10. richardko
    Posted December 5, 2013 at 8:47 am | Permalink

    Talking about regulatory genes. I think it would be amazing if some poor souls (s) could monitor a species of cuckoo and see if it ever produced an egg of a wrong colour. Then look if the wrong colour matches another host. Then we could say that cuckoo once parasitised that host. (I know that is not a word). Maybe gene analysis will one day ‘read’ all the different egg patterns hiding away, waiting for a chance to prove they were not so junk at all. (apologies to Sinatra)
    Vivant professores !

  11. Diana MacPherson
    Posted December 5, 2013 at 8:47 am | Permalink

    Look at Jerry not taking time to educate! (Joke referencing another post about another post :)) Thanks for taking time out of your busy book schedule to write this. I enjoyed reading it as I would not have been able to spot these errors.

  12. Posted December 5, 2013 at 8:52 am | Permalink

    Jerry, I am in agreement with your post. Just one historical quibble. J.B.S. Haldane’s apocryphal pub comment was based on a better-than-superficial understanding of the issues. Here is a quote in 1955 where he gets close to the Hamilton formula, though the case he is discussing is group selection rather than kin selection:

    From: Haldane, J. B. S. 1955. Population genetics. New Biology 18: 34-51.

    on page 44:

    “What is more interesting, it is only in such small populations that natural selection would favour the spread of genes making for certain kinds of altruistic behaviour. Let us suppose that you carry a rare gene which affects your behaviour so that you jump into a river and save a child, but you have one chance in ten of being drowned, while I do not possess the gene, and stand on the bank and watch the child drown. If the child is your own child or your brother or sister, there is an even chance that the child will also have the gene, so five such genes will be saved in children for one lost in an adult. If you save a grandchild or nephew the advantage is only two and a half to one. If you only save a first cousin, the effect is very slight. If you try to save your first cousin once removed the population is more likely to lose this valuable gene than to gain it. But on the two occasions when I have pulled possibly drowning people out of the water (at an infinitesimal risk to myself) I had no time to make such calculations. Paleolithic men did not make them. It is clear that genes making for conduct of this kind would only have a chance of spreading in rather small populations where most of the children were fairly near relatives of the man who risked his life. It is not easy to see how, except in small populations, such genes could have been established. Of course the conditions are even better in a community such as a beehive or an ants’ nest, whose members are all literally brothers and sisters.”

    • Posted December 5, 2013 at 9:23 am | Permalink

      Joe:

      Yes, I’m aware of that comment; it’s discussed in Ullica’s book. She related how Hamilton himself, though, said that he didn’t see this as a serious anticipation of his own work. And, at any rate, you have to admit that Dobbs was flatly wrong in claiming that Fisher, Haldane, and Wright did the math that solved the problem of cooperation

      • Posted December 5, 2013 at 12:25 pm | Permalink

        I agree completely that Fisher, Haldane, and Wright did not do theory that solved the problem of cooperation, and yes, Hamilton should get almost exclusive credit for the kin selection formula. I was reacting to your comment that Haldane’s pub remark was all he supposedly said about the evolution of cooperation. Haldane did do some published verbal theory relating to group selection, and in doing so showed that he understood the bookkeeping behind inclusive fitness.

        While I’m here commenting, thanks again for stepping forward and defending contemporary evolutionary biology against views like Dodd’s, Shapiro’s, and all those people who think epigenetics is a valid alternative explanation of evolution of lineages. (Not to mention creationists).

        • BillyJoe
          Posted December 6, 2013 at 3:40 am | Permalink

          Like you, I was thinking “Shapiro” and “epigenetics” while I was reading Dobbs’ article. Yet he mentioned neither!

      • Dominic
        Posted December 6, 2013 at 2:47 am | Permalink

        Here is the Orange Tree – sadly gone in the post war wrecking of Euston Rd
        http://pubshistory.com/LondonPubs/StPancras/OrangeTree.shtml

  13. Posted December 5, 2013 at 8:58 am | Permalink

    Thank you for this excellent explanation.

  14. Ron Dorscht
    Posted December 5, 2013 at 9:04 am | Permalink

    Nice post…except deer grow antlers on an annual basis, not horns which are permanent!

  15. Sergio Graziosi
    Posted December 5, 2013 at 9:07 am | Permalink

    Jerry,
    I don’t know if my tw**t had anything to do with this, but thank you anyway.
    I knew you would produce a much better reply than I ever could: my little contribution is both more polemic and less comprehensive (I was happy to challenge the central point alone).
    Plus of course you have plenty more readership and reputation to make the sure the point will come across.
    I am still trying to understand why/how so many (non-genetist, non evo-something) scientists expressed their appreciation for Dobbs article on Tw****r. It’s well written and is rhetorically convincing, but it’s still plain wrong, not just muddled or obfuscated.

    • Ken Elliott
      Posted December 5, 2013 at 11:44 am | Permalink

      I am not a scientist, nor am I someone who understands thoroughly the nuts and bolts of any field of scientific study, but I am an atheist and therefore get into discussions on rare occasions with the emotionally challenged, or the religious. One hurdle I have is convincing them of the type of scientist making ID or Creationist claims. The movie by comedian Ben Stein, “Expelled: . . . ” is a great example, where scientists with ID agendas muddy the waters of the truth for those who are not familiar, and not likely to be familiar, with the differences between those with true expertise and those with only opinions of a field in which they have no expertise. Someday evolution and all it pertains will be more commonly accepted, it’s just not there yet. But scientists like Jerry and many of his blog followers, and of course Richard Dawkins, and all the wonderful true evolutionary experts are paving the way. They are the truth, the way, and the light. (Tongue in cheek emoticon inserted here)

  16. Posted December 5, 2013 at 9:10 am | Permalink

    Even if species differences rest on changes in how genes are “read,” those differences in “reading” must themselves reside in the DNA, and thus must evolve as all selfish replicators evolve.

    This is the fundamental misunderstanding of the whole epigenetics / “Darwin was worng!” crowd.

    If they were suggesting that there is an additional conceptual layer on top of Darwinistic genetics that is necessary for a full understanding of organismal development, I’d fully agree with them.

    Where they go off the rails is by claiming — or even merely suggesting — that this additional layer is all there is, or that it’s somehow independent of genetic inheritance.

    And, for the full measure of appreciation, one cannot lose sight of the fact that this developmental flexibility is, itself, absolutely subject to Darwinistic genetic evolution. Those species with DNA that gives them beneficial forms of flexibility will prosper over those with DNA that also lets them bend into harmful forms, if nothing else.

    Cheers,

    b&

  17. µ
    Posted December 5, 2013 at 9:37 am | Permalink

    I agree with Dobbs that we need to improve our teaching of the selfish-gene concept. I strongly disagree that the selfish-gene concept “needs to be replaced” (quote from Dobbs’ blog at http://j.mp/TLDRdie ).

    A common misperception is to view the selfish-gene as a “driver” (quote also from the Dobb’s blog). But what is simply meant is that, if one snippet of nucleotide sequence (allele) is replaced with another, different sequence in the same genetic background and in the same environment, and if that second sequence (allele) then has a greater probability of surviving and reproducing than the first sequence, it will be naturally selected. We should therefore expect genomes to accumulate over time nucleotide sequences (alleles) that are good at ensuring their own perpetuation into the next generation, and that are superior to alternate earlier versions. [See Dawkins in the Extended Phenotype for much better explanations and analogies of this process.]

    Whether these differentially replicating alleles are protein-coding or regulatory is irrelevant to the argument (Coyne is right about that; Dobbs seems to be wrong here).

    Now, teaching that view is not that easy. In my experience, many students are stumped mostly by the term “selfish” (which our society considers morally inferior), but not by the differential replication inherent in natural selection. Robert Trivers suggested therefore (in a lecture, years ago) that we should perhaps use the term “self-interested gene” (which is morally less stigmatized in our competition-driven society). The meaning is the same (allelic versions that are superior in contributing to survival and reproduction will come to populate a genome), but using the term “self-interested” may take some of the edge of “selfishness” that aggravates many students.

    • Posted December 6, 2013 at 4:57 am | Permalink

      But what is simply meant is that, if one snippet of nucleotide sequence (allele) is replaced with another, different sequence in the same genetic background and in the same environment, and if that second sequence (allele) then has a greater probability of surviving and reproducing than the first sequence, it will be naturally selected. We should therefore expect genomes to accumulate over time nucleotide sequences (alleles) that are good at ensuring their own perpetuation into the next generation, and that are superior to alternate earlier versions.

      I think you’ve hit on why there are objections to this idea, and why answers of “But even the regulatory genes are naturally selected and so selfish” really miss the point. Expressing it this way is simple — well, if it was put into less technical terms — but is so simple that for most of the traits and even genes we have it’s probably not true. Sure, things CAN happen that way, but they likely don’t most of the time.

      Consider free riders (one of Fodor and P-P’s big points). In those cases, you have a snippet that changes, but that snippet in and of itself, considered only as itself, has no greater probability of reproducing, and in fact might even have a lesser probability, but it happens to luck out into an organism that has other snippets that DO. It, then, propagates through the species through no fault of its own. Then, perhaps, the environment changes so that it DOES become beneficial and can itself be considered to be selected for, but the explanation for that trait and its prominence in the species is not that it was selected for at all, or that it had a greater probability in and of itself of reproducing.

      Now, consider the expression example. In this one, what you have are a set of snippets that determine expressable traits and how they are expressed. As part of that, there are snippets that will allow the expression of a certain trait, and snippets that will activate that expression if the environment is right. This, somehow, spreads through the population, but is not selected for in and of itself because these are never actually expressed because the environment is not yet right. Eventually, the environment changes, and the expression occurs, and the trait appears, and can then be selected for. But it was the environment change that was the catalyst, not any change in the genes, and it didn’t spread into the population because of that ability; that was, therefore, not selected for in the sense you describe.

      And talking about how genes all have to work together doesn’t solve the problem. If you say that, you really should just concede that it is a simplifying metaphor but no one should take it as an example of how most of our traits are actually produced, so looking for a genetic difference and trying to determine a trait — which Dobbs refers to early — is simply a non-starter; most of the time, you aren’t going to be able to tell what the traits will be looking at specific genes or gene sequences if the expression mechanism is more determinate, and you won’t be able to determine why that specific trait exists by looking for what benefits it has if expression and free riding are common.

      So, sure, it’s a decent summary of natural selection, but not one what you should use when you start looking at specific traits themselves.

      • µ
        Posted December 6, 2013 at 7:36 am | Permalink

        Note that I wrote: “if one snippet of nucleotide sequence (allele) is replaced with another, different sequence in the SAME genetic background and in the SAME environment” (caps added now).

        If the environment changes, or if the genetic background changes, then of course selection can change on any gene. Does that invalidate the utility of the concept of a “self-interested gene”? I don’t think so.

        Does any of that make the gene, or the genetic background, or the environment the “driver” [sensu Dobbs] in the process? None of the above can be called a “driver”, and this is also why neither epigenetics nor GxG nor GxE nor GxGxE invalidate the utility of the concept of a self-interested gene?

        re: “Consider free riders”.
        That too does not invalidate the utility of the concept of a self-interested gene. Hitchhiking genes are well-understood and their behavior in populations can be predicted from selection coefficients and linkage. [I think the more tricky issue here is whether the hitchhiking sequence should be considered part of the gene that is under selection, and the hitchhiker becomes a separate gene only once the environment changes and linkage is broken].

  18. Posted December 5, 2013 at 9:37 am | Permalink

    I’m not a serious student of evolution, but …
    1. I was totally confused by the Dobbs article and couldn’t get thru it. Thanks.
    2. When I first read Dawkins (can’t remember which book), I ran a simple mac program he wrote (or perhaps didn’t write) that was pseudo evolution, where you controlled the “selection” from a set of genetic mutations, and watched as your computer-graphic species evolved. The most eye-opening thing, for me, was the impact of the regulatory/developmental genes. Not what’s taught in my high-school-level knowledge.

    • darrelle
      Posted December 5, 2013 at 9:57 am | Permalink

      “The most eye-opening thing, for me, was the impact of the regulatory/developmental genes.”

      Yes. Just wanted to take the opportunity to comment that gene expression is not simply “on” or “off.” It is a continuum. Like a rheostat rather than a simple switch. And that adds immensely to the landscape of possibilities.

    • Ken Elliott
      Posted December 5, 2013 at 11:51 am | Permalink

      If you think of which book, please share with me. I am WAY behind in my reading. I still have all of Dawkins’ book except “The God Delusion”, Jerry’s WEIT, and others to read. I’m currently reading Pinker’s “The Better Angels of our Nature” which is fascinating. Someone that incredibly intelligent and communicable is rare, although Jerry, Richard, Neil, et al all have that ability to some extent, and for that this layman is thankful.

      • Diana MacPherson
        Posted December 5, 2013 at 11:58 am | Permalink

        You’re behind in your reading because Better Angels is long and takes a while to read! It took me ages to get through, as I read slowly & mostly at bedtime, but I loved reading it. Other books seem to go by such faster after Better Angels!

    • gbjames
      Posted December 5, 2013 at 12:17 pm | Permalink

      You are probably remembering The Blind Watchmaker.

      Great book.

      • Achrachno
        Posted December 5, 2013 at 7:19 pm | Permalink

        Yes, my favorite from Dawkins, and one of the best period.

        • BillyJoe
          Posted December 6, 2013 at 4:00 am | Permalink

          I would have to agree with Richard Dawkins, that “The Extended Phenotype” is his best book.

    • Posted December 5, 2013 at 4:08 pm | Permalink

      “I ran a simple mac program he wrote…”
      Button pushed! URL link procedure activated!
      Stand by…Vwwwwooooommpp!

      There are different evolution simulators out there. You can play Dawkins Blind Watchmaker and also his Weasel programs online.

      Here is the Weasel one:
      Weasel .

      My fav. is not a Dawkins program. It is Evolve a Car. This drops a series of random polygons and ‘wheels’, and selects which ones goes furthest, mutates those, and selects again. Fun to watch, but amazing when you just let it run in the background and check on it from time to time.

  19. Pete
    Posted December 5, 2013 at 9:47 am | Permalink

    typing errors?
    -Similar striking changes in form occur also occur
    -turned on ad off

  20. gbjames
    Posted December 5, 2013 at 9:48 am | Permalink

    I’d like someone to write a book explaining the strange phenomenon of Dawkins-bashing. It’s one thing to argue about the substance of his arguments in The Selfish Gene (or wherever). But for some reason critics seem incapable of simply doing so. They inevitably slide into ad homonym and usually uninformed third hand reputation sniping.

    • Posted December 5, 2013 at 10:37 am | Permalink

      Lots of people just seem to dislike Dawkins very much. I think 99% of that comes down to misunderstanding the phrase “Selfish Gene” to mean, “people are genetically programmed to be selfish.” It’s too bad.

    • Diana MacPherson
      Posted December 5, 2013 at 10:54 am | Permalink

      Yeah, I’d love to figure something like this out. I don’t know if it would fill a whole book but it would be an interesting study.

      I suspect a lot of it is people just don’t like what he says because he says things that upset them in a straightforward, unapologetic way and he was really one of the first in recent memory to be recognized for doing so. He therefore stands out in people’s minds when they think of someone who challenged their beliefs & when their brain gave them a little chemical punishment for that, they associated the pain with Dawkins.

      I think it would also be an amusing meme to start: absurd things we can blame on Dawkins like random rashes, nose bleeds, crops failing, lack of parking spots, etc.

      • Posted December 5, 2013 at 11:06 am | Permalink

        I thought we had already started that meme…?

        b&

        • Diana MacPherson
          Posted December 5, 2013 at 11:11 am | Permalink

          Yeah we had but I was thinking formalize with pictures and all for maximum comic effect.

          • Posted December 5, 2013 at 3:48 pm | Permalink

            Oh…you mean like an official LOLcat?

            I’d do something like that…but, thanks to Dawkins, I haven’t a clue where I’d find the time….

            b&

        • gbjames
          Posted December 5, 2013 at 11:42 am | Permalink

          I blame Dawkins for making me forget that thread.

          • Ken Elliott
            Posted December 5, 2013 at 11:59 am | Permalink

            I blame him for missing that thread.

            Sarcasm and comedy aside, MAN!! i appreciate to no end what Dawkins, Coyne, Barker and others have done for me. I have not been this comfortable with my place in the universe in . . . well my whole life. It’s quite nice.

      • pacopicopiedra
        Posted December 5, 2013 at 5:24 pm | Permalink

        Not sure if you are a (American) football fan, but your blame Dawkins idea was done recently with Chicago Bears quarterback Jay Cutler.

        http://bleacherreport.com/articles/1478994-blame-jay-cutler-hashtag-sweeps-twitter-after-horrible-espn-segment

        I, for one, think all the Dawkins bashing is clearly Jay Cutler’s fault.

        • Diana MacPherson
          Posted December 5, 2013 at 5:26 pm | Permalink

          I’m not really any sort of sports fan but I did like the blame for the failed Mayan apocalypse. That was a good one.

          • pacopicopiedra
            Posted December 5, 2013 at 5:28 pm | Permalink

            And of course we can’t forget Blame Canada, from the South Park movie.

            http://en.wikipedia.org/wiki/Blame_Canada

            • Diana MacPherson
              Posted December 5, 2013 at 5:30 pm | Permalink

              Yes. I remember how displeased we Canadians were when Robin Williams sang that song because he didn’t like that a lot of movies and TV series were filmed in Canada.

      • Posted December 6, 2013 at 3:27 pm | Permalink

        WHOA! If you blame everything on Dawkins, RWNJs won’t have anything to blame on Pres. Obama. That simply will not do!

        • Posted December 6, 2013 at 5:30 pm | Permalink

          Oh, that’s easy.

          Richard is Obama’s fault….

          b&

      • Bob W.
        Posted December 9, 2013 at 4:48 pm | Permalink

        Really, it’s not that hard to figure out; Dawkins is a vocal atheist. Even a lot of folks that accept that evolution as the best scientific theory for explaining the diversity of life on this planet can’t bring themselves to admit that that’s all there is. There must be some ‘extra’ force responsible beyond mutation and selection. Apparently our genes are coded to propagate this delusion, along with an affinity for hereditary rule. That’s the interesting study that I’d like to see. But the I’m a childless atheist so maybe having a brain wired to believe in mystical beings and a mystical after life makes one more likely to reproduce? I suppose sucking up to rich people is also beneficial in they are more likely to toss crumbs your way, and less likely to turn on you and more likely to turn on the people that don’t suck up to them. And, in almost any environment, some organisms will ‘get lucky’ and accumulate or control a disproportionate share of whatever resources are available, thus an ‘optimal’ strategy would be to ‘get lucky’ and failing that, support those that did. Maybe we aren’t all that different from dogs.

        • Posted December 10, 2013 at 1:48 am | Permalink

          Beware of where you’re headed Bob… you are drifting into the conjectures of Evolutionary Psychology where every theory is plausible and none is provable. I recently went to a talk by Steve Jones at the Royal Society where he was banging the drum for the existence of a “religious gene” as you are doing now. But why is the explanation of religious tendencies in human society derived from such a “religious gene”? Why not a “gullibility gene” or a “believe what your parents told you” gene etc. etc. etc. There is great danger in Evolutionary Psychology in sorting out proximate from ultimate causes. Best not tread there.

          • gbjames
            Posted December 10, 2013 at 6:08 am | Permalink

            “Why not a “gullibility gene?”

            Heh. For a minute I was with you. But then I got to the end where you tell Bob to not “tread there”, the sort of advice I find distressing. Open minds need not fear to tread.

            • Posted December 10, 2013 at 2:14 pm | Permalink

              “Open minds need not fear to tread.”

              True – as long as you don’t mind what can possibly end up on the soles of your shoes.

  21. eric
    Posted December 5, 2013 at 10:00 am | Permalink

    He seems to have mistaken some genes “losing” the selfish competition to be preserved with the entirely different idea of them not competing at all.

    Gene A causes some structure to be built. Gene B causes Gene A to be turned off. The presence of B does not mean Gene A is less “selfish;” it is still propagating in future generations. What’s changed with B is that A may not propagate as accurately if its “off” because mutations in A will no longer alter the organism’s fitness. B has cut A’s ability to selfishly propagate off at the knees, so to speak.

    The problem with his second point might be summarized as: quantity /= importance. Whether we are 20%, 50%, or 99% similar to a cow, small differences can have enormous impacts. Consider two 1,000-character cake recipes which are identical in every respect, except one line. The first recipe reads: “Bake cake at 350F for .5 hour” while the second reads “Bake cake at 350F for 5 hour.” These recipes will be 99.9% similar (one character difference out of 1,000). Yet they will lead to remarkably different outcomes. Can the difference between a fluffy cake and a lump of coal reside in a mere 0.1% of its recipe? Why yes, yes it can. Can the difference between a human and a chimp reside in a mere 1% of its recipe? Why yes, yes it can.

    • Torbjörn Larsson, OM
      Posted December 5, 2013 at 12:47 pm | Permalink

      I was thinking, but forgetting, to note this before I read your comment:

      Dobbs says “you are 80 percent cow,”

      This also forgets the shared roots. Both the cow and I are 100 % “fish”, with shared organization, probably shared development, et cetera. (I guess in your example both cake and coal are heat processed carbon compounds. =D)

      So naively Dobbs can’t expect too low sequence similarity either. But he draws an unsupported linear “quantity = importance” measure from out of his straw hat.

    • Paul-G
      Posted December 5, 2013 at 3:24 pm | Permalink

      Also, if you compare how similar a human is to a cow and then compare how similar both are to a rock or a blob of mercury or a China tea cup then 80% seems somewhat understated.

      • js
        Posted December 5, 2013 at 4:21 pm | Permalink

        If humans are 80% cow, then what are cows?
        Are they 80% human?
        I’m sorry, but anyone that could make such a statement shows a complete misunderstanding of the subject.
        I’d never heard of this Dobbs fellow but thankfully I now know to steer clear (pun warning).

  22. Brian Prendergast
    Posted December 5, 2013 at 10:05 am | Permalink

    Thanks for this. Time well spent.

  23. terminus
    Posted December 5, 2013 at 10:09 am | Permalink

    Nicely written Jerry! We read your book in my AP Bio class, short pieces of Dawkins’ Selfish Gene, and reference many of the scientists in Dobbs’ article.
    Your clear and concise response has both confirmed and strengthened my understanding that coding and non-coding sequences evolve.

  24. Arthur
    Posted December 5, 2013 at 10:10 am | Permalink

    I don’t know enough about genetics to critique either the original article, or Jerry’s response, but I can confirm that Richard Dawkins has sadly of late come across as a buffoon. Mainly due to his ill conceived Twitter activities.

    These days, most of his critics are dyed-in-the-wool atheists who formerly supported the guy, but are now embarrassed by his social media failings.

    • Posted December 5, 2013 at 10:42 am | Permalink

      I disagree completely. He does not “come across as a buffoon” and I doubt that most of critics are atheists who formerly supported him. I think most of his critics are people who’ve never read past the title of his first book. They misunderstood that, and continue to misunderstand him at every chance they get.

      • gbjames
        Posted December 5, 2013 at 10:45 am | Permalink

        The other large block of critics are those who never read The God Delusion but are offended by the attack on religion and simply parrot comments about shrill/harsh/strident atheists they hear being parroted by others.

    • Grania Spingies
      Posted December 5, 2013 at 12:23 pm | Permalink

      I would have been half-way sympathetic once upon a time when people were critical of Dawkins on Twitter, it being as it is, a medium where communication is severely truncated.

      However, after the honey pot episode it became blindingly obvious: those who complained and fomented didn’t misunderstand his point for one second, they just pretended to so that they could dog-pile on someone they already manifestly dislike intensely. I now suspect that the same can be said for any of the Twitter “misunderstandings” surrounding what he has said. Those claiming to be outraged are already offended before he even picks up his iPhone.

      • Posted December 5, 2013 at 5:20 pm | Permalink

        As somebody who’s been very much out of the loop on Richard’s Twitter exploits (and Twitter in general)…I don’t suppose you could point me (and others) to some sort of a summary, perhaps including some of the more infamous Twits and responses…?

        Thanks,

        b&

        • Arthur
          Posted December 5, 2013 at 7:13 pm | Permalink

          Long time supporter and science writer for the Telegraph Tom Chivers made an open plea for Dawkins to cease twitter in August.

          http://blogs.telegraph.co.uk/news/tomchiversscience/100230250/

          This is one example of the many former supporters who are now embarrassed by Richard’s twitter activities.

          • Achrachno
            Posted December 5, 2013 at 7:32 pm | Permalink

            They shouldn’t be, and I’ll bet there are very few anyway. None of the tweets from Dawkins in the Chivers article was worthy of any criticism whatsoever. It’s just not PC to say certain true things. So what?

            • Diana MacPherson
              Posted December 6, 2013 at 6:02 am | Permalink

              Yeah, I don’t find his tweets so bad either. They are conversation starters anyway and I think the ensuing discussion is fruitful.

            • Posted December 6, 2013 at 3:37 pm | Permalink

              Couldn’t agree more. I “hate” this expression but “Haters gonna hate,” and if you’re religious no one has a bigger target on his front, back and elsewhere than Richard Dawkins. Occasionally, he reads some of his “hate mail” on video. Would be funny except for the genuine malevolence that slithers forth. My solace? A recent poll by a respected mainstream magazine voted Dawkins the world’s greatest living thinker (or something very close to that). Few people could be more worthy.

          • Posted December 5, 2013 at 9:01 pm | Permalink

            Thanks for the link. This isn’t the venue to discuss that topic…but, it seems to me that a big part of the problem is that nobody quite yet understands what Twitter is about. I think Richard’s detractors are reading more into the Twits than Richard wrote, and I think Richard doesn’t understand that people actually do take that shit seriously.

            Personally, I think it’s high past time that Twitter simply dies already. It has yet to serve a meaningful function and was created to solve an artificial problem that didn’t even exist any more at the time.

            …but that’s just me….

            Cheers,

            b&

  25. Posted December 5, 2013 at 10:14 am | Permalink

    Thank you Jerry. Much appreciated! You do good work.

  26. Rob
    Posted December 5, 2013 at 10:27 am | Permalink

    Good article. Very helpful. Very clear. Thank you.

    I’ve learned a lot from Dawkins’ writings. Additionally, his tweets have expanded my thinking in some areas, which I appreciate.

  27. Dominic
    Posted December 5, 2013 at 10:30 am | Permalink

    Originally he called Sewell Wright British – something I pointed out on Twitter yesterday.

    PZ Myers even praised it
    http://freethoughtblogs.com/pharyngula/2013/12/03/higher-order-thinking/

    • DV
      Posted December 5, 2013 at 2:35 pm | Permalink

      Will have to wait to see what Jerry writes tomorrow. But I don’t see how genetic accomodation must mean that the gene-centric view is wrong. Genetic accomodation still means that evolution works on genes as the units of selection. There’s no conflict at all. Although genetic accomodation is just getting attention and new to me, a related idea of the Baldwin effect has been written about in popular books before. (I don’t remember which book I read it from, but I checked wikipedia and Daniel Dennett’s name was mentioned, so I must have read it from Dan’s book, probably ‘Darwin’s Dangerous Idea’). And there was no calls for “die, selfish gene, die” then.

  28. Thanny
    Posted December 5, 2013 at 10:38 am | Permalink

    Looks like this is a perfect example of someone getting it completely wrong due to not knowing what the word “gene” actually means.

  29. Divalent
    Posted December 5, 2013 at 11:04 am | Permalink

    In the Selfish Gene, Dawkins defined “gene” thusly: “A gene is defined as any portion of chromosomal material that potentially lasts for enough generations to serve as a unit of natural selection.” (pg 28 in 1989 edition)

    This definition would included (along with everything else on a chromosome) regulatory sequences.

    Thus, Dobbs seems to be arguing against a strawman version of the “selfish gene” metaphore.

    • Jeff Walker
      Posted December 5, 2013 at 11:37 am | Permalink

      This is the crux of the argument. “Gene” is defined differently by different groups (as are many terms in biology). There is not a committee (that I’m aware of) that has standardized One True Meaning. So to take one meaning (a protein coding region of DNA) to debunk concepts that use another meaning (Dawkin’s definition above) is poor scholarship indeed. Everyone has made that mistake (poor scholarship). Own it and move on.

    • DV
      Posted December 5, 2013 at 3:05 pm | Permalink

      Dobbs would be right, if regulator genes (even the ones that don’t code for proteins) are not selected for. I don’t think even Dobbs would suggest that this is the case. So he is just plain wrong.

      So he’s now clarifying that his piece is really about the stories about nature, not about nature itself. What kind of excuse is this? He’s trying to salvage his reputation and say he didn’t get the science wrong, just the stories about the science?

    • Posted December 5, 2013 at 3:39 pm | Permalink

      MOST sources would now describe a gene as something like a ‘region of DNA that codes for a functioning molecule of RNA’, b/c of course there are ‘genes’ that code for tRNA and rRNA and so on. I have never liked that definition since it leaves out the regulatory regions like the promoter, and other regulatory units. My definition, which I have made up as far as I know, is: ‘A gene is a region of DNA needed to make a functioning molecule of RNA.’ This includes those regulatory regions since they regulate transcription of DNA –> RNA. It is completely compatible with Dawkins’ definition, although his does not necessarily require a gene to have any direct role in making RNA. By his definition centromeres and telomeres and origins of replication are genes (!)

      • ratabago
        Posted December 5, 2013 at 8:05 pm | Permalink

        Here is Wikipedia on the definition of genes:

        A modern working definition of a gene is “a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions, and or other functional sequence regions “.

        Oddly enough, this is almost precisely the definition I was given in first year genetics, first year general biology, and second year molecular biology of the gene (as part of a course in biochemistry). This was standard undergraduate stuff back in 1989/1990. It nicely covers encoding regions, regulatory regions, tRNAs, rRNAs, sRNAs, and anything else I can think of except structural DNA. I’m wondering how it is possible that the scientists Dobbs is quoting don’t know this? It’s hardly new, it’s by no means esoteric, and it’s hardly radical.

        Dawkin’s definition is wider than mine because he wants to include everything that is exposed to selection. It is broader than my interests were, but I’ve no objection to that. I do object to Dobbs and those quotes in his article, as they have redefined gene to the point that there definition is both inadequate and unrepresentative. Apparently so that they can strawman their own broken definition.

        • Posted December 6, 2013 at 4:59 am | Permalink

          I have certainly heard of that one too, but it always seemed vague to me. The definition puts the vague phrase ‘unit of inheritance’ at the core of the definition without defining what that means. I know what is intended, but to the uninitiated it will be very vague.

  30. Matthew
    Posted December 5, 2013 at 11:11 am | Permalink

    If I recall correctly, Dawkins spends quite a bit of time in The Selfish Gene explaining that genes work in concert to build organisms, and the most successful are those whose contributions lead to greater reproductive fitness. I think people simply don’t understand just how complex and baroque the interplay between genotype to phenotype really is.

    Also a bit amusing that Dobbs uses the phrase “‘Selfish Gene’ meme,” perhaps forgetting that Dawkins coined the term “meme” in that very book. ;-)

    • eric
      Posted December 5, 2013 at 12:05 pm | Permalink

      “I think people simply don’t understand just how complex and baroque the interplay between genotype to phenotype really is.”

      I’ll do you one better and say I think people simply don’t understand how barque the genotype (alone) is. Jerry’s skewer of Dobb’s first point is not that surprising, because I’d bet a lot of people think just like Dobbs – that there is some hierarchy in genetics. Instruction set A tells cells how to build something, instruction set B tells cells when and how to use A, and B and A are distinct things. To paraphrase Dobbs, gene expression mechanisms (B in my example) undermine the idea that genes are predominant (A in my example). The hidden assumption in Dobbs’ argument is that the expression mechanisms are not the same thing as the genes. There’s some sort of distinction or hierarchy. But oops, there isn’t. Bs and As are the same. Whether something acts as a B or an A merely depends on sequence, location, etc., and through mutation, A’s can become B’s or vice versa. And both A-type and B-types are selfish (in the metaphorical sense).

      I’m just guessing, but I expect Dobb’s position is actually pretty common, in part becaues to our common-sense human way of engineering systems, that haphazard mixing of different hierarchies of instructions seems messy and wrong. Look at a basic cookbook, and you’ll see a section on what “saute” or “bake” means. Then you have recipes that tell you to saute or bake. It would be crazy to hide the generic instructions for how to bake things in one of the individual recipes, randomly placed somewhere in the book. That makes no sense. But that is what our genome is like. Dobbs is assuming a structure or organization of our genetic instructions that seems natural and sensible to him, but its a structure that (AIUI) isn’t there.

      • NewEnglandBob
        Posted December 5, 2013 at 12:39 pm | Permalink

        I like your ‘sauté’ analogy. I think of it as a soup of proteins, swirling around, mixing and matching or neutralizing each other.

  31. Daniel Engblom
    Posted December 5, 2013 at 11:32 am | Permalink

    This constant nonsense about gene expression, epigenetics and changing ways genes behave as something going against “the selfish gene” (which is, as Dawkins emphasized himself, only neo-Darwinism from a slightly different angle), is really starting to piss me off.

    To simplify the metaphors: You think a selfish gene gets to propagate using only one tool? Opportunism is useful, a “good” selfish gene “knows” when to shut up and when to speak up, crudely put.

    And regulatory genes are, again very simplistically put, doing some genes “a favour” by suppressing them at the right time: They still get propagated, and possibly not selected against, if suppressing them means the vehicle surviving to reproduce.
    Genes changing behaviour at times is good for the genes.

    I apologise for the anthropomorphic language, but that is at least clear to me and in the realm of the metaphor. The “selfishness” in the metaphor does not mean genes are simple, it is only meant to highlight one element of their “behaviour”, meaning the logic of natural selection and what survives. Of course there are other facets on the ways of gene replication and selection, many of which Dawkins has written about.

  32. DV
    Posted December 5, 2013 at 11:51 am | Permalink

    >> All heritable differences between species, in fact, must reside in the DNA; we know of no cases in which they don’t. Where else could they be?

    I can just imagine Stephen Meyer raising an objection. The reasoning in the above statement, I can imagine him saying, betrays a prior commitment to the materialist narrative that it rejects a better explanation from ordinary experience of conscious agency. Where else could the differences come from? Why, they can come from an intelligent designer of course! Saying the differences “must” reside in the DNA is just being close-minded. They could come from magic, you know.

  33. Kevin
    Posted December 5, 2013 at 11:58 am | Permalink

    Great post. I sometimes wonder how interested I am in biology (as a subject) but reading stuff like this makes me appreciate the subject more. Very thoughtful and interesting. Thanks very much; now I need time to digest this.

  34. Torbjörn Larsson, OM
    Posted December 5, 2013 at 12:16 pm | Permalink

    Thanks, Jerry! Anecdotically, individuals of your readership benefits hugely from your clarifications. [I know this, because I do. =D]

    Dobbs is an erratic writer, which is why I don’t read him often and when I do, I do it carefully. As I remember it, it was a similar piece of fractal errors that warned me off, you never know when it is actually supported science. (I wish I could remember what it was though – so no reference.)

    Young’s opinion is more surprising. But I’m familiar with his writings and his nearly closeted accommodationism, so though one can never tell on individual samples, statistically accommodationists blow up on your screen when they meet 100 % skeptics that treat religion’s clearly stated magic as any other erroneous claim on nature.

    So maybe it is “Save Yule and Beat Up Dawkins Day”.

    • Torbjörn Larsson, OM
      Posted December 5, 2013 at 12:55 pm | Permalink

      Ahem! Yong’s opinion …

  35. questionauthorities
    Posted December 5, 2013 at 1:25 pm | Permalink

    Just because we don’t comment on your biology articles does not mean that we don’t read them Jerry. Personally, I love it when this kind of discussion takes place in public. It is very difficult for laymen to know which side is correct without seeing the arguments from both sides. I thought that the article was wrong, but with a recommendation from a bona-fide biologist (PZ) I could not be sure if that was just me. So thanks for putting in the time to help us understand the issues.

  36. Posted December 5, 2013 at 2:14 pm | Permalink

    This might be relevant: Dawkins interviewing Steven Rose about this topic.

    http://www.youtube.com/wat…ch?v=Ir64odzG98Q

    (link broken to prevent the vid from posting here – remove the the 3 dots from “watch”)

    • Posted December 5, 2013 at 5:22 pm | Permalink

      That was a superlative interview, well worth watching. Thanks!

      While Steven had many great insights to offer, I kept feeling Richard’s frustration when Steven seemed to go awry (such as in not getting that it’s the genes, and only the genes, that are the link from one generation to the next, and the non-dualistic sense of self that Richard was referring to).

      Cheers,

      b&

  37. Posted December 5, 2013 at 3:27 pm | Permalink

    Late to the party (long day in classes in our last week). The other day I had stumbled across the article by David Dobbs while following a trail of links. I read it, saw that it made no sense to me, but I just thought ‘maybe I just did not understand it’. So thank you for illuminating this! Good to know I am not yet crazy.

    To all writers about science for the general public: If you are thinking about writing an article about how ‘most scientists’ are really rong about something dealing with genomes, behavior, evolution, or some other complicated, well established paradigm — then please thing that has a well established paradigm, please STOP before you publish your ‘revolutionary’ idea. Send your draft to a couple of those mainstream scientists first. Have them look at it, OK? OK.

  38. Posted December 5, 2013 at 3:47 pm | Permalink

    These guys have good answers.
    http://sappoblog.blogspot.com/2013/12/answers.html

  39. js
    Posted December 5, 2013 at 4:39 pm | Permalink

    I can understand why people have difficulty accepting evolution.
    As I read this article, just outside the window are some tomato plants.
    Every now and then a bee comes along and lands on a flower.
    Before it lands, its buzzing is of a certain frequency but once on the flower, the frequency changes.
    I only fairly recently learned that this is because the pollen is inside the central part of the flower and that it will only open if it vibrates at that second frequency.
    Now, it’s mind boggling to think how could that possibly have happened but us humans live very short lives and often fail to appreciate the many minute changes over millions of years in both species that have caused this to happen.

    • Posted December 5, 2013 at 7:38 pm | Permalink

      That is interesting, and I have not heard of it before. If it is true, though, it should be a result of evolution. Queen bees that produce workers who succeed in getting a flower to part with their pollen will have greater fitness than who do not. So bees today are good at pollen robbery. There are even more remarkable behaviors, like how a spider knows to build an orb web. Just watch it, it blows my mind.
      Actually, a simpler reason also presents itself, which is that a bee might simply ascend through a continual series of vibration frequencies until the pollen starts to shake free, then it locks onto that frequency. This strategy would work with all kinds of flowers. We humans would just see the end result, and not the process that led to it.

      • Posted December 5, 2013 at 9:03 pm | Permalink

        Remember that the plants also have an interest in being pollinated. It could be that there’s an advantage to being pollinated by these particular bees, and that the bees already changed frequency for reasons of aerodynamics and that the plants adapted to that. And there could also be feedback loops involved….

        Cheers,

        b&

  40. Ken Pidcock
    Posted December 5, 2013 at 4:58 pm | Permalink

    Do these people not realize that gene expression is itself caused by differences in DNA sequence, and that those regulatory bits of DNA evolve precisely like “structural” genes themselves?

    When I encountered the Dobbs piece this morning, I had that exact thought. Thank you, Professor Coyne, for taking the time to respond to this misunderstanding.

  41. superatheist
    Posted December 5, 2013 at 6:20 pm | Permalink

    I think Niles, Gould and Lewontin talked enough about this argument as to the adequacy of the selfish gene metaphor. Even Mayr I think disagreed with it. Regulatory genes are of course genes that produce transcription factors, but the interactions of these genes with structural genes along with the environment directs the making of the phenotype. The phenotype isn’t a vehicle for the gene. That is why in eve-devo some people are arguing for developmental mapping instead of gene-phenotype mapping function. Cuz as lewontin said the character that is supposed to be selected for isn’t just a gene.

  42. pacopicopiedra
    Posted December 5, 2013 at 6:50 pm | Permalink

    I finally just had time to read the original article. Boy, is he confused. The worst part is that he says right there in his piece that he called Dawkins, Dawkins explained the source of his confusion, and then he either ignored or misunderstood Dawkins and went right on.

    It’s bizarre. When the stealth hunting predator who lives in the forest has a gene mutation that makes it faster, the mutation is not very beneficial. But when the stealth hunting predator from the forest moves to the savannah and must become a speed hunting predator, now a mutation to make it faster is beneficial. So, obviously, genes are overrated, and not very important at all. This is the fascinating breakthrough which makes the Selfish Gene metaphor wrong, wrong, wrong, and worthy of death.

  43. Posted December 5, 2013 at 9:24 pm | Permalink

    In para 15 above that starts with”sorry” it concludes with the statement, “All heritable differences between species, in fact, must reside in the DNA; we know of no cases in which they don’t. Where else could they be?”

    In Denis Noble’s 2011 paper titled Neo-Darwinism, the Modern Synthesis and selfish genes: are they of use in physiology?, he states “Crossing a common carp nucleus with a goldfish enucleated egg cell produces an adult fish that has an intermediate shape and a number of vertebrae closer to that of the goldfish. These factors can therefore determine a phenotype characteristic as fundamental as skeletal formations {ref Sun et al. (2005)refers}. Over 50 years ago, McLaren & Michie (1958) showed a similar phenomenon as a maternal effect in mice. The number of tail vertebrae (4 or 6 in the different strains) was determined by the surrogate mother, not the embryo.” Don’t the studies referred to here question the assertion all heritable differences must reside in the DNA?

    • Posted December 6, 2013 at 3:57 am | Permalink

      I’ve already written about Noble’s paper and work, which you can find by searching this site. Maternal effects and environmentally induced (epigenetic) modification of the DNA are heritable only for a very few generations at most. They therefore provide no basis for long-lasting heritable differences (i.e., evolution). Please check this site before you start questioning me about work like this.

      There is not one example of an adaptation that is based on environmental modification of the phenotype or nongenetic maternal effects.

      • Posted December 7, 2013 at 5:36 am | Permalink

        Thanks. Read your Noble piece and the follow-ons to this post. Not saying your methodical and thorough rebuttal to Noble doesn’t pick apart much of the manner he articulates his argument, am saying that the predominate views expressed herein by yourself and other contributors don’t adequately assimilate the cellular gene/environment (cytosol/cytoplasm)dance. On that front, section of your Noble post titled, “3. The gene-centered view of evolution is wrong.” glosses over some fundamental cellular biology. You state, ” Cells are transitory, and DNA is not. A cell is not passed on from one generation of individuals to the next, but the DNA molecule, which is in some sense immortal, is.” One can’t/shouldn’t argue with both of your assertions yet you fail to include comments as to what occurs in that ever repeating instant in cell reproduction when the nuclear membrane has dissolved, and for a brief period prior to cytokinesis there is simply the two copies of the DNA and pretty much the ‘cytosol’ which now includes much of the parent cell’s machinery (golgi, ER, etc) dissolved (or no longer readily visible)in the medium. The pending finale of cellular division is rarely if ever described as = or identical; rather asymmetric division (but close to identical) seems to be the standard used. It also seems to be accepted that the two copies of the DNA present are not a true parent/daughter relationship, but rather there are ‘bits’ of the former in the two new identical daughters. Is there thought as to which of the two DNA is ‘lead’ or ‘point-man’ during this period …seems illogical to enter in that discussion. This is the part of ‘life’ that perplexes me, it is a time when very early in our development (particularly the meiosis phase) some daughter cells are destined to become liver or brain etc and some get more mitochondria/bigger machinery then their sister (am not a plant guy but similar analogies must be there for stem and flower). This is the dance; it is a dance that can’t occur without the genes or the cytosol ‘communicating’ in some manner and doing the best they can to survive (Darwinian :<D)given both the resources and raw ingredients available within, and the external conditions imposed on them. I won't speak for Noble or Dobbs, just saying I see our present understanding lacks clarity in the area I present

        (This is a hobby for me too, one linked to my interest in root cause of cancer..day job unrelated) Thoughts (besides don't give up my day job)?

    • Dominic
      Posted December 6, 2013 at 7:47 am | Permalink

      Reminds me of August Weismann’s mice tail experiments…
      http://en.wikipedia.org/wiki/August_Weismann

  44. abrotherhoodofman
    Posted December 5, 2013 at 9:51 pm | Permalink

    Ed Yong wakes up, reads Dobbs:

    @david_dobbs’ deconstruction of the selfish gene metaphor is truly an exemplary piece of sci writing.

    Ed Yong proceeds to suck-up to Dobbs:

    @David_Dobbs As freelancers, same for me and DD. We shld band together to overthrow tyrant employers

    Ed Yong then reads Coyne:

    @whyevolutionistrue deconstructs @david_dobbs’ selfish gene piece.

    Ed Yong then goes to work:

    Spent a day on a sunny beach, watching frigatebirds and pelicans flying metres away. This is for work, you understand.

    Yes, Ed, we understand.

    ***************************

    Not to be outdone, former Dawkins pal PZ Myers reads Coyne and mutters incoherently:

    I’m seeing the same responses to Dobbs’ article — it’s still all just genes at the bottom of it, ain’t it? Oh, sure, but the interesting parts are the interactions, not the subunits. We need to take the next step and build tools to study networks of genes, rather than reducing everything to the genes themselves.

    Right, Peezus. I think that’s called throwing the baby out with the bathwater.

    “The interesting parts are the interactions between people, not the people themselves.”

    Yeah. Uh-huh.

    • abrotherhoodofman
      Posted December 5, 2013 at 9:57 pm | Permalink

      (Sorry, either one of my bold-tag regulatory mechanisms screwed up or it could have been a structural gene expressing itself in the wrong location.)

  45. Posted December 6, 2013 at 12:40 am | Permalink

    Thank you! I saw Dobbs’ article linked from PZ Meyers but when I was reading it I couldn’t help feeling that none of it was making any sense. I just couldn’t see where there was a real objection and was a little worried that maybe it was because I lacked enough background knowledge in the topic. Glad to see I was right. Looking forward to the next piece.

    • Posted December 6, 2013 at 5:08 am | Permalink

      I had exactly the same experience. One good thing that came out of it is that I found other interesting articles in Aeon magazine, so I have bookmarked the site. Time will tell if the magazine is worth looking at, or is just another source of fluff.

  46. Posted December 6, 2013 at 1:23 am | Permalink

    Thanks Jerry, fantastic (and much needed) post.

  47. Posted December 6, 2013 at 2:08 am | Permalink

    When encountering the praise for Dobbs’ dissing of the selfish gene metaphor at G+,I tried my best to show that the selfish gene handle is alive and well as Dobbs’ essentially presents a straw man. Professor Ceiling Cat needs to take heart and be aware of the skeptical ripple effect he sets in motion.

    Dobbs’ lively and vernacular writing style having such a convincing effect on people has psychological interest as there was not much substance in his article even though it seemed that it had.

    Anyway, I will link to Jerry’s debunking and look forward to the second part.

    • Diana MacPherson
      Posted December 6, 2013 at 6:47 am | Permalink

      Having the talent to communicate well gets you far. I know that in the past, I got myself out of tight spots simply because of being able to communicate well.

      Meyers is a good speaker and writer which convinces his audience that the content behind the words is legit. It’s all very pernicious.

      • W.Benson
        Posted December 7, 2013 at 6:31 am | Permalink

        PZ gets it about right 90-99% of the time, but when he’s off the mark, he stonewalls. Very pernicious, si!

  48. Posted December 6, 2013 at 2:46 am | Permalink

    Dobbs: “I apparently did not make clear that “Die, Selfish Gene, Die” is a story less about how genetics and evolution work than about the stories we tell about how genetics and evolution work — and, most crucially, about how those stories about nature percolate out beyond academia and into the minds of the lay public.”

    Ha! Yeah, but when stories are told at a higher level, that is, farther removed from the nitty gritty of hands-on-understanding, that is, from a working evolutionary biologist’s perspective, you must still distill the facts, my dear, you don’t over-ride them. Because if you do, then that comprises intellectual dishonesty and no matter how appealing your writing style is, you won’t last in the journalistic arena

    Sean Carroll (the physicist) has given a great talk about how story telling needs to be done correctly. (An AHA talk if I remember correctly)

  49. Dominic
    Posted December 6, 2013 at 3:44 am | Permalink

    There is a war it seems to me, in biology & in palaeontology, & there has been since the 19th C. depending on how they take to Natutral Selection.

    You could write a book on it. Someone should.

    • Dominic
      Posted December 6, 2013 at 3:45 am | Permalink

      Sorry – NATURAL selection!

  50. TJR
    Posted December 6, 2013 at 4:07 am | Permalink

    As many people have pointed out above, the whole Dobbs article is demolished once someone says “You do realise that regulatory genes are genes too?”.

    Does he even use the term “regulatory gene” or anything similar in the article?

    Jerry’s reply is a perfect illustration of the importance of communication by proper experts in the field, rather than just journalists.

    • Posted December 6, 2013 at 5:20 am | Permalink

      There are good writers about science who are not scientists themselves (admittedly such a being has a difficult and delicate role to play). Carl Zimmer comes immediately to mind.

      • TJR
        Posted December 6, 2013 at 6:38 am | Permalink

        Fair point. I meant “only” in the sense “only people who are” not the sense “people who are only”.

    • John Scanlon, FCD
      Posted December 7, 2013 at 7:50 am | Permalink

      Does he even use the term “regulatory gene” or anything similar in the article?

      I think not, but instead uses various awkward phrases based on abstract nouns. Poor writing, poor thinking.

  51. Posted December 6, 2013 at 6:15 am | Permalink

    If you’re looking for serious scientific objections to “the selfish gene,” see E. O. Wilson’s and M. Nowaks’ recent stuff on group selection. IMHO Wilson is wrong, but at least his arguments are coherent. Dobbs piece is better understood as ideological narrative than science. Kind of a last gasp of the Blank Slate. Dobbs claims his ideas aren’t Lamarckian, and yet somehow epigenetic changes are supposed to be dancing around in rapidly changing environment, free of genetic strings. Where does he think the capacity for those changes came from in the first place? These objections are obvious. What isn’t obvious is why so many apparently respectable scientists are taking him seriously, and can’t see through the charade. If you really want to understand where this is coming from, forget the scientific journals. Read, “Drugged Individualism,” in the November 1934 issue of The American Mercury, or “The Myth of Individuality” (by Theodore Dreiser, no less) in the March 1934 issue. After a few articles like that, you’ll recognize the ideological line. Google “American Mercury Unz” to find The Mercury online. It was edited by H. L. Mencken from 1924 to 1933.

    • Dominic
      Posted December 6, 2013 at 7:01 am | Permalink

      A great resource – thanks. First one for 1934 is “How Long Can Hitler Stay? by Leon Trotsky,”!

      • Posted December 6, 2013 at 7:19 am | Permalink

        Trotsky? Why, I’ve never heard of a man named Trotsky! ;-)

    • Dominic
      Posted December 6, 2013 at 7:42 am | Permalink

      There is definitely a reluctance on both left & right politically, to grasp the thistle of Natural Selection.

      Individuals v groups;
      Gradualists v punctuationists;
      Materialists v ‘the whole is greater than the sum of the parts’-ists
      etc

      • W.Benson
        Posted December 6, 2013 at 8:07 am | Permalink

        Political ideologies stink.

        • gbjames
          Posted December 6, 2013 at 8:14 am | Permalink

          Well we all have some fragrance.

          But bad science among otherwise sensible people does seem to commonly motivated by political ideology.

          • gbjames
            Posted December 6, 2013 at 8:39 am | Permalink

            …seem to *be* commonly…

            (My kingdom to be able to edit a comment!)

  52. W.Benson
    Posted December 6, 2013 at 8:06 am | Permalink

    R. A. Fisher (The Genetical Theory of Natural Selection, 1930, p. 159) used kin selection as a possible explanation for the evolution of chemical protection in insects for those cases in which the predator had to kill the prey to detect its nauseous properties. Fisher noted that a strong kin advantage might arise when the prey was gregarious or when close relatives lived in proximity where they could be encountered by the same individual predators. A predator, when killing a noxious prey, might learn to avoid others of the same species, thereby protecting the dead individual’s brothers and sisters, half of which should, by the laws of genetics, be carriers of copies of the same identical. Although the explanation did not ‘catch on’, it seems certain that Fisher was aware of both the quantitative implications as well as the importance of ecological context. In Fisher’s words (p. 159), “The selective potency of the avoidance of brothers will of course be only half as great as if the individual itself were protected; against this is to be set the fact that it applies to the whole of possibly numerous broods.” It seems possible that Haldane read and understood the import of Fisher’s insight before making his own comment on the topic.

  53. Posted December 6, 2013 at 8:39 am | Permalink

    Thanks for writing this Jerry.

  54. Posted December 6, 2013 at 8:55 am | Permalink

    “polyphemism” :-) I guess that was on purpose.

    • Diana MacPherson
      Posted December 6, 2013 at 1:50 pm | Permalink

      Polyphemus would be happy & his dad wouldn’t kick up a fuss like he did with Odysseus.

  55. Dave
    Posted December 6, 2013 at 9:18 am | Permalink

    Thanks Jerry for writing this.

  56. Posted December 6, 2013 at 11:09 am | Permalink

    Thanks for this. I enjoyed Dobbs’ article because it highlighted the complexity of interplay between genes and environment. But your explanation of the errors was also helpful in understanding that gene expression is a result of genes, too.

  57. Posted December 6, 2013 at 12:34 pm | Permalink

    My own research, if it is to be believed, shows that regulatory mutations are very important in adaptive evolution. Lactose Tolerance in Europeans is the result of regulatory elements and not a protein mutation. But as you rightly say, the regulatory mutation is in turn controlled by other genes that are expressed as proteins or RNA regulatory elements. I think that regulation is massively under-appreciated at the moment, but it is still a gene centered view of the genome.

    Date: Thu, 5 Dec 2013 14:08:00 +0000 To: t_aid@hotmail.com

  58. Posted December 6, 2013 at 3:26 pm | Permalink

    First thing I’d like to do is thank you Jerry for taking the time to refute this totally absurd article. Only someone who holds such a highly respected and recognised position on evolutionary biology can properly repudiate such nonsense, because any counterarguments that we ordinary contributors would make in response to Dobbs article would have very little effect on the perceptions of his followers, and certainly have even less corrective effects on Dobbs himself. And all these false perceptions really really really need fixing.

    I was totally astonished by the article, in my particular case mostly by his description of the historical backdrop to the theoretical mathematics that underlie the selfish gene concept. And I do not think that your criticism could be interpreted as just “nit picking” on historical matters – his errors here are fundamental to the main thrust of his article. Evolutionary Game Theory is the foundation mathematics of theoretical biology. And it is not just an exercise in theoretical modelling – it has proven time and time again to be both fully explanatory and exceptionally predictive of biological properties. Altruism and cooperation are only small part of a vast continuum of the explanatory outcomes from these models. And the fundamental assumption that underlies ALL of these models is that at the lowest level of selection the elements of selection are “selfish” – that their strategy is limited and encapsulated in promoting their own individual success in replication. Anyone who shows no familiarity to the depth of these explanations and the scientists who derived these explanations – Maynard Smith, Hamilton, Price, Grafen, Nowak etc etc could not possibly have the least appreciation of how solidly the selfish gene explanation is theoretically verified.
    Science needs good scientific journalists and scientific journalism to keep a wider public informed on this crucial subject. Journalists here bear a high responsibility to be accurate and informed. Dobbs violates these critical dictates. He seems a sensationalist rather than a reporter. He seems to bear a vendetta in his treatment of Dawkins, he attacks the man and not just his ideas. Unacceptable!

    Perhaps just writing another article discussing established science might not gain him attention or increased journalistic revenues, but if Dobbs only desires to make a living by producing sensational column inches he needs to change his focus to political reporting.

  59. Posted December 10, 2013 at 7:26 am | Permalink

    Slightly aside from the thrust of this article but:

    The number of changes in DNA is not material anyway, in some cases a single difference could make a big change in phenotype.

    In the computer world there is a form of encoding, or cypher writing, where the meaning of each bit depends on the current state of the reader and that depends on the bits that went before. A single bit changed from a 0 to a 1 early in the sequence can produce a whole different read out pattern.

    Fortunately much of the DNA sequence is not quite that sensitive to differences but sensitive enough to mean that a few select base pair changes could make a bigger difference to a thousand other changes.

  60. Posted December 10, 2013 at 10:33 am | Permalink

    I think Dobbs tried to make it too simple. However, I’m also a big fan of West-Eberhard’s work too. But in any case, just as a tiny voice in the throng, I’d like to say that I disagree with The Selfish Gene hypothesis. Moreso because I consider it a flawed metaphor, not necessarily that one can’t twist it to be true:

    http://scienceoveracuppa.com/2013/11/17/the-symbiotic-gene/

  61. Stevie Smith
    Posted December 10, 2013 at 5:58 pm | Permalink

    Jerry’s post is much appreciated. Gratuitous slurs upon Richard Dawkins have also come from Peter Turchin in his recent Social Evolution Forum http://socialevolutionforum.com/2013/12/05/selfish-genes-made-me-do-it-part-ii/#comments

  62. Posted December 10, 2013 at 8:23 pm | Permalink

    Reblogged this on Toblog and commented:
    Wise words on evolution and science journalism

  63. Posted December 13, 2013 at 1:07 pm | Permalink

    I’m the author of the article under discussion. I’ve posted a revision of ‘Die, Selfish Gene, Die’(http://aeon.co/magazine/nature-and-cosmos/why-its-time-to-lay-the-selfish-gene-to-rest/) that seeks to clarify some issues and answer some of the critiques. I also put up a post at my blog (http://daviddobbs.net/smoothpebbles/die-selfish-gene-die-has-evolved/) providing some context about the revision (including its take-home) and links to resources, including a highlighted version that make it easier to spot the added and altered passages.

    • What. The. Hell.
      Posted December 13, 2013 at 1:25 pm | Permalink

      Thank you for taking the time and effort to try to clarify your message, because now I see why you think people misconstrued your point. Unfortunately, my insider issues still remain. As someone studying host-pathogen co-evolution in a plant-fungal context – I guess I see things a little differently. I say this perhaps to help alleviate some of your concerns, because I understand why this would freak someone out. I don’t know what it’s like in entomology where you find your examples, but none of this was news to me. Most of our gene studies already incorporate mRNA analyses during periods the gene should be expressed, so we can see how many copies of each gene are involved in each process. No one is ignoring this – we are using it as an asset. I am sorry we failed to convey that and you felt misled, but thank you for appreciating science enough to be outraged when you think something is holding us back, and highlighting an important factor people outside gene researchers need to be made aware of.

  64. wannanah33
    Posted December 19, 2013 at 5:34 pm | Permalink

    TYPO?

    In the 9th paragraph which begins with “Another example of…”, the sentence “The different cases of worker ants…” should say “castes” instead of “cases”. If I’m wrong, I apologize.


20 Trackbacks/Pingbacks

  1. […] via David Dobbs mucks up evolution, part I « Why Evolution Is True. […]

  2. […] First, and most especially, this caustic point-by-point rebuttal by Professor Ceiling Cat over at Wh…. This piece is a hard read, since it gets into a lot of details, but it really gets into some interesting changes to the way we think heredity and evolution. […]

  3. […] http://whyevolutionistrue.wordpress.com/2013/12/05/david-dobbs-mucks-up-evolution-part-i/ […]

  4. […] Dobbs goes looking for new metaphors in a world of non-Mendelian genetics. But see also; and […]

  5. […] David Dobbs mucks up evolution, part I (whyevolutionistrue.wordpress.com) […]

  6. […] PZ Myers liked it and expanded on some of the ideas, Jerry Coyne loathed it and deconstructed it in two posts,  Larry Moran agreed with Coyne’s criticism but has his own gripes with the metaphor, […]

  7. […] Jerry Coyne: “David Dobbs Mucks Up Evolution, Part I” […]

  8. […] two towers. Jerry Coyne delivers a double wallop contra David_Dobbs. Part 1 Part 2 

 Read of the […]

  9. […] Dobbs takes on the Selfish Gene. Dawkins responds (as does Jerry Coyne, three times). I’m generally with Dawkins and Coyne on the theme (if not every detail) of […]

  10. […] friend Jerry Coyne, to the point that he not only read the rather lengthy article, but penned a pair of rebuttals on his Why Evolution is True website.  It wasn’t […]

  11. […] Part 1 […]

  12. […] Part 1 […]

  13. […] its inaccurate and a bit too puffed up on its own bravado. My brief statement is below, however Jerry Coyne, Richard Dawkins and PZ Myers provide a more thorough […]

  14. […] David Dobbs writes an adversarial piece on the concept of the selfish gene and Richard Dawkins and Jerry Coyne rebuff it. Meanwhile, Michael Behe [link redacted] says something that makes everyone ask […]

  15. […] David Dobbs mucks up evolution, part I […]

  16. […] David Dobbs mucks up evolution, part I, Coyne, Jerry. Why Evolution Is True, 12/05/2013. Jerry Coyne’s thorough response discrediting Dobb’s recent article in AEON, Die, Selfish Gene, Die. Website. Read 12/14/2013. […]

  17. […] David Dobbs mucks up evolution, part I, Coyne, Jerry. Why Evolution Is True, 12/05/2013. Jerry Coyne’s thorough response discrediting Dobb’s recent article in AEON, Die, Selfish Gene, Die. Website. Read 12/14/2013. […]

  18. […] – see also Adversarial Journalism and The Selfish Gene by richard dawkins – see also David Dobbs mucks up evolution, part I and David Dobbs mucks up evolution, part II by jerry coyne – see also There is no revolution […]

  19. […] David Hobbs Mucks Up Evolution: Part 1, Part […]

  20. […] he later shifted/clarified his views as part of a very interesting and often confusing discussion, especially with Jerry Coyne– here). It doesn’t matter if it’s Dawkins (or Dobbs) or some other famous scientist and their […]

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