This article in the Guardian really says nothing new beyond what a dozen articles have said already: “There are things we know about evolution that Darwin never imagined, and we’ve made many discoveries that weren’t part of the ‘modern synthetic theory of evolution’ forged in the Thirties and Forties.”  I’ve posted a ton about these issues already, many of which are said to form an “Extended Evolutionary Synthesis”, or EES. It turns out that yes, things like the neutral theory and epigenetics weren’t imagined by Darwin, who knew nothing about heredity, or even by the great Theodosius Dobzhansky, but the exponents of the EES sometimes try to pretend that it’s more than an extension of evolutionary biology, but a Kuhnian “revolution” mandating a “new theory of evolution”. Indeed that’s what the article below maintains. (The answer to the headline question is “yes.”)

But in fact we do not need a new theory of evolution: the basic theory proposed by Darwin in 1859, which includes gradualism, variation, natural selection as a critical factor responsible for adaptation, splitting of lineages, and the resultant common ancestry of all species and individuals, still holds. But we know a lot more now, and most of it can easily be incorporated into evolutionary biology. In fact, if you look at evolution textbooks from a few years ago, you’ll find phenomena like epigenesis, the neutral theory, “niche construction”, plasticity, and the like not only discussed, but shown to have been part of discussions about evolution for half a century or more. Now they’re simply part of “evolutionary biology”, which, yes, has expanded, but not in a manner that mandates replacing the old theory. Like cosmology, we just add new stuff to the field as it turns up, and ditch the stuff that turns out to be wrong.

Yet the author, Stephen Buranyi, a Guardian science writer, cannot help himself from not only distorting the history of evolutionary biology, but arguing that evolutionary biology needs a thorough rehaul (It doesn’t, for it’s not like “Darwin was totally wrong!”) And Buranyi takes great delight in couching the scientific debate about the importance of various factors in organismal evolution as “a culture war.” That’s nuts, it’s just a normal debate in science, and the outcome hinges on facts, not ideology.

Click to read the piece.

There’s simply too much to criticize and correct here, so I’ll take just five of Buranyi’s misguided claims.

a.) We don’t understand how important evolutionary features developed, like the eye. It’s true that we don’t know the exact sequence in which some complex adaptations developed, and we won’t because we weren’t there. But we do know from the fossil record about how whales evolved from terrestrial hoofed ungulates over about 10 million years, and we have the fossils to show it. Ditto for many other evolutionary transitions, like from fish to amphibians. But by using the eye, Buranyi resurrects the old (and refuted) creationist criticism that “how could an eye possibly evolve in a stepwise fashion from a simple light-sensitive spot?” The implication is that our ignorance of how this actually happened means that something’s seriously wrong with evolutionary theory.

Actually, this problem was first considered (and in principle solved) by Darwin, and discussed more extensively by Richard Dawkins in several places (e.g., here). No, we don’t know exactly how and when it happened, but eyes evolved independently several times, and we have a plausible sequence about how one can go, via an evolutionary sequence of small adaptive steps, from a light-sensitive eyespot to the complex “camera eye” of vertebrates and cephalopods. And, using estimates of parameters, we can show that there was plenty of time for this to happen via selection. If we can do that, with each step being adaptive (and in fact, actually seen in species living today), then the evolution of the eye is not a difficulty for simple Darwinism.

In fact, in 1994 Nilsson and Pelger published a paper showing that, with conservative assumptions about mutation rates and selection, you could model the evolution of a camera eye from a light-sensitive spot in a few hundred thousand years. If you want a precis, read Dawkins’s Nature article about the paper: “The eye in a twinkling.”

I discuss this in a bit of detail because Buranyi cites the eye as one of our insuperable evolutionary problems:

You may recall the gist from school biology lessons. If a creature with poor eyesight happens to produce offspring with slightly better eyesight, thanks to random mutations, then that tiny bit more vision gives them more chance of survival. The longer they survive, the more chance they have to reproduce and pass on the genes that equipped them with slightly better eyesight. Some of their offspring might, in turn, have better eyesight than their parents, making it likelier that they, too, will reproduce. And so on. Generation by generation, over unfathomably long periods of time, tiny advantages add up. Eventually, after a few hundred million years, you have creatures who can see as well as humans, or cats, or owls.

This is the basic story of evolution, as recounted in countless textbooks and pop-science bestsellers. The problem, according to a growing number of scientists, is that it is absurdly crude and misleading.

For one thing, it starts midway through the story, taking for granted the existence of light-sensitive cells, lenses and irises, without explaining where they came from in the first place. Nor does it adequately explain how such delicate and easily disrupted components meshed together to form a single organ. And it isn’t just eyes that the traditional theory struggles with. “The first eye, the first wing, the first placenta. How they emerge. Explaining these is the foundational motivation of evolutionary biology,” says Armin Moczek, a biologist at Indiana University. “And yet, we still do not have a good answer. This classic idea of gradual change, one happy accident at a time, has so far fallen flat.”

Both Buranyi and Moczek are dead wrong. We know about light-sensitive pigments, and we know they exist in microorganisms that can use them to detect the presence of light, which is itself adaptive.  The meshing of the various components has been modeled, and we can see every posited step in the process instantiated as an adaptation in one or more living species. What we don’t know is when and in which order things happened. Nevertheless, we see a plausible order in nature and we can model the process without difficulty. To say that “the classical idea of gradual change has fallen flat” is just (pardon my Spanish) caca de vaca. Does Buranyi think the eye appeared as a single “macromutation”? (More on that issue later.) So his distortions of history—he doesn’t mention, for instance, the paper of Nilsson and Pelger—begin at the article’s outset.

b.) Plasticity is a profound evolutionary problem that was neglected by evolutionary biology. Plasticity refers to the ability of an organism’s genome to respond to different environments in different ways (usually adaptive), either permanently or reversibly. We get tans when there’s too much sun, and this protects us from UV damage. Many mammals grow long hair in the winter and lose it in the summer.  Arctic mammals can turn white in the winter and brown in the summer as a means of camouflage. Rotifers and other small organisms grow fish-deterring spines if they develop in water containing fish, and plants can alter their form depending on where they’re growing.

We’ve known this for decades, so the evolution of plasticity is not something that’s stumped evolutionists. It’s easy to envision a genome that can respond to different environments in different ways. (One fantastic example is how the same genome can produce a caterpilllar and then a butterfly depending on the environment and time of development.) All that’s required for plasticity to evolve is that there be reasonable chances that an organism can find itself in different environments, i.e., a decent probability that you’d find yourself in environments, A, B, C, or so on.  Wild cats that live in environments that go from hot to cold over the year (or over altitude), would have greater reproduction if they had genes that could induce hair growth when the weather is cold and hair loss when it gets warmer. For arctic hares, the probability that the environment will be white in winter and green/brown in summer is 100%, but the probability that we’ll be out in the sun enough to get a tan is lower than 100%. But it doesn’t have to be 100% if enough people are out in the hot sun and could get melanoma. That’s enough to keep the tanning response encoded in our genome.

Indeed, plasticity can even reveal genetic variation that can be subject to selection; this idea of “genetic assimilation” was discussed and demonstrated eighty years ago.

Yet Buranyi sees plasticity as another startling non-Darwinian, mysterious, and neglected phenomenon. He’s wrong, though he gives some cool examples of plasticity. His words (my bolding):

One of the most fascinating recent areas of research is known as plasticity, which has shown that some organisms have the potential to adapt more rapidly and more radically than was once thought. Descriptions of plasticity are startling, bringing to mind the kinds of wild transformations you might expect to find in comic books and science fiction movies.

. . . Plasticity doesn’t invalidate the idea of gradual change through selection of small changes, but it offers another evolutionary system with its own logic working in concert. To some researchers, it may even hold the answers to the vexed question of biological novelties: the first eye, the first wing. “Plasticity is perhaps what sparks the rudimentary form of a novel trait,” says Pfennig. [JAC: Pfennig is just guessing here.]

Plasticity is well accepted in developmental biology, and the pioneering theorist Mary Jane West-Eberhard began making the case that it was a core evolutionary force in the early 00s. And yet, to biologists in many other fields, it is virtually unknown. Undergraduates beginning their education are unlikely to hear anything about it, and it has still to make much mark in popular science writing.

What is the new “logic” involved in plasticity? The evolution of plasticity, like the examples Buranyi gives, simply follows the logic of natural selection acting when there are environmental conditions or changes that can be encountered with some frequency. In such a case it pays for your genome to evolve flexible adaptive responses to different environments.

As for the claim that students aren’t exposed to this, well, it’s sure in the evolution textbooks. I just pulled Doug Futuyma’s 1998 (third edition) textbook Evolutionary Biology off my shelf (it’s the one I used when I taught introductory evolution), and, sure enough, there’s a whole section on plasticity and “norms of reaction”, as they used to be known. (A norm of reaction is simply when a given genome can respond to different environments by producing different phenotypes.) Doug’s book was published nearly 25 years ago, and the phenomenon was discussed at length by others long before that.

c.) Biologists have unduly neglected macromutationism: the idea that a complex feature can come into being in a single step.  This was indeed a discussion in the 1930s and 1940s, with scientists like Richard Goldschmidt proposing a “hopeful monster” hypothesis: that major evolutionary features could come into being via a single mutation that affected many systems at once. To Goldschmidt and his followers, “mutationism” was considered an alternative to natural selection.  Ernst Mayr once told me that he heard Goldschmidt make this remark: “I firmly believe that the first creature considered a bird hatched from an egg laid by a creature considered a reptile.” (That implies a huge step rather than a gradualistic evolution of reptiles into birds.)

Macromutationism, though briefly revived by Steve Gould as part of “punctuated equilibrium” (see below), eventually lost plausibility for several reasons. First, it’s unlikely that a mutation could occur that would create a complex feature (or a new group, like birds) in one step, for there’s a very low probability that a coordinated and cooperative set of features could arise in one step. In fact, although we can see big “homeotic” mutations in the lab (like an eye developing on a wing, or a leg as part of an insect mouth), these are developmental anomalies that are maladaptive. More important, genetic dissection of even minor phenotypic changes that have occurred in nature, like the shape of insect genitalia, have repeatedly shown them to be based on several mutations of small effect. We have virtually no evidence for mutations of large effect being important in evolution.

Of course, even macromutations have to obey the rules of population genetics, so even if one occurred, it could not spread through a species without natural selection to drive it. That means, of course, that “mutationsm” is not an alternative to selection!

Finally, we have the data. The fossil record documenting major changes, like the evolution of birds, whales, amphibians, hominins and the like, show no such “macromutations”: we see a gradual change in phenotype from ancestor to descendant with different traits showing up at different times. Of course mutations do vary in size, but I can’t point to a single adaptation in nature that requires us to postulate macromutations because the feature supposedly can’t be produced by a stepwise accumulation of smaller mutations. (This latter claim, by the way, is promulgated by IDers like Behe, who posit God instead of macromutations to bridge the gap.)

Yet Buranyi implies that macromutation, which died after a spirited scientific debate, is unduly neglected (my emphasis):

Even more ominous for Darwinists was the emergence of the “mutationists” in the 1910s, a school of geneticists whose star exponent, Thomas Hunt Morgan, showed that by breeding millions of fruit flies – and sometimes spiking their food with the radioactive element radium – he could produce mutated traits, such as new eye colours or additional limbs. These were not the tiny random variations on which Darwin’s theory was built, but sudden, dramatic changes. And these mutations, it turned out, were heritable. The mutationists believed that they had identified life’s true creative force. Sure, natural selection helped to remove unsuitable changes, but it was simply a humdrum editor for the flamboyant poetry of mutation. “Natura non facit saltum,” Darwin had once written: “Nature does not make jumps.” The mutationists begged to differ.

These disputes over evolution had the weight of a theological schism. At stake were the forces governing all creation. For Darwinists especially, their theory was all-or-nothing. If another force, apart from natural selection, could also explain the differences we see between living things, Darwin wrote in On the Origin of Species, his whole theory of life would “utterly break down”. If the mutationists were right, instead of a single force governing all biological change, scientists would have to dig deep into the logic of mutation. Did it work differently on legs and lungs? Did mutations in frogs work differently to mutations in owls or elephants?

. . . The modern synthesis was such a seismic event that even its flatly wrong ideas took up to half a century to correct. The mutationists were so thoroughly buried that even after decades of proof that mutation was, in fact, a key part of evolution, their ideas were still regarded with suspicion. As recently as 1990, one of the most influential university evolution textbooks could claim that “the role of new mutations is not of immediate significance” – something that very few scientists then, or now, actually believe. Wars of ideas are not won with ideas alone.

This gets everything wrong. It misses the evidence against “mutationism” and implies that “mutationists” simply emphasized that mutations are an important part of evolution—something that NOBODY DENIES. In fact, mutationists implied not only that mutations of very large effect are pivotal in evolution, but drive evolution without the need for natural selection. As we all know, mutation and selection are both important for adaptive evolution: mutations are the gas and evolution is the car. You can’t say that one is more important than the other. By giving a misleading account the history of biology here, and conflating “mutationism” with “the importance of mutations in evolution,” Buranyi has done the reader a huge disservice.

d.) Punctuated equilibrium was only about the pace and timing of evolutionary change.

Other assaults on evolutionary orthodoxy followed. The influential palaeontologists Stephen Jay Gould and Niles Eldredge argued that the fossil record showed evolution often happened in short, concentrated bursts; it didn’t have to be slow and gradual.

In fact, the real critique of evolutionary orthodoxy in Gould and Eldredge’s theory of punctuated equilibrium was the linking of a jerky pattern in the fossil record to a novel and almost non-Darwinian process, involving macromutations, evolution in isolated populations, the crossing of adaptive valleys via strong genetic drift, and then sorting out the variable groups via “species selection” instead of conventional Darwinian “genic selection.” While I have envisioned one form of species selection that operates in nature (see the last chapter of my book Speciation with Allen Orr), that process operates on rates of speciation to which characters are linked, but is neither identical to nor as ubiquitous as the process Gould postulated.

The failure of the various parts of Gould’s theory to work (including adaptive valley crossing via drift) was demonstrated by a number of experiments and pieces of theoretical work (see here and here); I summarized the failure and demise of Gould’s mechanistic theory here. I’m not sure if the “jerky” fossil record that gave rise to the postulated processes is still accepted as ubiquitous by paleontologists, but as for now, the reasons Gould and Eldredge advanced for such a pattern—the important attack on neo-Darwinism—are incorrect. (There are of course several causes for “jerky” evolution, including an incomplete fossil record or a jerky process of natural selection itself.)

e.) The scientific debate about the ambit of evolutionary biology is a “culture war.”  This bit really got my knickers in a twist:

To release biology from the legacy of the modern synthesis, explains Massimo Pigliucci, a former professor of evolution at Stony Brook University in New York, you need a range of tactics to spark a reckoning: “Persuasion, students taking up these ideas, funding, professorial positions.” You need hearts as well as minds. During a Q&A with Pigliucci at a conference in 2017, one audience member commented that the disagreement between EES proponents and more conservative biologists sometimes looked more like a culture war than a scientific disagreement. According to one attender, “Pigliucci basically said: ‘Sure, it’s a culture war, and we’re going to win it,’ and half the room burst out cheering.”

Bad call, Massimo! No, it’s not a culture war, even if sometimes scientists get heated and use terms like “evolution by jerks” to characterize advocates of punctuated equilibrium. The debate was conducted, and largely settled, by scientific argument that didn’t include that kind of acrimony. It is simply a debate about what mechanisms are important in evolution. My own view is that yes, the Modern Evolutionary Synthesis includes stuff that we didn’t even dream of 80 years ago (the “neutral theory” is one), but there is simply no reason to pronounce neo-Darwinism obsolete. “Expansion” is an okay word, but saying that “we need a new theory of evolution” is both ignorant and hyperbolic.

I could write for several days on the errors and distortions of Buranyi’s piece, but I’m tired. What’s given above is meant to serve merely as a few examples of the misguided nature of his article. What’s worse is that it misleads laypeople into thinking that there’s something seriously wrong with modern evolutionary theory. That itself could hearten creationists, and I’m sure the IDers are already lapping up the Guardian piece.