Does evolution need a revolution?

November 24, 2014 • 9:55 am

I’m a bit late on this one, but the Albatross has kept me occupied. This post will be of interest mainly to science buffs, particularly those who already know a bit about evolution. But I’ll weigh in anyway, for, like an egg-eating snake expelling the shell, I had to get this out.

On October 9, the journal Nature published a longish comment by two groups of investigators called “Does evolutionary theory need a rethink?“. (Reference below; I believe the pdf is free. If not, you can get one by judicious inquiry.) It’s a “Point/Counterpoint” in which one group of evolutionists (whose part is called “Yes, urgently,”), suggests that modern evolutionary theory needs a rethink, and will be replaced by something quite different, while the other group (“No, all is well”) maintains that the “revolutionary” discoveries fit comfortably within the existing evolutionary paradigm, so no drastic overhaul is needed.

I read the “Yes, urgently” part first and decided to respond here without having read the other part, as I wanted to critique their views without being influenced by the “No, all is well” side.

Let me say first that I’m a bit puzzled by the continual appearance of these “Does evolution need a revolution?” pieces. If our field really was undergoing a revolution, we wouldn’t have to debate it. I doubt, for instance, that when there was a genuine paradigm shift in physics—from classical to quantum mechanics—we saw many physicists writing “Does physics need a rethink?”  articles. The answer was obviously “yes.”

But even among those who see a paradigm shift in evolution, there’s nobody who sees anything like a complete overturning of our worldview, as happened when quantum mechanics appeared as a deeper and weirder supplement to classical mechanics. Although I haven’t read the “all is well” side, I agree with their conclusion as expressed in the title, and would probably agree with their arguments, which I’ll read after I write this. For the “revolutionary” phenomena touted by the “yes, urgently” side are either not new, fit comfortably within the modern view of evolution, are limited in scope, or, even if fairly frequent, wouldn’t cause a paradigm shift.  By paradigm shift, I mean the view of evolution as gradual, based on variation in DNA sequences that change by either selection or genetic drift (or a few rarer processes), often propelled by natural selection, and producing branches—new species—that yield reproductively isolated populations that cannot interbreed (that’s what species are).

It’s also telling that nearly all the authors calling for an “urgent rethink” of evolutionary theory are those who have published or proposed the “revolutionary” ideas that motivate their views. And they severely overrate the nature of the scientific discussion going on:

This is no storm in an academic tearoom, it is a struggle for the very soul of the discipline.

“Struggle for the soul of our discipline”? That seems a bit dramatic and self-aggrandizing, and is simply untrue. There is no such “struggle” going on, except, perhaps, in the minds of those who feel that their work is not sufficiently appreciated or advertised.

That aside, let me discuss briefly the new phenomena that, the “yes” authors say, call for a new paradigm, an overthrow of what they call “standard evolutionary theory” (SET). There are four, which I’ll take in order:

1. The evolution of development (“evo devo”). The “yessers” claim that developmental biology was never properly incorporated into SET, and would change it drastically were this to happen. They further argue that evo devo has shown that some developmental pathways are more likely to evolve than others:

In our view, this concept — developmental bias — helps to explain how organisms adapt to their environments and diversify into many different species. For example, cichlid fishes in Lake Malawi are more closely related to other cichlids in Lake Malawi than to those in Lake Tanganyika, but species in both lakes have strikingly similar body shapes. In each case, some fish have large fleshy lips, others protrud- ing foreheads, and still others short, robust lower jaws.

SET explains such parallels as convergent evolution: similar environmental conditions select for random genetic variation with equivalent results. This account requires extraordinary coincidence to explain the multiple parallel forms that evolved independently in each lake. A more succinct hypothesis is that developmental bias and natural selection work together. Rather than selection being free to traverse across any physical possibility, it is guided along specific routes opened up by the processes of development.

I’m not sure why the authors feel that “developmental bias” is a more “succinct” hypothesis than convergent evolution. In fact, I see it the other way around. While some developmental pathways surely are easier to evolve than others, the remarkable plasticity of animals and plants under selection suggests that parallel selection may be a more important cause of convergent evolution. After all, icthyosaurs (reptiles), porpoises (mammals) and fish (fish) all evolved similar streamlined shapes independently. It’s more “succinct” to see this as groups of unrelated organisms responding to an environmental challenge (a watery milieu) by using different genes to produce similar shapes than by invoking similar developmental channels. After all, fish, reptiles, and mammals are only distantly related, and it seems unlikely that these shape changes reflect the constraints of development. (In fact, it would be hard to see them as anything other than selection having acted on different developmental pathways.)

And the same may be true for the cichlids in Lake Malawi and Lake Tanganyika. Why would one think that the repeated paths of evolution, which we also see in Australian marsupials versus distantly related placental mammals (both have “flying squirrels,” “moles,” and other similar forms) reflect similar developmental biases? There’s no evidence for developmental channelling here, but there’s evidence from many fronts (e.g., the remarkable plasticity of species under artificial selection) that animals have genetic variation to change into almost anything you want.

Evo devo is a fascinating field, and has come up with some stunning results: one is the discovery that developmental switches can be similar for traits even in distantly related organisms, like the Pax-6 gene controlling eye formation in flies and mammals. But that doesn’t argue for developmental channelling of entire phenotypes, for the eyes involve many different genes in mice and flies. There is still no good empirical evidence for “convergence” due to similarity of developmental pathways that are constrained.

2. Developmental plasticity.  This is the notion that a single organism can change its appearance (phenotype) or physiology in different environments.  Mammals may grow longer fur, or change their color from brown to white, when the weather gets colder and snowier; plants can grow toward the sun, or change their leaf shapes depending on how much sun they get; the two different claws of the lobster (crushing versus pinching) develop differently depending on which claw grabs an object first.

This is nothing new, for that plasticity is often adaptive and has evolved by natural selection. Those mammals who had genes for changing coat color in winter left more offspring (they were hidden from predators or prey), and those plants that could change their leaf shape or direction to catch the sun would photosynthesize more.

But the “revolution” advocates also propose another form of plasticity: an adaptive change in an organism is caused by phenotypes alone, with the genetic change lagging well behind:

If selection preserves genetic variants that respond effectively when conditions change, then adaptation largely occurs by accumulation of genetic variations that stabilize a trait after its first appearance. In other words, often it is the trait that comes first; genes that cement it follow, sometimes several generations later.

But all this really is is what we call “genetic assimilation”: that those traits that prove adaptive in a new environment, though perhaps a result of a malleable appearance, still have genes underlying them, and it is the accumulation of those genes that cause evolution.

Let me give an example. Suppose there are some Tiktaalik-like fishapods swimming near the shore. A few individuals venture out onto the land, as they show “behavioral plasticity” and are adventurous. It turns out that getting on the shore gives you all kinds of new food, particularly insects. They leave more offspring. Over time, the fishapod becomes a proto-amphibian. This is, in fact, the way that terrestrial tetrapods may have evolved.

But this is nothing new: in fact, it was suggested by Ernst Mayr in his famous 1963 book Animal Species and Evolution. Mayr said that many drastic changes in lifestyle may have begun with simple behavioral plasticity.

But the important thing to recognize is that behavioral change and its sequelae (like all the other adaptations for living on land) cannot evolve unless those changes have a genetic basis. What we see here is simply phenotypic (trait) variation that has some underlying genetic basis, and proves to be adaptive. The genetic changes accumulate, and eventually we get a big change in form, lifestyle, and so on. That’s simply conventional natural selection, not a revolution in SET. Further, we don’t know how often major changes in lifestyle happen this way. But whatever the case, this is not a paradigm shift.

There are other theories that the changes in phenotype are adaptive but have nothing to do with genetic variation, and the genes simply come along later to somehow “stabilize” the phenotype.  This isn’t likely because it’s not obvious how lifestyle or form changes could evolve in such a way, since the initial changes would be lack any genetic underpinning. There’s one possible case involving loss of eyes in cave fish, but until that phenomenon is shown to be frequent, we can’t use it to tout a “revolution.”

3. “Nongenetic” forms of evolution. If evolution really weren’t based on heritable and permanent changes in DNA sequence, that would be surprising, and at least a major change in perspective.  The “revolution” proponents argue that this does happen in two ways.

First, there is cultural evolution: stuff is passed on not by genes, but by learning. This, of course, is nothing new: Dawkins wrote about memes—units of cultural inheritance—way back in 1976, drawing a parallel between genetic and cultural evolution. But that was a parallel, and one that I don’t find terribly enlightening. But cultural inheritance is of course important in some species, including all animals that teach their young.  The authors give some examples:

In addition, extra-genetic inheritance includes socially transmitted behaviour in animals, such as nut cracking in chimpanzees or the migratory patterns of reef fishes.

So what’s new? Yes, we can model how this works, but learning it itself an evolved ability, and modeling social evolution will involve things beyond the purview of evolutionary theory. Cultural evolution is not genetic evolution, and hence not part of the SET, which rests on changes in genes. Cultural evolution is important, but it’s no more part of SET than is the “evolution” of changes in automobile style over the years.

The “revolution” authors also include epigenetics as an important component of nongenetic inheritance, one that will revolutionize evolution.  By “epigenetics,” they mean environmentally induced changes in the DNA (e.g., methylation of DNA bases) that somehow become coded in the DNA, so that the environment by itself can change the genome and eventually produce adaptive evolution.

While adaptive methylation has been known for a while (male versus female DNA in zygotes is often differentially methylated, and in ways that favor one parent’s genes), all of this adaptive methylation depends on changes in the DNA code itself—changes that tell the DNA to let itself be methylated. That’s different from the new proposal, which claims that such changes aren’t initially coded in the genes, but directly produced by the environment. (This is “Lamarckian” evolution for those of you who know what that means.)

The problem with this is that such cases of environmental changes in DNA are always temporary, for they’re not coded in the DNA and thus cannot persist forever. And if they’re temporary, they cannot cause long-term adaptive evolution. In fact, there is not a single known case of any new organismal trait based on environmentally-induced change of DNA that has persisted for more than a few generations. And we know of no adaptive change based on such a process. In contrast, there are lots of cases of evolutionary changes and adaptations based on heritable, non-environmentally-induced changes in DNA—that is, “conventional” changes caused by mutations.  In view of this paucity of evidence for environmentally-caused epigenetic change as an evolutionary factor, why are the authors calling for us to overturn SET?

4. “Niche construction.” This is a recent buzzword in evolutionary biology that is an interesting notion, and one that certainly holds true in many cases of evolution. It is the idea that the organism’s own activities modify its environment in a way that changes the direction of natural selection acting on that organism. The classic example is the beaver. These rodents have evolved to build dams and live in those dams, and thereby have modified their environment in a way that affects their subsequent evolution. Due to its own evolution, the beaver now lives in a lake it made itself, and lives inside a house of sticks that it also built. That must surely influence its future evolution, and which mutations could be adaptive (ones promoting better swimming and tree-felling, for instance). Ditto for social insects, who now live in complex burrows (built by them, of course) that must surely affect their later evolution.

While this idea is getting new attention, and deservedly so, it doesn’t call for a revolution in SET. First of all, it’s not particularly new. The idea of “gene-culture” coevolution has been around a long time. One example is pastoralism, in which humans changed their environment by keeping domestic animals that give milk.  And that has changed our evolution, for cultures that are pastoral have undergone evolution involving the use of lactose. Genes that break lactose down into digestible components are usually inactivated after weaning in humans, who, over most of our history, didn’t have a source of milk after they stopped suckling. That’s why many of us are “lactose intolerant.” When we suddenly got a rich source of nutrition from our sheep and cows, pastoral cultures evolved so that the genes metabolizing lactose weren’t inactivated,but were turned on for life. (Individuals with genes allowing them to digest milk had up to 10% more offspring on average than intolerant individuals!) Thus, our own culture affected our subsequent evolution. This did not cause us to dismantle SET; rather, it was an interesting sidelight on how culture itself caused genetic change.

Second, we don’t know how pervasive this process is. That is, while many organisms do affect their environments, we don’t know how often that environmental change feeds back to the organism to cause additional evolution. In some cases it probably doesn’t: fish adapt to an unchanging fluid medium, the coat color of polar bears cannot affect their environment of ice or snow, and the hooves of the chamois don’t affect the granitic structure of the Swiss Alps. So how often “niche construction” is important is an open question, albeit an interesting one. But I don’t see it overthrowing SET, for it’s simply a novel way that the environment can change and affect organismal evolution.

That is not to disparage this phenomenon—or any of these phenomena. Niche construction seems more likely to be important than “genes follow phenotype” plasticity, or than adaptive epigenetic evolution, of which we have not a single example. All these ideas deserve empirical study. But none call for a new paradigm.

Now I can read what the “conservatives” (Wray, Hoekstra, Futuyma, Mackay, Lenski, Strassmann, and Schluter) have to say.

Laland, K., T. Uller, M. Feldman, K. Sterelny, G. B. Müller, A. Moczek, E. Jablonka, J. Odling-Smee, G. A. Wray, H. E. Hoekstra, D. J. Futuyma, R. E. Lenski, T. F. C. Mackay, D. Schluter, and J. E. Strassmann. 2014. Does evolutionary theory need a rethink? Nature 514:161-164.

112 thoughts on “Does evolution need a revolution?

  1. I’m surprised Nature would publish something like this. Even I know enough about evolutionary biology to have written a reasonable facsimile of Jerry’s response….


    1. I thought the same, although my attempt would in no way be described as a “reasonable facsimile”. However, even I (which should be italicized) could see some of these “yes” arguments don’t stack up.

    2. Yeah I thought the same and although I wouldn’t have all the answers Jerry had, I would certainly be highly suspicious of those “yessers” with something like evolution because I’d expect to notice this “revolution” if there were big paradigm shifts occuring.

    3. But I’m sure this article will be cited often – disparagingly by its detractors and in a “see we are relevant because Nature mentioned us” way by its supporters. And that in the end is what Nature lives off; its citation index. This is the scientific equivalent of clickbait.

  2. Jerry – thanks for taking the time to write this very nice summary. It should be required reading for upper level undergraduate students in genetics and evolutionary biology, as well as for all faculty in the biological sciences.

  3. They further argue that evo devo has shown that some developmental pathways are more likely to evolve than others:

    I thought we already knew this, and it was part of the standard theory. Specifically, “random” mutation is not random in the sense of every single replacement or duplication being equally likely, but random in the sense that the phenotypic result does not change the odds. So yeah, its entirely possible for some mutational events to be more common than others and thus some developmental events to be more common than others. Am I missing something here? Because I’m not seeing what’s revolutionary about this idea.

    there is not a single known case of any organismal trait based on environmentally-induced change of DNA that has persisted for more than a few generations.

    Is this really true? I think epigenetics can be easily shown to occur for some trivial cases. For example, cosmic rays are part of our environment. Every time one zips through someone’s gonads and alters the DNA of some sperm, that is technically an “epigenetic” change (at least the way you’ve described it, Jerry). Drinking teratogenic chemicals might do it too. AIUI, horizontal gene transfer from a virus would technically count too, because the viruses and bacteria that cause it are technically part of the ‘victim’ organism’s environment.

    I think the disagreement over epigenetics probably concerns more “normal” environmental factors (temperature, macro scale animal and plant life in the environment, and so on), and how those could possibly indirectly cause any sort of heritable change in DNA. Its thus an argument over the extent to which epigenetic environmental factors matter, not an argument over whether any environmental factor can change DNA, because clearly some do.

    1. The changes induced in germ cells by cosmic rays (for example) would be genetic not epigenetic, in the sense that such a mutation would be part of the normal genome of the offspring. We all have around 150 mutations that are not present in the somatic DNA of our parents. This is the wellspring of variation of the “shit happens” variety.

      There has been work and much gnashing of teeth on the possibility of multigenerational epigenetic effects. I’m aware of work in the area of endocrine disruptors, such as the work by Mike Skinner at Washington State. But I don’t know how long that’s been followed and how well it has been independently validated.

      1. If the example of changes in germ cells by cosmic rays is genetic, what would be an example of epigenetic change? I understand there aren’t any known examples, just trying to figure out what one might be.

        1. Epigenetic changes involve altering gene expression without a change in DNA sequence. The radiation example would involve sequence changes.
          Gene silencing can be achieved by a number of epigenetic mechanisms. A classic example is methylation of promoters which inhibits transcription, but there are lots of mechanisms, including histone modification and microRNA regulation (type epigenetics into wikipedia for examples). Every time I think I’ve understood this someone comes up with something else – sat through a fascination talk on piRNA a couple of weeks back – a whole class of molecules of whose existence I’d managed to be oblivious.

          There is debate and discussion over how heritable such effects can be. In general it’s not considered to be inherited – but there are some strong dissents from that position, especially among some of the evo/eco/devo crowd. (This field hadn’t been invented when I was at school so I was interested that my daughter had a formal undergrad class in epigenetics).

          1. If its not heritable, the presumably each generation of the species would have to have the same contact with the environmental agent, yes? Or maybe a mother undergoes the epigenetic change before/during pregnancy, influencing the gene expression of the child? But if that’s the case, I don’t see why the grandchild wouldn’t just revert to the original mother’s (i.e., its grandparent)gene expression.

            If, OTOH, you say that the agent causes some non-genetic change which in turn causes some genetic change that is heritable – either in it, or in a daughter organism – then you’re right back to indirect genetic changes.

            1. Ah yes, the mechanism question. Which is why there is so much skepticism. (Including from me.) However the papers are out there to read and discuss.

              For a couple of recent reviews see:
              (I can e-mail the pdfs if you contact me)

              There was also a more lay audience-targeted review in Scientific American (Vol 311, Issue 2) – have the hard copy but (ironically ) can’t get the pdf easily

          2. Read the wiki and / 3-examples-transgenerational-epigenetic-inheritance /
            Still confused, but I’m working on it.

        2. Folic acid might be one example. When digested in high concentrations during pregnancy, it can increase levels of methylation, because it is metabolized to S-adenosinemethionine which acts as a donor of methyl groups. So basically, it can cause changes in gene expression in developing embryo. I think that they actually did some studies on mice, and showed that depending on levels of methylation of certain gene (Agouti, I think) you could change type of epistatic interactions between two allels of that gene.
          Also you have various chemicals that might alter development, for instance cyclopamine or ethanol and high temperature. And while these examples aren’t epigenetic in a sense that they alter methylation profile, they do cause phenotypic change without changes in nucleotide sequence.

          1. Right, I get that. But unless there is some change to the daughter’s DNA, when the daughter has kids of her own they will not have high methylation rates unless she consumes lots of folic acid too. Instead, they will revert to what the grandmother was like.

            Thanks for the articles Simon, I will look into it. Right now (prior to reading them) I still feel like: if its is heritable, its just indirect mechanisms for standard mutation and natural selection. If its not heritable, then its just an standard environmental influence on selection. Either way, not a ‘revolution’ in the TOE.

            1. Right, but I was just giving an example of environmentally-induced epigenetic changes in offspring. I really haven’t done an extensive reading to weigh in on issue of long term transgenerational effects of epigenetic changes. However, I think that Bryan Turner did some theoretical (or speculative?) work on conversion of epigenetic changes into genetic changes.


    2. I made note of this series of intro articles on epigenetics when it appeared (3 parts) on the NCSE blog over a few week period recently. I seem to come across a lot of discussions where people want to make all kinds of wild claims for epigenetics (mainly from a lack of understanding) and could do with a simple, introductory-type overview. I think this might fill the bill.

      The link is to the first article (of 3). Click the authors name to get links to parts 2 and 3.

  4. Thanks for the thoughtful analysis! Your examples from nature really helped to get some of the concepts across to me. Are you planning on writing a follow-up post on the “conservative” side of the issue? I’d be interested to hear how much overlap there is in your opinions.

  5. Very good. I had earlier read both sides of the commentary, and I think you will find that the ‘No, all is well’ crowd do a good job at rebutting the revolutionaries. All of their arguments are ultimately ‘gene centered’, even as they seek to criticize the SET for being too gene centered. It is a wonder that they do not see it.

    1. Why don’t they see it? Perhaps because in science you get brownie points based on the degree of novelty of your ideas, so there is an ever-present incentive to exaggerate the novelty of an idea or finding, or to cast it as “revolutionary”. I also wonder if this periodic re-thinking is starting to reflect a failure to absorb what has already been stated in the earlier pertinent literature.
      Stephen Jay Gould was a master of exaggerating the revolutionary nature of his own ideas, and eventually had to back off of his dramatic pronouncement in the 80s that “neo-Darwinism is dead!” I seem to recall that Professor CC played a role in puncturing the novelty claims embedded in the punctuated equilibrium idea.

      1. Well, you broached a topic that I was not sure about bringing up, which is why there are so often a few revolutionaries calling for an overhaul of the evolutionary paradigm just because some nuances have been discovered. I have thought that this push is on b/c they want to be famous. They want to be the ‘bringers of the new paradigm’, so they speak loudly and agitate for a revolution. But there aint’ no revolution.

  6. Sadly, the one thing that will assuredly happen is a blizzard of “Evolution in Crisis” headlines in the ID/creationist world.

    1. This is a real possibility. That there is discord in the ranks of science will be misunderstood as a schism. Since a schism is terrible in religion, signs of such a thing in science must also be a sign that the walls are coming down, right?

    2. Yeah but they don’t need an article in Nature to start on that. If you live in that culture bubble, you believe that most scientists reject evolution.

      1. It’s true that they don’t need it, but articles such as this do give them ammunition and an (admittedly false) sense of legitimacy. Much like the infamous “Darwin was wrong” cover a few years ago.

  7. Sean Carroll talks about this article as well:

    My understanding is this. The consensus is mostly: complex stuff happens fast and slow. And there is no need for a revolution, in fact, it sort of makes no sense or at least has no privilege to be considered in the present state of how the theory of evolution engages with explanations of natural phenomena.

  8. Thanks. I found your commentary helpful in addition to the “conservatives'” commentary. I also found the “revolutionaries'” commentary useful in that it challenges my understanding. But I haven’t been able to see yet how their challenges undermine SET.

    1. I wonder if part of the problem is the multiple meanings of ‘revolution.’

      Meaning one: ‘contradicting things science is confident are true.’ There doesn’t seem to be much of a revolution in SET or even needed in SET. None of the four arguments Jerry summarizes above really do this.

      Meaning two: ‘significantly changing the direction in which research effort and money are spent.’ Yeah, some of the ideas here might lead to that sort of revolution in the future. And it is likely that the proponents of the four arguments above asipire for this to be true – by calling their ideas revolutionary, what they are really hoping to do is to attract more scientists and more research funding to areas of research they think could be very interesting, useful, or beneficial in the future.

  9. Thank you for taking this on. I was hoping that we’d get your perspective, so that we could share it with others.

  10. How is “niche construction” different from the effects that Dawkins described in The Extended Phenotype, which seem to clearly be a function of normal genetic inheritance? (Out of my depth here!)

    1. There was a nice discussion of the extended phenotype in the journal Biology and Philosophy in 2004, in which Dawkins addresses just this issue:

      Let’s see if I can accurately summarize: Niche construction may be considered an example of an extended phenotype, but only if we are talking about adaptive evolution based on differences in genes, which is what Dawkins wrote about in his 1982 book. Otherwise, niche construction refers to the broader concept of any environmental change that results as a byproduct of an organism’s activities and that in turn influences its future evolution.

    2. I think the difference is the Niche Construction theory holds the extended phenotype (organism + behavior + modified environment) as a cause of evolution, wheras the phenotype is conventionally understood only as a product or consequence of evolution.

      I’m not sure I follow where the controversy is, apart from vocabulary: beavers are exposed to selection in an environment they configure, which is different from preceding environments that selected for beaverness, but ultimately the mechanism is the same so it’s not clear to me how it changes Dawkins’s theory, as opposed to adding color and detail.

      1. So, humans (organism) raise cattle (behavior) and as a result have milk available (modified environment). This food gives an advantage to those that can utilize it and leads to selection for retaining lactase expression into adulthood (selection of a specific marker) with a selective advantage for the lactose tolerant progeny.

        Ultimately to cope with the excess meat the hamburger is invented and to cope with the problems caused we develop statins.

        Still not clear if the difference is just semantics.

    3. As a non expert my thoughts are as follows.

      1) It should not be surprising in the slightest that an organism affects the environment in which it exists.

      2) Since environment has been considered the primary cause of natural selection since Darwin on through SET, it should not be surprising at all that changes to the environment caused by an organism can then in turn affect the evolution of that organism by natural selection by the environment.

      3) This is so obvious it must have occurred to many biologists many times in the past, probably from the very earliest days of the TOE.

      4) There just doesn’t seem to be a need for any new mechanism for an organism’s impact on its own environment to then affect its future evolution. Natural selection seems perfectly adequate, and parsimonious, to explain that.

      4) It seems fairly ludicrous that some biologists would call this new or a revolution. Ludicrous enough that I question my understanding as outlined above, or my understanding of the “New’s” niche construction.

  11. Evo-Devo comment: It seems intuitively appealing that in recently diverged species such as the cichlids, convergent evolution of features that seem to lack a clear selective advantage (fleshy lips, bulging foreheads), or perhaps stem from weak selection pressures, would result at least in part from a widely shared genome hosting mutations that are easier to make and thus more likely. For more distantly related organisms displaying features of clear selective advantage, such as dolphins and ichthyosaurs, similar selection pressures must be the answer.

    1. I think that the features in the cichlids might well be drawn from developmental programs that are ‘ready’ to have certain alleles selected for — so they appear quickly and recurrently. Lots of genes are linked on the same chromosomes, so alleles can appear together, once selection is applied for one allele. We see this when we domesticate animals for docility. they often show other traits that come along for the ride, like piebald spotting, and curly tails.
      Actually, the fleshy lips are adaptive for nibbling on rocks and corals, and lots of cichlids have them, including marine species. The high forehead is, I think, a sexual selection trait and this too is common in different cichlid species around the world. That different species have it seems as remarkable has different species of birds have big tail feathers in males.

      1. There’s also the p-factor fallacy. If there’s only a five percent chance that this level of convergence would “just happen”…well, as soon as you’ve examined twenty situations in which it could arise, you’d expect to see something like this happen just by chance alone.

        Human intuition sucks donkey balls when it comes to estimating probabilities. We’re all absolutely certain that everything happens for a reason, and convincing ourselves otherwise is nigh on impossible.


        1. Ben,
          It doesn’t seem intuitive to me, I mean the sucking of donkey balls. Are you sure there is not another explanation? Like this method of telling time by donkey balls?

          1. Sorry about that. It’s counter intuitive that copying an address would bring up the video and not simply the address.

          2. There may well be…but, to be honest, I’ve never had the inclination to fully explore all the possibilities of what could be done with donkey balls….


            1. On occasion I modify my epithet of “by the four balls of Jeebus, Mary and Joseph” to call upon the “six balls of Jeebus, Mary, Joseph and the donkey” ; your invocation of donkey dangly bits might be better saved for extracting some fluids from the BuyBull.
              Someone, somewhere, must have a bovine artificial insemination supply company called “Buy Bull”. Surely? It’s too … scatological to have been missed.

      2. The hyperbole of the authors stuck me that for these convergent traits to appear would require “extraordinary coincidence “.

        Oh really?

        In two sets of fish with a fairly recent common ancestor (all cichlids IIRC evolved from one ancestor species in one of the lakes), living in two similar lakes in the same climate? Extraordinary coincidence?


    2. This is almost certainly true. I fail to see how this is either new or revolutionary though. All the traits we see are a result of drift and/or selection acting on previously existing genomes. Those previously existing genomes obviously make some things closer in mutational space than others, which will both result in the possible re-emergence of lost features as well as putting constraints on the space of possible novel features. So? We’ve always known this. That’s what the whole comparative embryology evidence for evolution is about: biology isn’t God, it can’t build a human in just any old way, it has to start with an existing developmental program and tweak it in some sense. Thus our development has odd features you wouldn’t expect if we were designed from scratch.

      To me, the whole debate about whether or not these ideas are revolutionary is just a stupid semantic argument. It’s like two people arguing about whether a particular cat should be called a “long haired cat”, with one insisting “no it’s a short hair” and the other “no, it’s a long hair”, but both agreeing on the actual length of the hair in inches.

      It’s a dumb argument.

  12. … when there was a genuine paradigm shift in physics—from classical to quantum mechanics—we saw few physicists writing “Does physics need a rethink?” articles. The answer was obviously “yes.”

    You are a scientist and speak in academic language — thus your quite reasonable use of the term “paradigm shift” to describe classical-to-quantum mechanics.

    But when members of the general public uses the term “paradigm shift” to explain what happened with quantum mechanics, I have found that they assume that classical mechanics was then throw out completely — along with materialism. The world became re-enchanted as we learned that the moon is only there when you look at it and quantum consciousness permeates the universe!!11!1!

    In common parlance, the two “paradigms” are spiritual vs. atheistic naturalism.

    And thus there were and are plenty of “does physics need a rethink?” articles among the woo-sters. What about that paradigm shift, where we all learned how atheists are wrong? Why are so many physicists still stuck in the 19th century?

    Mister, “Paradigm Shift” is fightin’ words where ah come from. But I reckon you didn’t mean no harm.

    1. The world became re-enchanted as we learned that the moon is only there when you look at it and quantum consciousness permeates the universe!!11!1!

      Yeah, immediately following Kuhn there was a huge academic and populist race to out-Kuhn Kuhn. 🙂

    2. There’s a different problem with this :

      I doubt, for instance, that when there was a genuine paradigm shift in physics—from classical to quantum mechanics—we saw many physicists writing “Does physics need a rethink?” articles. The answer was obviously “yes.”

      Not only did Classical Physics never die – it remains an excellent approximation for the first couple of hands full of significant figures – but pretty much every serious physicist I’ve ever talked to is perfectly happy to accept that fundamental physics needs a re-think, and that “something ain’t right”.
      General Relativity is a classical theory. It’s not got a quantum in it. It’s also one of the most accurately tested descriptions of the universe that we’ve got. 12-plus significant digits in many tests, and I think some parts of testing have gone above 15 significant digits. Which is great.
      But the universe is also “quantum” – I’ve seen it myself by constructing with these fair paws a double-slit interferometer which could only have had one photon in flight at a time.
      There is this fundamental split in physics. Something ain’t right.
      The big debate – which seems to mostly happen in extreme astrophysics and cosmology – is where to go to shift the paradigm. And most physicists just duck the question because it’s outside their pay grade. I worry (slightly) about quantum on those occasions when I’m thinking about radiometric dating, atomic absorption spectroscopy for chemical analysis and photoelectric effects as composition indicators. And I worry about classical effects for electrical work, optics, and stopping the helicopter from crashing into the water to kill me through hypothermia or shark attack (depending on country) ; not that I’m a physicist, but I really don’t have time or braincells spare to devote to the question of resolving the contradiction.
      I don’t mind my tax Euros going to support a small proportion of physicists who do want to find a solution though. We’ll probably get that money back in either entertainment, or technology anyway (CERN, WWW, anyone?), so it’s a “Meh” to me.
      The dichotomy is still there though.
      In other news … who was it that said that revolutions in science proceeded one funeral at a time?

      1. I’ve seen it myself by constructing with these fair paws a double-slit interferometer which could only have had one photon in flight at a time.

        Got any details on that, especially if it’s something the “average Joe” could pull off?

        I’ve got plans to first play around with the classic double slit experiment with a laser, and also plans to see if I can do the “see individual photons” trick by putting enough filtering material in front of a green laser pointer to get the photon rate into the several per second range (coupled, of course, with a very dark room at night and plenty of time for dark adaptation). Then, the last trick would be to add a double slit at the right distance for interference patterns….


        1. Yeah, sure. Details.
          Use a red LED as a light source. Voltage drop and current give you the power output, and it’s pretty high efficiency. Wavelength well established, so your power, via E=h*c/wavelength (can’t be bothered with an excursion into Unicode – client’s computer anyway), gives you the number of photons per second, and your double-slit geometry gives you the distance form LED to eye.
          Set up a standard double-slit in a darkroom. Now turn the power of the LED down (in-line resistance) until you can only just make out the diffraction fringes. Read the current through the LED. Do the maths. You should find out that the Mk-1 human eyeball can easily detect the diffraction pattern while there’s only one photon in flight at a time.
          Nuffield physics A-level course (“high school”) from the mid-70s onwards. They took 2 years leading you through all the relevant physics – waves, interference, electromagnetic waves, speed of light in rolls of co-ax cable, photoelectric effect, electronics … and left this as pretty much the last experiment of the course. They fed you through as far as deducing that there was only one photon in the apparatus at a time, but it was still interfering with other photons which had ceased to exist, or had not yet been generated … and left you there.
          It wasn’t until about 3 years later that I realised that I had seen the wave particle duality of the universe with equipment that I’d built with my own hands. That hit me harder than three crack-heads and a granite cobblestone. Those educational psychologists at Nuffield sure knew how to make things stick in your head.

          1. Thanks for that! That’s very much what I was groping towards, save for the actual illuminant and the means for controlling its brightness. Yours is likely simpler and safer.

            And, honestly, whether or not you get all the math to accompany it, it’s an experiment that you probably should have to do before being allowed to graduate high school. I can’t imagine a more visceral demonstration of the fact that the Universe really is much stranger than you think it is…and I can’t wait to find out for myself….


            1. Visceral – that’s a good word for it..
              ISTR that we had to use a special low-current ammeter, but since our general purpose ammeters were analogue AVOmeters with an input impedence of only a few MΩ … quite likely any modern digital meter would be adequate. your current will be in the µA range, but I don’t think you’ll go down to nA.😹

              1. Even if the power source won’t directly drive the LED down to the dozens-of-photons-per-second range, it’d hopefully get it close enough that some simple optical filters will. Mylar film might do the trick nicely, or perhaps a variable neutral density filter (which is just a pair of polarized glass plates in a rotating assembly). Though I suppose the latter could conceivably cause some other interesting (whether desirable or not) effects due to polarization….


              2. Say your optical bench (OK, solid table) is 2m long. To have one photon in flight at a time, then you emit (to a single significant figure) 300000000/2 ~= 150000000 photons per second. If that’s a 700nm red LED, each photon packs E=hc/wavelength J, which I make 2.8*10^-19J
                LED power is then about 4*10^-11W. With a 0.7V drop across the LED, I make the 6*10^-10A.
                Hmmm, I may have slipped a decimal place somewhere. I remember that we had to use the teacher’s “good” ammeter, not the standard bench ones. But that would have to be a pretty good ammeter.
                Mind you, put it across a 100M Ohm resistor with another 100M variable resistor in the circuit for adjustment and you should get a millivolt-ish signal across that. Which is very measurable.

              3. I’ve archived these posts off for a starting reference.

                There’s two experiments I have in mind that I want to combine into a single one.

                One, of course, is the plain-Jane double slit.

                Another…I’ve read references from multiple sources that the human eye is actually capable of seeing single photons at a time, and I really want to try that one out as well. At least get a source into the range of an hundred photons per second, ideally with variability that could get it down to a few photons per second.

                Doing a bit more research…that’s almost certainly going to require not a red LED but something close to 500 nm, slightly more green than blue. Red light is invisible to scotopic vision. Typical green laser pointers are 532 nm, which is likely plenty “close enough”…but will need all kinds of filtering to get to that power output range. A green LED might be a better choice….

                Obviously, if I can get the latter to work, I’ll combine the two….


              4. Try digging through your photo kit – or your astronimy supplies. A “eclipse filter” (or something like “Solar Skreen”) should give you about a factor of 10^5 light attenuation, with a reasonably flat profile across the visible spectrum.

              5. Yes, I do. I’ve got a 6″ diameter one for the 400mm lens, and then a pair or three of cardboard-framed eclipse glasses. And, obviously, if one still leaves the light source too bright, another one or two will do the trick….


  13. Great overview of the ‘challenges’ to evolution. Like many such challenges (think punctuated equilibrium) they seem less important the closer they’re examined. I don’t quibble with Nature for publishing it, but perhaps the title should have implied that the challenges are actually small. “Can revisionist fleas topple the Big Dog?”

  14. These debates about theory often remind me about taxonomic classification debates. It seems to me that it is often about whether you are, by general nature, a “lumper” or “splitter.”

    Do you split theories and models into discrete tiny bins (e.g. to use an historical example…see Fisher vs. Wright in population genetics as different theories) or tend to lump theories into bigger bins (e.g. a general view of population genetics, with some variation and debate allowed).

    In classifying species and their respective genomes, both lumpers and splitters may err in that-subconsciously, at least–they both think of species as static entities, instead of thinking with a more phylogenetic species concept where diverse species merge into each other and drift, over time. I tend to be a “lumper” and thus want to agree with this post, but–at the same time– I also wonder if we would be better to take a more “phylogenetic-like” view where we focus more on “theory-trees” of common origins and divergences, than argue about static classifications of changing theoretical models.

  15. It seems we get these “does evolution need a rethink?” articles every once in a while. My response is; well bloody well rethink it then and let the rest of us know if you come up with anything. I’m only a lay observer but they never do seem to come up with anything new.

  16. I find the preamble to the “no storm in an academic tearoom” comment interesting:

    Yet the mere mention of the EES often evokes an emotional, even hostile, reaction among evolutionary biologists. Too often, vital discussions descend into acrimony, with accusations of muddle or misrepresentation. Perhaps haunted by the spectre of intelligent design, evolutionary biologists wish to show a united front to those hostile to science. Some might fear that they will receive less funding and recognition if outsiders — such as physiologists or developmental biologists — flood into their field.

    However, another factor is more important: many conventional evolutionary biologists study the processes that we claim are neglected, but they comprehend them very differently …

    In other words, evolutionary biologists are hyper-sensitive, emotional, irrational, closed-minded, cybabies who subvert scientific integrity to motivations like shutting down creationists, and they are fearful of non-scientists stealing their sweet, sweet grant money (certainly not out of any credible professional standards).

    And the “on the other hand” is delightful: not that “we might be wrong,” but that other scientists can’t see the forest for the trees (or maybe the tree for the tree’s genome).

    I can’t help but notice that the “No” team managed to make their points without any name-calling or characterizing of other people’s motives. Not that this proves anything about the science, but I think it’s telling.

  17. It seems that a lot of people try to make a name for themselves by constantly agitating for a “revolution” in field x or subject y, when one really isn’t called for.

    Unfortunately, it seems that a disproportionate portion of the funding, praise, publications, and promotions go to the kind of people who do this.

    There’s a professor in my department who has had huge success by jumping from one bandwagon to another. A review of their career shows a history of buzzword-filled papers and trendy (if unproven) techniques – each one discarded after they stop getting attention/money.

    1. Reminds me of that old chestnut: All publicity is good publicity. Stir the pot, become famous.

      I am sure that Sithrak has a spit for pot-stirrers.
      The FSM doesn’t have any problem with pot-stirrers.

      1. I’m sure Sithrak also has a spit for the non-pot stirrers. And for the pot non-stirrers, and the non-pot-non-stirrers, and for any and all who may or may not be included in those sets.

        Sithrak has never been known for being stingy with the spits….


  18. The mathematics of classical physics and quantum mechanics are very different, so the change was clearly revolutionary. I don’t see anything remotely like this in the given examples of “paradigm shifts” in evolution. The one example I know something about is the difference between (pure) genetic evolution and gene-culture co-evolution. Mathematically they are similar, and one can see how to transition from one to the other. For example, there are models of pure genetic change called “adaptive dynamics” where mutations are rare compared to fixation times, while in models of cultural evolution the opposite is true. With a single parameter one can gradually move from one extreme to the other.

  19. Jerry,
    In an earlier thread, you were wondering whether your science-based articles were worth the effort you put into writing them. I just want to say that as an (extremely) ex-chemist I have nothing meaningful to add to this post (or to the insightful comments on it); but I am very grateful for the trouble you have taken to construct it, and the education I have gained as a result; and I hope you will carry on all this great work.

  20. Everyone would like to create the next revolutionary scientific theory that changes a whole field of study the way Quantum Physics did.

    Unfortunately, it seems the “yes” camp in this debate aren’t objective enough to see the confirmation bias at work here. “Why yes of course my work must be revolutionary, I want to be revolutionary after all!”

    No one forces revolution with hyperbolic rhetoric. Revolution comes about by an accumulation of evaluation and action.

  21. The Dolly experiment and others showed that the nuclear DNA of a somatic cell contains all the genetic information to orchestrate the embryonic development of a new animal of the same species. Is it not clear that an animal of a different species must of necessity go through a substantially different embryonic development? Different DNA sequences are essential for this to happen. In other words, evolution cannot happen without an accumulation of changes in DNA sequences.

    The DNA molecule (and the information therein contained):

    – can be copied (this is the base of heredity)
    – can be changed. The change is then copied and thus becomes hereditary. This opens the door to an accumulation of changes leading to a new species.

    Good luck to those who think a “drastic overhaul is needed”. I suspect they will need a great deal of it. But hey! I am not a biologist so I am perhaps only presumptuous.

  22. I too am bewildered at to the point. “Is conceptualized” by whom? “Has ossified around genetic concepts” for whom? The general public? Well, I have no argument there – but then it is a question of proper education about evolution, is it not?

    Would not the adoption of an “extended evolutionary synthesis” codify the very central concept that they are rejecting? That in itself should give the “yessers” pause.

    Does it need to be repeated that Darwin did not know about genes? Goodness me. The environment is a “background condition”? That went out a long time ago. I too wonder if the “yessers” aren’t motivated by quantum theory envy, and I must ask, doesn’t biology in particular draw upon older publications and sources in ways that other sciences do not? A “revolution” at this point is not tenable – in fact, it is not even what the “yessers” themselves are proposing, though they think that they are. Their argument is confused.

    I also second Steve Pollard’s comment. Please continue to write blog posts like this one!

  23. I couldn’t even see how most of those (except the Lamarckian one) would go against the SET, I also have many faint recollections of reading about them – in a favourable light – before all this revolution hyperbole, from people like Dawkins, Ridley, Dennett, Coyne and Pinker.

  24. I just wanted to thank for this post and analysis of the scientific topic. You recently lamented that you get a smaller response to science focused posts. I greatly appreciate and read virtually all of the science posts. Regrettably, my business and legal education have left me without the background to contribute much to the conversation in those areas.

  25. I remember PZ Myers covered this topic interestingly some time ago. Of course he is a conservative on this issue.

    1. I haven’t followed PZ’s blog for some time (more than eighteen months), but I do remember a post of his about this, because he explained evo-devo which was new to me.

  26. I read through Massimo Pigliucci’s essay on this over as Scientia Saloon the other day, and to me the issue seems largely whether one thinks the modern synthesis can incorporate all the modern advances in evolutionary theory, or whether we should recognise those advances have changed the modern synthesis enough to recognise it’s a somewhat different beast we are dealing with.

    I wonder if this episode is evidence against the Kuhnian notion of a paradigm shift. There’s no revolution here; even with the most radical thesis there’s only an advancement on what’s already there.

    1. Paraphrasing :
      “Has the Modern Synthesis of Evolutionary Theory evolved?”
      Answer : the question pretty much answers itself.

  27. As I read this (very interesting BTW Jerry), the first thing I thought was that here was another confirmation that questions in headlines are always No. What I kept wondering, though, is why people might feel a need to upset SET (non-creationists, that is). Does this go back to the older nature/nurture argument? It seems kind of woo-ish or New-Agey to suggest that there are ways we could influence our own development.

    1. Nah, I think it’s just ambition. Lots of scientists are fueled by ambition. The dream is to be the next Darwin or at least the next Crick/Watson. The problem is that science actually answers questions and those answered questions can’t be answered again.

  28. When your trying to remove a mountain you would think, start at the top and work your way down. Not so with these ‘revolutionaries’ they are beginning to tunnel at the base running the risk of collapse, unfortunately it seems on themselves.
    Nice counter post Prof. with some doors still open for further considerations..

  29. After reading the summary of the “yessers”, I’m left with an overwhelming feeling of 2is that all they’ve got?”
    There are certainly problems with the popular understanding of evolution – but the same can be said of pretty much any other branch of science. As a geologist I am used to metaphorically coshing members of the public with the immensity of “Deep Time”. The American experience of creationist verbal diarrhoea is pretty traumatic even for those of us who only have to deal with it’s side blasts. Public patent offices still need to have rules about not accepting perpetual motion machines without a working model to examine. But these are issues of science education (with substantial doses of the psychology of wish-fulfillment and fear, for the perpetual-motioners and god-squaddies), not of the underlying science.
    Good post though Jerry, thanks.

  30. I think the main problem of the ‘yessers’ is their straw man: “and natural selection is the sole cause of adaptation”. If stated like that, any minor kind of change (not all change is necessarily adaptive) that is not obviously naturally selected for appears a “revolution”.
    At present evo-devo, developmental plasticity, epigenetics, niche construction (an idea nearly as old as natural selection itself, btw) and the like are filling in some of the blank, or at least greyish, fields, expanding SET, not shifting the paradigm, meseems.

    For those who like slogans: ‘Not Revolution, but Evolution!’ 🙂

    1. It reminds me of the “symbiosis” well, what shall we call it, cabale(?) of 2 decades ago.
      Symbiosis somehow would negate natural selection, but at present it is a *cornerstone* of SET.

  31. I don’t have a lot to add to the comments other than to assure the proprietor that his excellent biology article is appreciated. This is why I read this site.

  32. All these “revolutionary” developments are nothing but potential outcomes of evolution by natural selection. “Non-genetic forms of evolution?” The Blank Slaters never give up, do they? When it comes to evolution, the ideological angle have ye always with you.

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