Douglas Futuyma, a biologist at Stony Brook University, defends the “Modern Synthesis” of evolution at the Royal Society earlier this month.

Tom Parker for Quanta Magazine

Douglas Futuyma, a biologist at Stony Brook University, defends the “Modern Synthesis” of evolution at the Royal Society earlier this month.

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Kevin Laland looked out across the meeting room at a couple hundred people gathered for a conference on the future of evolutionary biology. A colleague sidled up next to him and asked how he thought things were going.

“I think it’s going quite well,” Laland said. “It hasn’t gone to fisticuffs yet.”

Laland is an evolutionary biologist who works at the University of St. Andrews in Scotland. On a chilly gray November day, he came down to London to co-host a meeting at the Royal Society called “New Trends in Evolutionary Biology.” A motley crew of biologists, anthropologists, doctors, computer scientists, and self-appointed visionaries packed the room. The Royal Society is housed in a stately building overlooking St. James’s Park. Today the only thing for Laland to see out of the tall meeting-room windows was scaffolding and gauzy tarps set up for renovation work. Inside, Laland hoped, another kind of renovation would be taking place.

In the mid-1900s, biologists updated Darwin’s theory of evolution with new insights from genetics and other fields. The result is often called the Modern Synthesis, and it has guided evolutionary biology for over 50 years. But in that time, scientists have learned a tremendous amount about how life works. They can sequence entire genomes. They can watch genes turn on and off in developing embryos. They can observe how animals and plants respond to changes in the environment.

As a result, Laland and a like-minded group of biologists argue that the Modern Synthesis needs an overhaul. It has to be recast as a new vision of evolution, which they’ve dubbed the Extended Evolutionary Synthesis. Other biologists have pushed back hard, saying there is little evidence that such a paradigm shift is warranted.

This meeting at the Royal Society was the first public conference where Laland and his colleagues could present their vision. But Laland had no interest in merely preaching to the converted, and so he and his fellow organizers also invited prominent evolutionary biologists who are skeptical about the Extended Evolutionary Synthesis.

Both sides offered their arguments and critiques in a civil way, but sometimes you could sense the tension in the room — the punctuations of tsk-tsks, eye-rolling, and partisan bursts of applause.

But no fisticuffs. At least not yet.

Making Evolution as We Know It

Every science passes through times of revolution and of business as usual. After Galileo and Newton dragged physics out of its ancient errors in the 1600s, it rolled forward from one modest advance to the next until the early 1900s. Then Einstein and other scientists established quantum physics, relativity and other new ways of understanding the universe. None of them claimed that Newton was wrong. But it turns out there’s much more to the universe than matter in motion.

Tom Parker for Quanta Magazine

Audience members at the Royal Society’s “New Trends in Evolutionary Biology” conference.

Evolutionary biology has had revolutions of its own. The first, of course, was launched by Charles Darwin in 1859 with his book On the Origin of Species. Darwin wove together evidence from paleontology, embryology and other sciences to show that living things were related to one another by common descent. He also introduced a mechanism to drive that long-term change: natural selection. Each generation of a species was full of variations. Some variations helped organisms survive and reproduce, and those were passed down, thanks to heredity, to the next generation.

Darwin inspired biologists all over the world to study animals and plants in a new way, interpreting their biology as adaptations produced over many generations. But he succeeded in this despite having no idea what a gene was. It wasn’t until the 1930s that geneticists and evolutionary biologists came together and recast evolutionary theory. Heredity became the transmission of genes from generation to generation. Variations were due to mutations, which could be shuffled into new combinations. New species arose when populations built up mutations that made interbreeding impossible.

In 1942, the British biologist Julian Huxley described this emerging framework in a book called Evolution: The Modern Synthesis. Today, scientists still call it by that name. (Sometimes they refer to it instead as neo-Darwinism, although that’s actually a confusing misnomer. The term “neo-Darwinism” was actually coined in the late 1800s, to refer to biologists who were advancing Darwin’s ideas in Darwin’s own lifetime.)

The Modern Synthesis proved to be a powerful tool for asking questions about nature. Scientists used it to make a vast range of discoveries about the history of life, such as why some people are prone to genetic disorders like sickle-cell anemia and why pesticides sooner or later fail to keep farm pests in check. But starting not long after the formation of the Modern Synthesis, various biologists would complain from time to time that it was too rigid. It wasn’t until the past few years, however, that Laland and other researchers got organized and made a concerted effort to formulate an extended synthesis that might take its place.

The researchers don’t argue that the Modern Synthesis is wrong — just that it doesn’t capture the full richness of evolution. Organisms inherit more than just genes, for example: They can inherit other cellular molecules, as well as behaviors they learn and the environments altered by their ancestors. Laland and his colleagues also challenge the pre-eminent place that natural selection gets in explanations for how life got to be the way it is. Other processes can influence the course of evolution, too, from the rules of development to the environments in which organisms have to live.

“It’s not simply bolting more mechanisms on what we already have,” said Laland. “It requires you to think of causation in a different way.”

Adding to Darwin

Eva Jablonka, a biologist at Tel Aviv University, used her talk to explore the evidence for a form of heredity beyond genes.

Our cells use a number of special molecules to control which of their genes make proteins. In a process called methylation, for example, cells put caps on their DNA to keep certain genes shut down. When cells divide, they can reproduce the same caps and other controls on the new DNA. Certain signals from the environment can cause cells to change these so-called “epigenetic” controls, allowing organisms to adjust their behavior to new challenges.

Some studies indicate that — under certain circumstances — an epigenetic change in a parent may get passed down to its offspring. And those children may pass down this altered epigenetic profile to their children. This would be kind of heredity that’s beyond genes.

The evidence for this effect is strongest in plants. In one study, researchers were able to trace down altered methylation patterns for 31 generations in a plant called Arabidopsis. And this sort of inheritance can make a meaningful difference in how an organism works. In another study, researchers found that inherited methylation patterns could change the flowering time of Arabidopsis, as well as the size of its roots. The variation that these patterns created was even bigger than what ordinary mutations caused.

After presenting evidence like this, Jablonka argued that epigenetic differences could determine which organisms survived long enough to reproduce. “Natural selection could work on this system,” she said.

While natural selection is an important force in evolution, the speakers at the meeting presented evidence for how it could be constrained, or biased in a particular direction. Gerd Müller, a University of Vienna biologist, offered an example from his own research on lizards. A number of species of lizards have evolved feet that have lost some toes. Some have only four toes, while others have just one, and some have lost their feet altogether.

Tom Parker for Quanta Magazine

Sonia Sultan has shown that genetically identical organisms can be raised in such a way that they appear to be completely separate species.

The Modern Synthesis, Müller argued, leads scientists to look at these arrangements as simply the product of natural selection, which favors one variant over others because it has a survival advantage. But that approach doesn’t work if you ask what the advantage was for a particular species to lose the first toe and last toe in its foot, instead of some other pair of toes.

“The answer is, there is no real selective advantage,” said Müller.

The key to understanding why lizards lose particular toes is found in the way that lizard embryos develop toes in the first place. A bud sprouts off the side of the body, and then five digits emerge. But the toes always appear in the same sequence. And when lizards lose their toes through evolution, they lose them in the reverse order. Müller suspects this constraint is because mutations can’t create every possible variation. Some combinations of toes are thus off-limits, and natural selection can never select them in the first place.

Development may constrain evolution. On the other hand, it also provides animals and plants with remarkable flexibility. Sonia Sultan, an evolutionary ecologist from Wesleyan University, offered a spectacular case in point during her talk, describing a plant she studies in the genus Polygonum that takes the common name “smartweed.”

The Modern Synthesis, Sultan said, would lead you to look at the adaptations in a smartweed plant as the fine-tuned product of natural selection. If plants grow in low sunlight, then natural selection will favor plants with genetic variants that let them thrive in that environment — for example, by growing broader leaves to catch more photons. Plants that grow in bright sunlight, on the other hand, will evolve adaptations that let them thrive in those different conditions.

“It’s a commitment to that view that we’re here to confront,” Sultan said.

If you raise genetically identical smartweed plants under different conditions, Sultan showed, you’ll end up with plants that may look like they belong to different species.

For one thing, smartweed plants adjust the size of their leaves to the amount of sunlight they get. In bright light, the plants grow narrow, thick leaves, but in low light, the leaves become broad and thin. In dry soil, the plants send roots down deep in search of water, while in flood soil, they grow shallow hairlike roots that that stay near the surface.

Scientists at the meeting argued that this flexibility — known as plasticity — can itself help drive evolution. It allows plants to spread into a range of habitats, for example, where natural selection can then adapt their genes. And in another talk, Susan Antón, a paleoanthropologist at New York University, said that plasticity may play a significant role in human evolution that’s gone underappreciated till now. That’s because the Modern Synthesis has strongly influenced the study of human evolution for the past half century.

Paleoanthropologists tended to treat differences in fossils as the result of genetic differences. That allowed them to draw an evolutionary tree of humans and their extinct relatives. This approach has a lot to show for it, Antón acknowledged. By the 1980s, scientists had figured out that our early ancient relatives were short and small-brained up to about two million years ago. Then one lineage got tall and evolved big brains. That transition marked the origin of our genus, Homo.

But sometimes paleoanthropologists would find variations that were harder to make sense of. Two fossils might look in some ways like they should be in the same species but look too different in other respects. Scientists would usually dismiss those variations as being caused by the environment. “We wanted to get rid of all that stuff and get down to their essence,” Antón said.

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Andy Whiten, who studies the evolution of social learning and culture at the University of St. Andrews, takes it all in.

But that stuff is now too abundant to ignore. Scientists have found a dizzying variety of humanlike fossils dating back to 1.5 to 2.5 million years ago. Some are tall, and some are short. Some have big brains and some have small ones. They all have some features of Homo in their skeleton, but each has a confusing mix-and-match assortment.

Antón thinks that the Extended Evolutionary Synthesis can help scientists make sense of this profound mystery. In particular, she thinks that her colleagues should take plasticity seriously as an explanation for the weird diversity of early Homo fossils.

To support this idea, Antón pointed out that living humans have their own kinds of plasticity. The quality of food a woman gets while she’s pregnant can influence the size and health of her baby, and those influences can last until adulthood. What’s more, the size of a woman — influenced in part by her own mother’s diet — can influence her own children. Biologists have found that women with longer legs tend to have larger children, for example.

Antón proposed that the weird variations in the fossil record might be even more dramatic examples of plasticity. All these fossils date to when Africa’s climate fell into a period of wild climate swings. Droughts and abundant rains would have changed the food supply in different parts of the world, perhaps causing early Homo to develop differently.

The Extended Evolutionary Synthesis may also help make sense of another chapter in our history: the dawn of agriculture. In Asia, Africa and the Americas, people domesticated crops and livestock. Melinda Zeder, an archaeologist at the Smithsonian Institution, gave a talk at the meeting about the long struggle to understand how this transformation unfolded.

Before people farmed, they foraged for food and hunted wild game. Zeder explained how many scientists treat the behavior of the foragers in a very Modern Synthesis way: as finely tuned by natural selection to deliver the biggest payoff for their effort to find food.

The trouble is that it’s hard to see how such a forager would ever switch to farming. “You don’t get the immediate gratification of grabbing some food and putting it in your mouth,” Zeder told me.

Some researchers suggested that the switch to agriculture might have occurred during a climate shift, when it got harder to find wild plants. But Zeder and other researchers have actually found no evidence of such a crisis when agriculture arose.

Zeder argues that there’s a better way of thinking about this transition. Humans are not passive zombies trying to survive in a fixed environment. They are creative thinkers who can change the environment itself. And in the process, they can steer evolution in a new direction.

Scientists call this process niche construction, and many species do it. The classic case is a beaver. It cuts down trees and makes a dam, creating a pond. In this new environment, some species of plants and animals will do better than others. And they will adapt to their environment in new ways. That’s true not just for the plants and animals that live around a beaver pond, but for the beaver itself.

When Zeder first learned about niche construction, she says, it was a revelation. “Little explosions were going off in my head,” she told me. The archaeological evidence she and others had gathered made sense as a record of how humans changed their own environment.

Early foragers show signs of having moved wild plants away from their native habitats to have them close at hand, for example. As they watered the plants and protected them from herbivores, the plants adapted to their new environment. Weedy species also moved in and became crops of their own. Certain animals adapted to the environment as well, becoming dogs, cats and other domesticated species.

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Denis Noble now sees a need for an Extended Evolutionary Synthesis.

Gradually, the environment changed from sparse patches of wild plants to dense farm fields. That environment didn’t just drive the evolution of the plants. It also began to drive the cultural evolution of the farmers, too. Instead of wandering as nomads, they settled down in villages so that they could work the land around them. Society became more stable because children received an ecological inheritance from their parents. And so civilization began.

Niche construction is just one of many concepts from the Extended Evolutionary Synthesis that can help make sense of domestication, Zeder said. During her talk, she presented slide after slide of predictions it provides, about everything from the movements of early foragers to the pace of plant evolution.

“It felt like an infomercial for the Extended Evolutionary Synthesis,” Zeder told me later with a laugh. “But wait! You can get steak knives!”

The Return of Natural Selection

Among the members of the audience was a biologist named David Shuker. After listening quietly for a day and a half, the University of St Andrews researcher had had enough. At the end of a talk, he shot up his hand.

The talk had been given by Denis Noble, a physiologist with a mop of white hair and a blue blazer. Noble, who has spent most of his career at Oxford, said he started out as a traditional biologist, seeing genes as the ultimate cause of everything in the body. But in recent years he had switched his thinking. He spoke of the genome not as a blueprint for life but as a sensitive organ, detecting stress and rearranging itself to cope with challenges. “I’ve been on a long journey to this view,” Noble said.

To illustrate this new view, Noble discussed an assortment of recent experiments. One of them was published last year by a team at the University of Reading. They did an experiment on bacteria that swim by spinning their long tails.

First, the scientists cut a gene out of the bacteria’s DNA that’s essential for building tails. The researchers then dropped these tailless bacteria into a petri dish with a meager supply of food. Before long, the bacteria ate all the food in their immediate surroundings. If they couldn’t move, they died. In less than four days in these dire conditions, the bacteria were swimming again. On close inspection, the team found they were growing new tails.

“This strategy is to produce rapid evolutionary genome change in response to the unfavorable environment,” Noble declared to the audience. “It’s a self-maintaining system that enables a particular characteristic to occur independent of the DNA.”

That didn’t sound right to Shuker, and he was determined to challenge Noble after the applause died down.

“Could you comment at all on the mechanism underlying that discovery?” Shuker asked.

Noble stammered in reply. “The mechanism in general terms, I can, yes…” he said, and then started talking about networks and regulation and a desperate search for a solution to a crisis. “You’d have to go back to the original paper,” he then said.

While Noble was struggling to respond, Shuker went back to the paper on an iPad. And now he read the abstract in a booming voice.

“‘Our results demonstrate that natural selection can rapidly rewire regulatory networks,’” Shuker said. He put down the iPad. “So it’s a perfect, beautiful example of rapid neo-Darwinian evolution,” he declared.

Shuker distilled the feelings of a lot of skeptics I talked to at the conference. The high-flying rhetoric about a paradigm shift was, for the most part, unwarranted, they said. Nor were these skeptics limited to the peanut gallery. Several of them gave talks of their own.

“I think I’m expected to represent the Jurassic view of evolution,” said Douglas Futuyma when he got up to the podium. Futuyma is a soft-spoken biologist at Stony Brook University in New York and the author of a leading textbook on evolution. In other words, he was the target of many complaints during the meeting that textbooks paid little heed to things like epigenetics and plasticity. In effect, Futuyma had been invited to tell his colleagues why those concepts were ignored.

“We must recognize that the core principles of the Modern Synthesis are strong and well-supported,” Futuyma declared. Not only that, he added, but the kinds of biology being discussed at the Royal Society weren’t actually all that new. The architects of the Modern Synthesis were already talking about them over 50 years ago. And there’s been a lot of research guided by the Modern Synthesis to make sense of them.

Take plasticity. The genetic variations in an animal or a plant govern the range of forms into which organism can develop. Mutations can alter that range. And mathematical models of natural selection show how it can favor some kinds of plasticity over others.

If the Extended Evolutionary Synthesis was so superfluous, then why was it gaining enough attention to warrant a meeting at the Royal Society? Futuyma suggested that its appeal was emotional rather than scientific. It made life an active force rather than the passive vehicle of mutations.

“I think what we find emotionally or aesthetically more appealing is not the basis for science,” Futuyma said.

Still, he went out of his way to say that the kind of research described at the meeting could lead to some interesting insights about evolution. But those insights would only arise with some hard work that leads to hard data. “There have been enough essays and position papers,” he said.

Some members in the audience harangued Futuyma a bit. Other skeptical speakers sometimes got exasperated by arguments they felt didn’t make sense. But the meeting managed to reach its end on the third afternoon without fisticuffs.

“This is likely the first of many, many meetings,” Laland told me. In September, a consortium of scientists in Europe and the United States received $11 million in funding (including $8 million from the John Templeton Foundation) to run 22 studies on the Extended Evolutionary Synthesis.

Many of these studies will test predictions that have emerged from the synthesis in recent years. They will see, for example, if species that build their own environments — spider webs, wasp nests and so on — evolve into more species than ones that don’t. They will look at whether more plasticity allows species to adapt faster to new environments.

“It’s doing the research, which is what our critics are telling us to do,” said Laland. “Go find the evidence.”

Correction: An earlier version of this article misidentified the photograph of Andy Whiten as Gerd Müller.

This article was reprinted on TheAtlantic.com.

 

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  • In general this is a well-presented article. However, we see that a disproportionate number of workers are still embedded in the now obsolete paradigm that wa propagated in the seventies in the epidemic of "gene fever" that occurred in the wake of the elucidation of the structure of DNA. A gross over-simplification which sadly is uncritically accepted by most even today.

    The crucial aspect which is regularly overlooked or glossed over is that the "turning on" or "turning off" of a gene is a function of the cell and not directly attributable to the genome itself.

    The very common notion that "DNA creates the organism" is very wrong. Implications of this kind can all too easily help propagate the myth that morphogenesis and structural and behavioral changes are driven by the gene (or group of genes) rather than by of the overall evolutionary network.

    It is important to bear in mind that the genome is merely a rather small library of protein recipes. It is entirely passive. It is actively manipulated, maintained and accessed by RNA and other cellular machinery.

    Machinery that is directly inherited, complete with RNA, organelles, the transcriptome, and all other structures required for function. All as a result of cell division. DNA being merely a rather small reference library that is accessed for instructions for the manufacture of “spare parts”.

    In my writings, I employ the analogy of a piano to represent DNA. The piano itself is entirely passive, as is DNA. But a pianist can produce innumerable musical variations by using this passive array of strings.

    In biology, the pianist corresponds to the machinery of the cell together with the inputs from its environment. Some of which control differentiation.

    Biological evolution is, after all, a network function.

    The network model of inheritance and morphogenesis is explored more fully in my latest book "The Intricacy Generator: Pushing Chemistry and Geometry Uphill".
    Also of crucial relevance to this topic is Franklin M Howard's excellent "The Way of The Cell"

  • This was a fantastic read! I am excited to share this with my AP Biology students to illustrate that science is a process.

  • I'm very very disappointed with the RS meeting "New Trends in Evolutionary Biology". Reason? In the first chapter of the book “The Extended Synthesis” editors Gerd Müller and Massimo Pigliucci explained that the new synthesis (EES) overcomes the Modern Synthesis in three basic points:

    Gradualism:
    “The dynamics of biological systems illuminates the capacity of continuous selectional regimes to produce the nongradual phenotypic change frequently observed in the paleontological record.” (p. 13)

    Externalism:
    Instead of giving priority to all external factors and natural selection alone as the main cause of biological novelties the EES considers that “the specificity of its phenotypic outcome is provided by the developmental system it operates on. Hence the organisms themselves represent the determinants of selectable variations and innovation.” (p. 13)

    Gene-centrism:
    “Gen centrism necessarily disappears in an extended account that provides for multicausal evolutionary factors acting on organismal systems´ properties, including the non programmed components of environment, development and inheritance.” (p. 14)

    If one overcomes gradualism, the central role of natural selection and gene centrism in creating new phenotypic traits, as far as Darwinism is concerned, what have we got left? And what about information? I wish these scientific points were fully discussed on the RS meeting. A new general theory of evolution needs to replace the Modern Evolutionary Synthesis.

  • natural selection works on variations in the genetic code and evolution is merely the necessary time dimension (the infinite 'while loop' around the algorithm).

  • ctnd.

    Many of the examples above have to do with the plasticity of how organisms use the genetic code. An example of this plasticity is epigenetic inheritance. This plasticity can take extreme forms (biologists have many examples of this), but the molecular mechanisms behind this plasticity are all the result of the same core algorithm that is natural selection.

    In that view, that I hold as well, I stand with the crowd that sees no necessity for a paradigm shift.
    I have no problem with the name 'Extended Evolutionary Synthesis' as long it is clear that it doesn't replace anything, but at best adds new mechanistic (molecular) insights.

    These new mechanisms are amazingly complex strategies developed by natural selection to increase the dynamic range of organisms to cope with environmental changes (stresses) and thereby increase their fitness.

  • @ Kevin P: it is. everything that was described only 'adds' to it. The debate is whether those additions can be called a 'paradigm shift'. Since the discovery of genes etc. the molecular mechanisms of evolution became clear. We continbued to see more and more details of the picture, and you can imagine the picture is becoming very rich and complex.

  • Im not seeing the need for any paradigm shift. Genes have a tool box and it contains various tools to respond to particular variables.

    Also, this is not much of an issue in science. Interesting but most research is addressing be minutia of nitty gritty details confined to small fragments of biology. I've been in paleontology for 46 years and evolution is not a topic. We look at biostratigraphy but is is, again, at a complete practical 'habds on' level.

  • Ii hold the degree of M.D. (ret), now a retiree at rest. I have a bit of formal grounding in the classical biological sciences and the molecular sciences, at least as they apply to heredity, disease, and the practise of medicine. When I was in school in the 60's and 70's Watson and Crick were front page news. Mendelian genetics (with 'variable penetrance') was standard. The explanation of life itself suddenly seemed to become creepily approachable and even strangely mundane. My teaching had been that base particles follow random hyperactive 'Brownian Motion' and that in the penultimate analysis all systems run down to maximum randomness and minimum energy over time. And yet, from the soup of steamy primordial and putrid chaos there self-assembled hydrocarbons, and then previable organic substrates, and then self-assembling amino acids, followed by self-assembling proteins, which then led to self-assembling RNA which led finally to faithfully replicating and self-assembling DNA…..etc….it occurred to me that there was an awful lot of self-assembling going on. I don't hear it much talked about.

  • The Russian scientists heard of Lamarck and based their understanding of evolution on Lamarck's theory while also accepting concepts from Darwin. Sometimes, it seems like certain knowledgeable people are very concerned that anyone who does not agree with their ideas should not be acknowledged, so they refuse to investigate other possibilities. Due to recent studies, many hardheaded scientists are now forced to accept some of Lamarck's concepts without, of course, giving Lamarck any credit for what he understood over 200 years ago.
    In conclusion, neither Charles nor Chevalier got it perfectly correct and neither has anyone else; therefore, Lamarck should be given credit for describing the first reasonable theory of evolution. Before him the entire Earth had only been around for about 6,000 years.

  • @ Peter Kinon,

    "The crucial aspect which is regularly overlooked or glossed over is that the "turning on" or "turning off" of a gene is a function of the cell and not directly attributable to the genome itself"

    Actually the "crucial aspect which is regularly overlooked or glossed over is that" the regulatory proteins that turn genes on and off are coded for in the genome itself and got there by the ordinary Darwiniwn processes of random mutation and natural selection.

    "In my writings, I employ the analogy of a piano to represent DNA. The piano itself is entirely passive, as is DNA. But a pianist can produce innumerable musical variations by using this passive array of strings"

    Your analogy fails. Unless you are suggesting that the piano strtings contain all the inofrmation to produce the pianist.

    "The network model of inheritance and morphogenesis is explored more fully in my latest book "The Intricacy Generator: Pushing Chemistry and Geometry Uphill""

    I'm mot sure how this got past moderation. Quote: " Comments that are…self-promotional…will be rejected"

  • @William Dobni

    "it occurred to me that there was an awful lot of self-assembling going on. I don't hear it much talked about"

    You haven't heard much talk about Physics and Chemistry then?

  • The author, Carl Zimmer, is one of the most respected science popularizers writing on evolution today. That's why an extensive article he wrote on human blood types made such a strong impression on me. The article explained very clearly the difficulties in demonstrating the adaptive benefits of human blood groups, while noting the remarkable existence of the "Bombay" variation.

    The article did not explain the possibility that blood types are random variations. This article does not address is the issue of whether the current version of evolution merely gives lip service to the notion of random variation, while in practice taking a panadaptionist default. I suppose that's unsurprising given Mr. Zimmer's own problems in this regard. It seems to me a more objective view of the dissidents would note that most of these views are problems for panadaptationism, or the closely related gene selectionist perspective.

    If natural selection is the major force conserving the morphology of species, as appears to be the case, then adaptationism will always have an enormous role in evolutionary biology of variations in gene frequencies. It is entirely unclear why the Zimmers have such difficulty in thinking about the specific weight of natural selection in the multiplication of species.

  • Great article. I keep articles like these in a special file just to read and re-read.

    I am reminded of S.J. Gould's "The Structure of Evolutionary Theory" and how it was described by Gould during an interview with Charlie Rose as not an 'end point in Gould's thinking, but merely a way point' in the journey, thus, capturing the essence of the book's beautifully portrayed competing arguments between Hugh Falconer and Charles Darwin each using the Duomo as his metaphor!

  • The description of the discussion of my talk at the RS-BA meeting is seriously incorrect. The central point of my lecture was that organisms harness stochastic mutations in variable locations in their genomes to generate functionality. I gave clear examples of this in the immune system and in bacteria where such targeted functional stochasticity is common. The questioner could not have been listening to my lecture. To quote my abstract "Stochasticity at low levels does not therefore exclude order at higher levels. Organisms enlist stochasticity in their development of functional behaviour"

    Denis Noble

  • “I think what we find emotionally or aesthetically more appealing is not the basis for science,” Futuyma said.

    Of course. And yet, these feelings made it into the discourse, asserting their influence, (constructing a niche). Is this not a case in point? If they really are irrelevant, why mention them at all? It's a myth to think such human qualities of thought are somehow immune to natural science. There are higher-order influences acting on biology even if biologists aim to avoid them for cultural reasons. Just sayin.

  • Where exactly does plasticity end and evolution begin?

    How do we know something evolved as opposed to adapt?

  • DARWIN'S RESEARCH ASSOCIATE'S 1897 SOLUTION

    Beginning with an address to the Linnean Society four years after the death of his mentor, Darwin's research associate, George Romanes, developed a view of evolution that is recognized neither by the modern synthesists nor the extended evolutionary synthesists. His clearest account is the third volume of his series entitled "Darwin, And After Darwin" (1897). While adopting this view in a 1980 paper (without citation), Stephen Jay Gould relinquished it in his 2002 magnum opus. However, both before and after Gould's sadly premature demise in 2002, considerable evidence supporting Romanes view has accumulated.

  • @Kevin P
    There *is* no "settled science".
    That is part of what makes it science.
    Settle anything and it becomes dogma, which is the opposite of science.
    I cannot think of any scientific discovery or advance that didn't raise more questions than it answered, whether in evolution or anything else.
    Please understand that that does not mean that they are neither discoveries nor advances, but that they reveal more things to understand about a world of which our view still are very superficial, and give us more power to influence the world we live in. If we cannot manage that desirably, it is no good blaming principles of science, settled or unsettled, nor scientifically discovered principles, processes or products — the fault lies in ourselves.

  • Amazing that it is Carl Zimmer who wrote this article! While I much enjoy his writings (articles in NY Times and National Geographic, and book) I have long considered him a solid, non-imaginative, non-visionary conformist of Darwinism (or Adaptationism) who mostly just regurgitates the concepts of the Modern Synthesis in elegant and pedagogically useful prose – notably when reporting on new findings that fit the Darwinian orthodoxy. But the biosphere is full of phenomena that call for the extension – we are collectively blinded to those.

    Thus, it is refreshing to see how Dr. Zimmer is opening his mind in this report. Of course he is now a journalist and not a scientist.

    The believe that every biological trait we observe is the result of pure Darwinian adaption (random inheritable variation and selection) is absurd. (It assumes that evolution is an ergodic process which it is not). Yet it is the orthodoxy in biology. Dissent is considered blasphemy at worst, and silenced at best. Many a scientific career has suffered from this.

    At the single -cell level, such as in micro-organism and during somatic evolution of cancer cells, where there is no germline/soma separation, mechanisms abound that could explain directed or biased mutations. The “Neo-Darwinists” suppress these concepts that extend (but do not refute) the Modern Synthesis, at their own peril. (Except in cancer therapy and antibiotics research where patients are the victims: the continuing dominance of the Neo-darwinian view prevents new strategies in combating therapy resistance that develops so rapidly (sometimes within 2 generations) that cannot be explained by random mutations).

    But whence the rigid adherence to Darwinian adaptationism (or the Modern Synthesis)?? I suspect a dark psychological force at play which the human mind is heir to: Darwinian adaptation allows us to see a PURPOSE in all these traits – a concept that is taboo in evolution and that belongs to the realm of religion. Even if one explains the origin of a trait by separating it into the two steps of RANDOM variation, which is naturally purpose-FREE, and selection.

    Despite the emphasis on the purposelessness of RANDOM mutations, the adaptationists’ blind believe in the force of SELECTION opens a backdoor for PURPOSE to creep back in…. Purposefulness is a central element of religions –for it ultimately explains the existence of a designer behind creatures. Hence, ironically, to Darwinists, natural selection is essentially THE intelligent designer of the creationists. No wonder Richard Dawkins, the ultra-adaptationist, proselytizes evolution biology and atheism with religious fervor.

    Anyway, great, balanced article by an unlikely author.

  • Great to see the comments here by two of my heroes:

    Donald Forsdyke (Book: "Treasure your Exceptions", with great chapter on Romanes)
    and
    Denis Noble (must-read book for all students with courage to see beyond neo-Darwinism and Genes: "Music of Life")

  • In many ways I find the discussion very unsatisfactory; I get the impression (by now long-standing) that workers in various fields discover things that do not fit into the textbooks of yesteryear, or for that matter yestercentury, and conclude that their content is thereby negated. By way of analogy this is like arguing that because Newtonian physics superseded Galilean physics, it had banished friction and Galileo's work in general. And yet, in spite of Newton's laws of motion, it had done nothing of the type; it had merely broadened our view.
    Darwin didn't invent evolution and did not pretend to have done so; he had clarified views on the origin of species, and established the principle of natural selection as a crucial and central mechanism, and had done a huge amount of other work of great value.
    He knew that there was much that needed explaining, and after his death, amid much confusion gene-based genetics was integrated with natural selection to give the then "modern synthesis". Please note that it only was a synthesis in the sense that it united opposing schools of thought. In terms of scientific progress it was mainly an event of adding the discovery of the gene to the mechanism of what? Of natural selection, which still was where it started from when Darwin had established it. Barely a decade later nucleic acid molecular biology created an equally great upset, not by evicting either genetics or natural selection, but by clarifying mechanisms that had thitherto been largely mystical and empirical. This time no one needed to apply a term to the evolution revolution, though there was muttering about "neoDarwinism" etc.
    And then? Introns, jumping genes, lateral gene transfer, endosymbiosis, modifiers, non-junk junk DNA, degrees of gradualism, CRISPRs you name it…
    But none of those invalidated earlier knowledge, they just amplified it and especially amplified the perspective. Imagine someone who had leaned to steer a car, but had never seen what makes a car tick; He naturally thinks that the steering wheel is how a car works. One day he sees that the steering wheel is not the only wheel. This teaches him that there is more to the car than steering. Does he experience a new need to call it a "car"? Does he need yet another new name when he discovers brakes and engines?
    Biology is a great deal more complex than a car and evolution is a great deal more complex than natural selection, and I doubt that any members of the audience at the meeting generally doubted each other's factual material to a great extent, but the time to start worrying about renaming disciplines is when we have new perspectives that invalidate earlier ideas, rather than just elaborating them.
    That might not be important in itself, not so much arguing about angels on pins, as whether they dance on the point or the head, but what irks me is that every time someone conflates epigenetic mechanisms with Lamarckism, or demonstrates lateral gene transfer or the like, then TV evangelists crawl out of the woodwork explaining that "Darwinism" is exploded, when they clearly do not even understand the topic, let alone the implications of the work.
    "Extended Synthesis" indeed!

  • @Enezio E. de Almeida Filho
    The wearying failure to recognise punctuationism as an admittedly important, but not fundamentally different aspect of gradualism, has outlived any excuse for its continued existence. In nineteenth-century biology biologists appealed abjectly "very gradual changes" and "huge expanses of time" and imperfections in the fossil record, but that was only reasonable in the paucity of their contemporary knowledge. We still know far too little, but our understanding is based at least on a broader knowledge and on underlying mechanisms and principles. To amount to anything different from gradualistic natural selection, punctuationism either would have to involve a new causal theory or a new operational principle. It did neither. Even in pre-genetic days, Darwin et al recognised the concept of drastic mutations and hopeful monsters, so abrupt changes were not excluded, and in fact their role in punctuation is no different. Other views of natural selection and adaptation were not affected, except in the recognising the importance of long periods of comparative status between punctuation events, and the plethora of radiations, largely short-term, around the events. But the events themselves are strictly Old-Darwinian. They would not have required major adjustments of the theory even in Darwin's day, let alone the 20th century. Back in the seventies, when I first read about speciation in Lake Turkana molluscs, I was deeply impressed until I reached the point where they discussed the duration of the punctuation events: 5000 to 50000 years!!!!! Yes, palaeontologically that is an eye-blink, but evolution is not palaeontology; biologically, in particular adaptationally, it is a long, long time.
    In short, what they had demonstrated was perfectly ordinary gradualism.
    And on the basis of such we are to reject evolutionary theory?
    Or even rename it?
    I hardly think so!

  • @Enezio E. de Almeida Filho

    On Externalism
    You quote:
    'Instead of giving priority to all external factors and natural selection alone as the main cause of biological novelties the EES considers that “the specificity of its phenotypic outcome is provided by the developmental system it operates on. Hence the organisms themselves represent the determinants of selectable variations and innovation.” '

    Forgive me for pointing out that this isn't even coherent. It is a classic "Aunt Sally" argument, inventing the opposing point of view to suit one's attack. Even in the first edition of "The modern Synthesis" back in the 1940s, Huxley (J.) began with stating that Darwin had based his theory on three observations and two deductions. Of those he mentioned, the first and third implicitly recognised the nature of the populations subject to selection. Even if he had not done so, there is no way that one can talk meaningfully about selection, natural or otherwise, unless there not only is something to select from, but also some criterion according to which to select. Some basis for adaptation, if you like.
    Otherwise there simply isn't selection.
    You see?
    To omit *either* from the process and relationship, so dramatically fails to make sense, that it probably never would have occurred to anyone to "give priority to all external factors and natural selection alone" (which incidentally would be an eccentric use of the word "priority"; perhaps they would like to reword the claim in the next edition) any more than it would have occurred to them to adapt elephants by applying selection to roses. Of course the attributes of the subject organisms are crucial; that is what the selection works from.
    This is supposed to be an obscure and novel point? Surely not?
    I can hardly believe that they said anything like: "the organisms themselves represent the determinants of selectable variations and innovation". Far from being cogent, that omits one of the two essential elements of selection, whether "natural" or "artificial".
    And even if that is not what they had intended to convey, it still would not invalidate the prevailing body of work, whether that body is in any other way invalid or not.
    That is so far from making sense that I am sure you must have made a slip in your wording or choice of reference material, but although I sympathise, I must leave it to you to make your own corrections, for fear of distorting your thesis.

  • @Enezio E. de Almeida Filho

    On gene centrism
    This is another Aunt Sally. Darwin got along very nicely thank you, without any clear concept of the gene whatsoever. de Vries, Correns et al introduced the concept to evolution, also without much idea of what a gene might be. The one-gene-one-protein proposal was hardly more than an intelligent shot in the dark in the 1940s, but it too worked excellently for years. That it was simplistic, was hardly relevant in context.
    Molecular biology and its consequences has muddied the water, so that at present, although we have examples of genes, we lack any coherent, universal and cogent useful definition for a gene. Also, elementary information theory has rubbed a lot of noses in the various clandestine channels by which heritable information may be passed between generations or even between genetically unrelated associates, but that has nothing to do with Darwinism of any particular flavour, let alone scouting or redefining the discipline.

    I suggest that you reconsider the idea that Darwinism as she is spoke has much in any way to do with gene centrism as such. Darwinism deals with selection pressures and heritable attributes, and it did so even in the days of Darwin, never mind Huxley or Crick and Watson.

  • @Denis Noble,

    "The central point of my lecture was that organisms harness stochastic mutations in variable locations in their genomes to generate functionality"

    But how do organisms do this? How else but through their DNA? (What other mechanism is there?).
    In other words, the ability of organisms to "harness stochastic mutations in variable locations in their genomes" is coded for in their DNA. And it got there by the ordinary process of random mutation and natural selection. Of course, "random" does not mean "completely" random. Mutations are constrained by the laws of physics and chemistry…and by the contraints coded for in the DNA, and which got there by the ordinary process of random mutation and natural selection.

  • Biologists studying the evolution of the horse in the Holarctic, primarily in North America, discovering the variety of size and shapes in the modern horse, Equus caballus, believe one of the factors that confused early paleontologists when they tried to classify the newly found discoveries is the plasticity of the species. They theorized that the size of the horse was influenced by the type of environment that existed where the horse was born. For example, horses born 700,000 yrs ago in Alaska were much larger than the ones found in Alaska during the time the last period of rapid, abrupt global warming occurred. These horses, sometimes referred as Equus alaskae or Equus lambei are, in fact, members of the species Equus cabals, a species that evolved in N. America 1.7 million years ago. Because the horse left so many fossils here in North America that include not only the first horse ancestors, but also all of the many multiple species of horse that existed in N. America. There was a reason Darwin favored the horse as an example to explain evolution, but he did not get it all right. There was no straight line in horse evolution, but lots of shrubs with families and branches of families. The final genera that exists is Equus. There is Equus bruchelli, the modern zebra; Equus asinuss, or the donkey, and the modern horse, Equus caballus.

    Interestingly, none of the comments above discussed the possibility that the environment might be the trigger that turns some genes to turn off and others to turn on. In horse, for example, the weight and thickness of the horses' coat is not determined until the last 24 to 48 hours before birth. Horses born in colder, damper climates have heavier coats than horses born in warmer, drier climates. Furthermore, when one begins to look at the places where these horses chose as their habitat or refugia during climate climate extremes. Studying the factors that led to the emigration, transitions from one continent to another during times of climate change and the transition between stadial periods and interstadial times would do a lot to inform your understanding of evolution. Scientists have recently been able to tie the period when horse and other large mammals disappeared from North America to the arrival of humans and the coinciding abrupt & sudden rise in post-glacial temperatures. The land mass known as Berengia, that connected North America to Siberia provided low lying coastal grasslands for Mammoth, Mastadon's, Musk Ox and horses. The rapid warming that occurred after the
    Little Ice Age as well as the last major glaciation covered Berengia, (land that was nearly the size of Texas). The sea rose some 400 to 450 feet and there is no trace that there was ever any Berengia there.

    It is not true and is also true that the horse became extinct in N. America. It is true in the sense that the ones who did not get to the coast of Alaska before the water rose were trapped in Alaska. We know they survived until some 7,600 yrs. ago. Nonetheless, if the horses hadn't sensed the need to find refugia in Siberia and then moved on to Europe and Africa, the horse may well have become extinct.

    Scientists remark that even though horse emigrated from N. America to Europe or Siberia, the horse always returned to North America after the climate crisis or food crisis if you look at it through the eyes of a horse, and had the Spanish not intervened would return again when the climate changes tell them it is time.

    A good book to read on horse evolution that ties the horse changes to changes in the environment is The Rise of the Horse: 55 Million Years of Evolution, by Dr. Jens Lorenz Franzen. Another book written by the late Harvard biologist Steven Gould, Bully for Brontosaurus includes the story of horse evolution in the chapter, "Life's Little Joke."

    My study of the horse and study of the words used by those scientists in the field and in the lab leads me to the conclusion that many people have had difficulty getting their heads around the idea that the horse did most of its evolving in N. America because the first modern horse fossil was discovered in Sweden by none other than Carlos Linnaeus himself about 1750. The fossil was a horse's head, and the species name "caballus" was chosen due to the distinctive differences in the length of the molars, but also a special dentition. For years, mammals trotted around the arctic circle crossing at various locations based on the location of islands and depth of the ocean (horses are good swimmers).

    Which organisms are most likely to survive change? Those who able to adapt. The modern horse certainly exemplifies this ability through its ability to adapt to different environments and to survive on food that might not exist in nature in the form it is fed to them by humans.

  • One of the great delights to the layman in reading Darwin's "Origin" is to come back to it with the the examples and footnotes which are found in "Charles Darwin's Natural Selection: Being The Second Part Of His Big Book Written From 1856 to 1858" Edited By R.C. Stauffer. (1975). And while the commentary to this article reminds me of how much fun and informative it is to read the 'back and forth' between experts and academic rivals about what Darwin meant in the "Origin" it is in many ways more informative to read the footnotes and see the examples Darwin actually used.

  • I grow weary of two terms so often cited in evolutionary discussions that to me are either/both ill-defined and poorly understood: "random mutation" and "natural selection". Random mutations is an illusionary process. Without mutations in the genetic code, among all of the other types of genetic modifications that exist, evolution would grind to a halt as there must be diversity "thrown out" into the wild for organisms to exist. I much prefer the term "planned randomness" as a description of the inefficiency of DNA replication. A perfect copy of inherited traits leaves no choices, no diversity and no ability to adapt. The "random mutations" discussed are inherent to the evolutionary process, but by no means are they merely random events; they are a planned process.
    As for "natural selection, this term is bandied about to explain every adaptation from the color of fish on coral reefs to leaf size and shape as though every living part of every living organism is a matter of "fitness by natural selection". If this were so, why is there incredible diversity and not just a few "fit" species that dominate all life. If something is alive, it obviously must be fit. Sometimes fitness is not the driving force, but rather the idea that the organism or trait simply "works". This may be splitting hairs, but I have read the words "natural selection" so may times that it appears to be the explanation for everything. The real play-maker is diversity, as choices must come first.
    Natural selection is also way too broad a term to be used the sole descriptor for diversity. There is selection of both phenotypes and genotypes and this rarely if ever clarified. Natural selection could be caused by a volcano, a meteorite, a flood, a hot dry summer or the introduction of a retrovirus into a genome. To the evolutionary specialists, please refine the term "Natural Selection" as well as point out literature that may elucidate the trouble I have with the terminology.
    Again, thanks to Quanta for these articles that lead to much discourse and should I dare say to the "evolution of diversity of thought and opinion".

  • I'm glad to see that this article, unlike the report that referred me to it (http://bigthink.com/robby-berman/how-about-new-theory-of-evolution-with-less-natural-selection
    How About a New Theory of Evolution with Less Natural Selection?
    November 28, 2016 by ROBBY BERMAN) brings up the key role of mutation in the Modern Synthesis. The big question that science seeks to elucidate concerning evolution is not the readily-observed shifts in alleles (or their developmental effects) within populations, but how did this process drive the basic original single-celled ancestors over countless generations to produce all the systematically organized dynamic complexity of living things, from the molecular machines even in bacteria to all the various organs, limbs, and systems within macroscopic, multi-cellular life with a dizzying variety of sexual reproduction methods?

    Unfortunately, that seems to get overlooked in these petty squabbles between the hidebound establishment and the excited tinkerers. Even with talk of a "paradigm shift," nothing even approaching the surprises and adjustments made from Newtonian physics to Einstein's relativity theories and quantum physics is being considered. In a real shake-up, there would be more questioning if a truly large change in course (or view) is called for. Apparently the field is so set in its ways it can barely tolerate the thought of a slight addition.

    Look at the examples being presented: sickle-cell anemia, pesticide resistance, the timing of flowering and the size or distribution of plant parts, the loss of toes (and whole limbs), using brains to learn to farm, bacteria "rewiring…regulatory networks" to adapt from the artificial loss of a single gene — do any of these show real potential for illustrating a step toward truly new systematically organized dynamic complexity?

    Also, everyone seems to see nothing but positive possibilities in whatever their view is. For instance, the article says plasticity "allows plants to spread into a range of habitats, for example, where natural selection can then adapt their genes" — shouldn't we also consider that it might obviate the need for further genetic adaptation, and soften the effects of natural selection? Likewise, niche construction is presented as contributing to the evolution of humans (and beavers), but haven't some researchers also asked if niche construction provides a buffer from environmental swings which would drive natural selection?

    BTW, the link in the phrase "a dizzying variety of humanlike fossils" is to an article about the contribution of Denisovans and Neanderthals to the extant human genome — what other fossils were in mind? Two is not a number I find dizzying.

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