Category: evolution

My answers in a Mexican newsletter to questions about evolution

February 25, 2026 • 10:45 am

Not long ago I was asked by Jason Flores-Williams to contribute to his online/free paper newsletter Alma Asfalto, a Mexican publication (translation: “asphalt soul”) that has English translation. Flores-Williams wanted me to answer a few questions about evolution, and I agreed for two reasons. First, I wanted to help promote the understanding and acceptance of evolution among our southern neighbors. Second, if you click on the first link (to Wikipedia), you’ll see that Flores-Williams is a guy worth helping:

 Jason Flores-Williams (born 1969, Los Angeles, CA) is an author, political activist, and civil rights attorney. He is best known for his legal work on behalf of death row clients, political protesters, the homeless population of Denver, and his suit to have the Colorado River recognized as a legal person. Flores-Williams is an acknowledged expert in conspiracy law and First Amendment cases whose views are frequently sought by media organizations, including the Washington Post, the New York Times, and the Los Angeles Times. He was also a lead organizer of the protests against the 2004 Republican National Convention. He lives in Denver, Colorado.

How could I refuse a guy who did that? And so I agreed, answering his five questions. These answers appear on pp. 6-7 of the 16-page March edition of the paper, along with interviews and short essays by other scientists and humanities folks (these include author and filmmaker Sasha Sagan, the daughter of Carl Sagan and Ann Druyan). I’ll give here the five questions I was asked, but to see my answers you must to the paper by clicking on the screenshot below. (You can also download the whole paper. Warning: the site loads slowly.)
 

Here are the questions I was asked. Again, see the answers at the site.

  • In the simplest terms, what is evolution—and what do people most often get wrong about it?
  • Why does evolution still make some people uncomfortable, even though it’s one of the most well-supported ideas in all of science?
  • Does accepting evolution make human life feel less meaningful—or, in your view, more remarkable?
  • People sometimes say that evolution promotes selfishness or brutality. What does evolution actually tell us about cooperation, empathy, and morality?
  • If you could change one thing about how evolution is taught or talked about in public life, what would it be—and why does it matter right now?

Here are the contents:

Mexico City
March 2026 

Reality is being branded.
Truth manipulated.
Disengagement marketed.
But something real is gathering.

Across science, philosophy, art, and film, the real is now contested ground.

https://almaasfalto.com/marzo/

REALITY

Sasha Sagan
— The Integrity of Uncertainty

Zona Maco
— Art Week, Mexico City

Jerry Coyne
— Evolution and Meaning

Vlatko Vedral
— The Universe Owes You No Certainty

Asya Geisberg
— Necessary Friction

Franco “Bifo” Berardi
— Desertion from the Future

Kevin Anderson
— Against the Illusion

Mariana Rondón
— It Is Still Night in Caracas

Sarah Martinez
— Alchemist of Nothingness (FR/ES)

Printed in Mexico City.
Alma Asfalto circulates in Roma, in the Historic Center, and underground, on Metro platforms.

 

Darwiniana for Darwin Day

February 12, 2026 • 10:38 am

There’s an potpourri of Darwin-related material at the Friends of Darwin Newsletter website, especially extensive because today is Darwin Day.  Click below to read it; it discusses pollination (Athayde’s favorite topic), recommends two new books, and has a bunch of evolution-related links. I’ll put those below the screenshot. Today’s newsletter was written by Richard Carter.

The “missing links” (indents are quotes from article)

Some Darwin-related articles you might find of interest:

  1. The importance of Charles Darwin’s documentary archive has been recognised by its inclusion on the UNESCO International Memory of the World Register. The Darwin Archive comprises documents held at Cambridge University Library, the Natural History Museum in London, the Linnean Society of London, Darwin’s former home at Down House in Kent, the Royal Botanic Gardens at Kew, and the National Library of Scotland.
  2. Podcast episode: The History of Revolutionary Ideas: Darwin.
    David Runciman talks to geneticist and science writer Adam Rutherford about the book that fundamentally altered our understanding of just about everything: Darwin’s On The Origin of Species.
  3. Video: Darwin’s unexpected final obsession with earthworms.
  4. Darwin Online has published Charles Darwin’s address book. Here’s their introduction, and here’s the address book.
  5. The University of Edinburgh recently completed a five-year programme to catalogue, preserve, and enhance access to the Charles Lyell Collection. Geologist Lyell was a close friend of Darwin, and major influence on his work. Here’s the collection’s snazzy new website.
  6. Leonard Jenyns on the variation of species and Charles Darwin on the origin of species 1844–1860
    At the 1856 meeting of the British Association for the Advancement of Science, Rev. Leonard Jenyns (1800−1893) delivered one of the most significant statements on the nature and the origin of species in the years immediately preceding Charles Darwin’s On the Origin of Species. Jenyns was a long-standing friend of Darwin and had turned down the place aboard HMS Beagle subsequently taken by Darwin.
  7. The November 2025 issue of the journal Paleobiology contained a collection of papers exploring Niles Eldredge and Stephen Jay Gould’s 1972 paper on punctuated equilibria, in which they argued that species don’t always evolve through slow, steady change. Instead, the fossil record shows long periods in which species remain remarkably stable, interrupted by relatively brief bursts of evolutionary innovation linked to the origin of new species. The Paleobiology papers include a retrospective review of the importance of the idea of punctuated equilibria, and Niles Eldredge’s personal reflections.
  8. Talking of brief evolutionary bursts, a recent paper finds that most living species derived from large groups which evolved in relatively short periods of time; or, as they put it, rapid radiations underlie most of the known diversity of life.
  9. Talking even more of evolutionary bursts, another recent study suggests changes in solar energy fuelled high speed evolutionary changes 500-million years ago. (See also the original journal paper Orbitally‐driven nutrient pulses linked to early Cambrian periodic oxygenation and animal radiation.)
  10. The case for subspecies—the neglected unit of conservation
    To lump or to split? Deciding whether an animal is a species or subspecies profoundly influences our conservation priorities. (See also my old post Lumpers v Splitters.)
  11. Sexual selection in beetles leads to more rapid evolution of new species, long-term experiments show
    40 years of experiments following 200 generations of beetles show the importance of sexual selection in the emergence of new species. (See also the original journal paper: The effects of sexual selection on functional and molecular reproductive divergence during experimental evolution in seed beetles.)
  12. Why did life evolve to be so colourful? Research is starting to give us some answers
    If evolution had taken a different turn, nature would be missing some colours.
  13. Some of the biggest fossils Darwin sent home from the Beagle voyage were those of extinct giant ground sloths, Megatherium and Mylodon. Scientists have figured out how extinct giant ground sloths got so big and where it all went wrong.
  14. Large brains and manual dexterity are both thought to have played an important role in human evolution. A new study has found that primates with longer thumbs tend to have bigger brains, suggesting the brain co-evolved with manual dexterity. (See also the original journal paper Human dexterity and brains evolved hand in hand.)
  15. Thumbs and brains are all well and good, but paleoanthropologist John Hawks explores another human characteristic that remains an enduring evolutionary enigma: what the heck are chins for?

I haven’t looked at them all, but I did look at two related to my own field—speciation. I like article #10, called “In praise of subspecies,” which explains what subspecies are (they’re called “races” of plants and animals by many biologists), and  tells us how recognizing them will reduce the number of species. (This won’t satisfy all biologists, for many disagree with me that modern humans and Neanderthals are subspecies, not distinct species.) But I disagree with the author, Richard Smyth, who thinks that all subspecies should be units of conservation. That is, genetically and morphologically different populations of a species should all be conserved if they are considered “endangered”.  One should do that when possible, of course, but I feel the unit of conservation—the thing that must be saved, is the biological species. But Smyth gives a good summary of what subspecies are.

Biologists have long thought (and Allen Orr and I have a chapter on this in our book Speciation) that sexual selection promotes speciation by driving isolated populations in different directions, eventually leading to some of them becoming reproductively incompatible, through either unwillingness to mate or creating problems in hybrids. The experiments described in #11 are interesting, and show more divergence in populations of beetles that are subject to sexual selection than in those constrained to be monogamous, but they don’t show the advent of reproductive barriers between populations. They do, however, show more divergence in the sexually-selected population, which is posited to be the first step in speciation.

Remember, Darwin’s greatest book was called On the Origin of Species (a shortened title).  Yet he didn’t help us understand species very much, as he had no concept of species being groups separated by reproductive barriers. It wasn’t until the 1930s that biologists began to understand how new species originated when they realized that the key to understanding the “lumpiness” of nature—distinct species in one area—was figuring out how those groups could coexist, and that meant understanding how reproductive barriers arise. Darwin’s book would have been more appropriately titled On the Origin of Adaptations.

And that is my pronouncement for Darwin Day. I do recommend reading the first chapter of Speciation, but if you’re not an evolutionary biologist you can forget about the rest, which becomes technical at times.

xh/t: Athayde

Colin McGinn on the evolution of “knowledge”

January 23, 2026 • 10:15 am

Colin McGinn is a well-known philosopher of mind who has written a short piece on the “history of knowledge” on his personal website. He takes an evolutionary view of the topic, which is what he means by “history”. But I found the piece, despite McGinn’s reputation and his authorship of nearly 30 books (many of them on consciousness), confusing and probably misleading. You can read it yourself by clicking on the link below

No doubt McGinn will take issue with my criticisms, for I am but a poor evolutionary biologist trying to understand this the best way I can. However, I do know some biology.  I will put what I see as McGinn’s two main misconceptions under my own bold headings, with McGinn’s quotes indented and my own comments flush left.

McGinn conflates “knowledge” with “consciousness”.  In general, knowledge, which most people define as “justified true belief” is acquired, and does not evolve.  Since it involves belief, it does require a mind that is conscious.  (I’ll take consciousness as McGinn does. meaning “having subjective awareness” or “being able to experience qualia: sense perceptions like the feeling of pain and pleasure, the apprehension of color and touch, and so on”.)

The problem is that what evolves is consciousness, not “knowledge”.  We do not know whether consciousness is a direct, adaptive product of natural selection, or is a byproduct of evolution, but it is certainly a result of our neuronal wiring. I’ll leave aside the problem of which animals are conscious. Based on parallel behavior, I think that many vertebrates and all mammals are conscious, but of course I can’t even say if other people are conscious. (Remember Thomas Nagel’s famous article,  “What is it like to be a bat?” We don’t know.) So consciousness has evolved, perhaps via selection, and it’s likely that the consciousness of many vertebrates had a common evolutionary origin based on neuronal wiring, though again it may have evolved independently in different lineages.

But regardless of these unknowns, since “knowledge” is largely acquired rather than inherited (remember its definition), it’s difficult to see how knowledge can evolve genetically, rather than being learned or passed on culturally.  Monkeys and apes peel bananas differently from how we do it: starting from the flower (bottom) end rather than the stem end (try it–it’s easier), but surely that knowledge is not evolved.  Anything acquired through experience is not knowledge bequeathed by evolution, even though the capacity to acquire certain knowledge (like learning language) can be evolved.

Now in some cases “knowledge” seemingly can be inherited, so the conflation is not total. Male birds of paradise, for example, “know” how to do specific displays to lure females of their species, and that is an instinct (does that count as “knowledge”?) which is inborn, not learned. But different birds of paradise have different displays or songs, and those displays surely evolved independently based on evolved differences in female preferences. We cannot say with any assurance that the genes or neuronal wiring for one species evolved from homologous genes and wiring in another species. Is one songbird’s knowledge of how to find edible berries evolutionarily related to another the ability of another species of songbird to find food? Both may be learned or both may be evolved, but there’s no reason to think that “knowledge” of different species forms an evolutionary tree the way that their genes do.

You can see this conflation in McGinn’s opening paragraph, which assumes that there was a primordial “knowledge” that gave rise to descendant knowledge:

 This is a big subject—a long story—but I will keep it short, brevity being the soul of wisdom. We all know those books about the history of this or that area of human knowledge: physics, astronomy, mathematics, psychology (not so much biology). They are quite engaging, partly because they show the progress of knowledge—obstacles overcome, discoveries made. But they only cover the most recent chapters of the whole history of knowledge—human recorded history. Before that, there stretches a vast history of knowledge, human and animal. Knowledge has evolved over eons, from the primitive to the sophisticated. It would be nice to have a story of the origins and phases of knowledge, analogous to the evolutionary history of other animal traits: when it first appeared and to whom, how it evolved over time, what the mechanisms were, what its phenotypes are. It would be good to have an evolutionary epistemic science. This would be like cognitive science—a mixture of psychology, biology, neuroscience, philosophy, and the various branches of knowledge. It need not focus on human knowledge but could take in the knowledge possessed by other species; there could be an epistemic science of the squirrel, for example. One of the tasks of this nascent science would be the ordering of the various types of knowledge in time—what preceded what. In particular, what was the nature of the very first form of knowledge—the most primitive type of knowledge. For that is likely to shape all later elaborations. We will approach these questions in a Darwinian spirit, regarding animal knowledge as a biological adaptation descended from earlier adaptations. As species and traits of species evolve from earlier species and traits, so knowledge evolves from earlier knowledge, forming a more or less smooth progression (no saltation). Yet we must respect differences—the classic problem of all evolutionary science. We can’t suppose that all knowledge was created simultaneously, or that each type of knowledge arose independently. And we must be prepared to accept that the origins of later knowledge lie in humble beginnings quite far removed from their eventual forms (like bacteria and butterflies). The following question therefore assumes fundamental importance: what was the first type of knowledge to exist on planet Earth?

Note that he implicitly envisages an evolutionary tree of knowledge. It would be clearer if he used “consciousness” for “knowledge”, and defined both of them, which he doesn’t.  But even if you think that, well, McGinn may be onto something here, that “something” comes crashing down when he starts talking about what “knowledge” was the ancestral knowledge. This brings us to the second problem:

McGinn is dead certain that the first “knowledge” that evolved, by which he really means the first quale, or subjective sensation, is the experience of pain. There is no evidence , or even a convincing scenario, for this proposition.  Here’s where he proposes this, and not with much doubt, either:

I believe that pain was the first form of consciousness to exist.[1] I won’t repeat my reasons for saying this; I take it that it is prima facie plausible, given the function of pain, namely to warn of damage and danger. Pain is a marvelous aid to survival (the “survival of the painiest”). Then it is a short step to the thesis that the most primitive form of knowledge involves pain, either intrinsically or as a consequence. We can either suppose that pain itself is a type of knowledge (of harm to the body or impending harm) or that the organism will necessarily know it is in pain when it is (how could it not know?). Actually, I think the first claim is quite compelling: pain is a way of knowing relevant facts about the body without looking or otherwise sensing them—to feel pain is to have this kind of primordial knowledge. To experience pain is to apprehend a bodily condition—and in a highly motivating way. In feeling pain your body knows it is in trouble. It is perceiving bodily harm. Somehow the organism then came to have an extra piece of knowledge, namely that it has the first piece, the sensation itself. It knows a mode of knowing. Pain is thus inherently epistemic—though not at this early stage in the way later knowledge came to exist. Call it proto-knowledge if you feel queasy about applying the modern concept. We can leave the niceties aside; the point is that the first knowledge was inextricably bound up with the sensation of pain, which itself no doubt evolved further refinements and types. Assuming this, we have an important clue to the history of knowledge as a biological phenomenon: knowledge in all its forms grew from pain knowledge; it has pain knowledge in its DNA, literally. Pain is the most basic way that organisms know the world—it is known as painful. Later, we may suppose, pleasure came on the scene, perhaps as a modification of pain, so that knowledge now had some pleasure mixed in with it; knowledge came to have a pain-pleasure axis. Both pain and pleasure are associated with knowledge, it having evolved from these primitive sensations. This is long ago, but the evolutionary past has a way of clinging on over time. Bacterial Adam and Eve knew pain and pleasure (in that order), and we still sense the connection. Knowledge can hurt, but it can also produce pleasure.

When you poke an earthworm, it recoils.  Does it do so because it feels pain? I doubt it, as it seems to me unlikely that an earthworm is conscious. Perhaps it just has an evolved neuronal network and morphology that retracts the body when it senses (not consciously) that it’s been touched. It could simply be like our kneejerk reaction: a reflex that evolved, but is not perceived consciously (remember, we take our hand off a hot stove before we are even conscious of feeling pain). But even if you think earthworms are conscious, certainly single-celled animals are not, yet they exhibit adaptive behavior as well.  One-celled animals can move toward or away from light, are attracted to chemical gradients that denote the proximity of food, move away when disturbed by a touch, seek out other individuals for reproduction, and so on. All animals, whether you think they’re conscious or not, have some kind of evolved instinct to find individuals of the opposite sex when it’s time to have offspring. And surely that “knowledge” (if you will) is the most evolutionarily important of all.

Why, then, is awareness of pain supposed to be the very first “knowledge” to evolve?  Why not responses to touch, to chemical gradients, to a drive for reproduction, or all the qualia that involve senses: touch, taste, sight, hearing, hunger and thirst, and so on?  All of those can be seen as adaptive as a sense of pain, whether it be conscious or not.

Seeing various behavioral responses as constituting “knowledge”, then, adds nothing to our understanding of either evolution or consciousness. It muddles one’s thinking.  The problem is instantiated by sentences like this one:

The organism knows how to get about without banging into things and making a mess. We could call this “substance knowledge”.

Well, simple organisms like rotifers also avoid obstacles.  They are almost certainly not conscious, and you can’t have knowledge without consciousness.  Do they “know” how to get about without banging into things, or is it an evolved trait based on cues associated with “being touched”. What “knowledge” is being shown here?

McGinn then proposes, with near certainty, an evolutionary progression of “knowledge”:

So, let’s declare the age of sense perception the second great phase in the development of knowledge on planet Earth. The two types of knowledge will be connected, because sensed objects are sources of pain and pleasure: it’s good to know about external objects because they are the things that occasion pain or pleasure, and hence aid survival.

I will now speed up the narrative, as promised. Next on the scene we will have knowledge of motion (hence space and time), knowledge of other organisms and their behavior (hence their psychology), followed by knowledge of right and wrong, knowledge of beauty, scientific knowledge of various kinds, social and political knowledge, and philosophical knowledge. Eventually we will have the technology of knowledge: books, libraries, education, computers, artificial intelligence. All this grows from a tiny seed long ago swimming in a vast ocean: the sensation of pain.

The “knowledge” of right and wrong is a learned and cultural phenomenon, completely unlike our “knowledge” of pain, whether it be conscious or a simple reflex reaction to harmful stimuli. What bothers me about all this is not just the mere conflation of “knowledge” with “consciousness”, or the idea that pain was the first “knowledge”; it is the sheer certainty McGinn displays in his essay. Perhaps that comes from his being a philosopher rather than a biologist, as biologists are surely more cautious than philosophers. A quote:

 It was pain that got the ball rolling, and maybe nothing else would have (pain really marks a watershed in the evolution of life on Earth).

I could say with just as much evidence that the perception of touch (either conscious or as an evolved reflex) “got the ball rolling”.  And a response to touch in simple organisms cannot be construed as “knowledge” in any respect.

There is more in this article, but I find the whole thing confusing.  We don’t even know whether consciousness evolved as an adaptive phenomenon. We don’t know whether our consciousness is a post facto construct for perceiving qualia that the body has already detected (remember, you pull your hand off a hot stove before you feel pain). Above all, we don’t know the neuronal basis of consciousness, much less which animals are conscious and which are not.  In Matthew Cobb’s biography of Francis Crick, you can see his subject struggling with this issue in the last part of his life, and admitting that we know little about it. Crick laid out a program for sussing out the neuronal basis of consciousness, but, as Matthew noted in these pages, scientists haven’t gotten far with this problem.

I have no idea why McGinn is so certain about evolution and qualia. I don’t know any evolutionist who would agree with his thesis. I even broached it to a neurobiologist who knows evolution, and that person found the whole concept totally misguided.

As I said, McGinn is no slouch; he is a highly respected philosopher whose work I’ve read and respected. But I get the feeling that he’s driven out of his lane here.

On the origin of venom by means of natural selection

December 11, 2025 • 10:20 am

Many animals are venomous, but in most cases the exact proteins involved in causing pain or death are unknown, and even in those cases the genes producing them have not been identified, counted or mapped.  If you’re interested in the evolution of venom, what its precursors are, and how venomous animals avoid poisoning themselves, you have to know this kind of stuff.

A new paper in Proc. Nat. Acad. Sciences (click screenshot below to read for free, or find the pdf here) answered several of these questions in the venomous caterpillar of the mottled cup moth (Doratifera vulnerans), shown below.  It’s from Australia, and is described in Wikipedia this way:

It is known for its caterpillar having unique stinging spines or hairs that contain toxins, for which the scientific name is given that means “bearer of gifts of wounds”. Chemical and genetic analysis in 2021 show that its caterpillar contains 151 toxins, some of which have medicinal properties

That earlier paper, from 2021 and including some of the same authors as the one we discuss today, did indeed identify 151 proteins (peptide are bits of proteins or short chains of amino acids) that were in the toxins, but did not know which genes produced them, how the genes were arranged, what the closest relatives of the genes were, and how many of the 151 “toxins” were really toxic (the word “toxin” there and in the present paper do not mean that the substances were toxic, but that they were simply a component of the extracted toxins). However, the authors, some on the paper I’m highlighting today, did identify two genuine toxins that caused pain: the peptides Dv12 and Dv11.

Look at this thing! It’s clearly aposematic, meaning that it has bright warning coloration that predators can recognize and learn to avoid. And you can see those nasty spines.  In the earlier paper they extracted toxins from related species and tested them by injecting them into mice tails, guinea pigs, and human volunteers. That earlier paper also adds this about the species name:

This species, whose binomial name etymologically means “bearer of painful gifts,” is a common culprit of caterpillar envenomations in Australia.

That means that many Aussies get stung by these things, probably inadvertently. Would you touch an animal that looks like this?:

Photo by Fir0002,  Creative Commons Attribution-Share Alike 3.0 Unported license.

On to the new paper, and I’ll try to be brief as it’s long and complicated.

1.) First, the authors sequenced the entire caterpillar genome (remember, it’s the same as the adult moth genome).

2.) Then, knowing the sequences of the proteins known from previous work on toxins, they could find the genes producing them by matching the protein sequence to the DNA sequence that could produce these proteins. Of the 151 proteins in caterpillar venom known from the prvious work, they mapped 149 of them to 115 sites in the genome

3.) Of the 115 sites, 35 were products of single genes, while 80 (70%) of the total, were members of gene families consisting of two or more similar genes (sometimes many genes) with similar sequences.  Here’s a map of the “toxin gene” locations on the insect’s 13 chromosomes. The blue dots are the genes existing in single copies, orange dots are clusters of genes previously grouped together by protein-sequence similarity, and pink dots are genes that were newly identified, surely as part of gene families, in the present study. This conclusion comes from their sequence similarity and they physical grouping on two chromosomes.(The size of the dots indicates the number of genes that are part of a contiguous group. Click to enlarge:

So we know that genes found in venom are very often the product of gene duplications, either of single genes becoming two (this can happen via unequal crossing-over during meiosis or by other methods), producing two initially identical genes side by side or whole groups of them (“tandem duplications”). Once a gene has been duplicated, the original copy can then keep its original function, while the other copies, not being “needed,” are free to evolve other functions. Many genes we’re familiar with, like our own globins and immunoglobulins, evolved by gene duplication followed by divergence of the duplicated copies.

Where did the genes making venom proteins come from? This is the key evolutionary question answered here and, to some extent, in the previous paper. They evolved from ancestral genes in the moth’s immune system that evolved to attack microbes, the so-called “antimicrobial peptides” (AMPs), also known as cecropins. The ancestral AMP proteins, nearly identical to their original form and function, kill bacteria (prokaryotes) by disrupting the bacterial membranes. Insects still need to kill microbes!

Clearly, the proteins in venom have evolved by natural selection modifying ancestral genes used to kill bacteria. Now they are used to repel predators. Natural selection causing this divergence was implicated by looking at sequence differences, as there are ways of showing what sequence differences evolve faster than expected under either the slower processes of genetic drift or “purifying” selection that conserves structure.  They found that most of the venom-adapted proteins that evolved from cecropins did evolve under natural selection, while the descendants of cecropins that retained their original anti-microbial proteins were under purifying selection to retain their sequence. It’s clear, then, that the insect still needs genes to attack bacteria. It’s just that some of them have been repurposed, often through gene duplication and divergence, to repel predators. (The authors have a way of assessing “pain” by measuring the increase in calcium concentration in cells grown in vitro and exposed to venom. This happens when the two investigated proteins are used.)

Here is a complicated family tree of cecropin genes in black used to kill microbes. The genes found in venom are in the red box (“venom adapted”). You can see that they are related to cecropin genes but branched off fairly recently (probably four or five million years ago). The venom genes are in the red box that I’ve added, and their relationship as being derived from ancestral AMP genes is very clear. (The “canonical” genes in green are antimicrobial proteins closely related in sequence to the venom genes.

So, now we know where the genes in venom come from. What we do not know is how many of those genes are essential in venom, either causing pain or doing other stuff that venom needs to do. At least two of them cause pain, but there are probably more, for they haven’t all been tested. And some of the other genes are probably involved in dismantling cell walls in potential predators. The authors tested several of the venom proteins and also found that, as in their AMP ancestors, they disrupt cell covering, in this case eukaryotic cell membranes.

Finally, the big question: If the caterpillar makes venom, why doesn’t it poison itself? Here’s how the authors answer that question (I’ve put the answer for this species is in bold).

Animals that produce toxins, either for innate immunity or as venom toxins, must employ strategies to protect themselves from toxicity. Such protective mechanisms include production of toxin inhibitors, storage in inactive form, mutations in their own ion channels that confer resistance, alteration of lipid bilayer compositions, and compartmentalization of toxins separate from body tissues. In the case of limacodid venom peptides, the venom is compartmentalized into the cuticle-lined venom reservoir inside venom spines, preventing the toxin from coming into contact with cells other than the secretory cells that produce them. Thus, compared to canonical cecropins, venom-adapted cecropins may also be released from pressure to avoid activity against animal cells.

There are other findings in the paper that will be of interest primarily to those studying genomic evolution. For example, many of the venom proteins still retain some weak antimicrobial activity, so the idea that genes completely lose their ancestral function when they gain a new one doesn’t hold in this case.

Below you can see the adult moth because, remember, they studied caterpillar venoms, and many of those genes are probably turned off in the adult. But adult and caterpillar carry the exact same genes, of course; their different bodies, physiology, and behavior rest on the differential turning on and off of these genes at different life stages. And that remains a big mystery: how do such different life stages evolve, with each step of the evolution being adaptive?

From The Australian Museum, photo credits at bottom (click to enlarge), image by Lyn Craggs.

 

Human and chimp genome comparison: apples and origins

December 7, 2025 • 10:00 am

How much genetic difference separates us from our closest relatives? The conventional wisdom about humans and our closest ape relatives (chimps and bonobos) is that we share 98% of our DNA. That’s a big similarity, and implies that if we lined up our genomes side by side, only about 2 out of 100 DNA bases would differ. This figure is often used to show that we have only a tiny genetic difference from our closest relatives. To quote W. S. Gilbert of Gilbert and Sullivan, “Darwinian man, though well-behaved, at best is only a monkey shaved.”  Well, the differences go farther than mere shaving.

The “98% similarity figure” is wrong. And it’s wrong for several reasons. First, most ape genomes (chimps, gorillas, orangs, etc.) have not been as thoroughly sequenced as was the human genome. A lot of the data that went into the 98% figure was missing.  Second, you can’t just compare genomes by lining them up and looking for differences in base pairs at similar sequences.

Why not? Because the notion of “similar sequences” is ambiguous and, sometimes, meaningless. Since we diverged from our ape ancestors, there have been a lot of changes in every species’ DNA that prohibit us from simply “lining up the genomes”.  Transposable elements have invaded some species but not others, bits of the DNA have been duplicated, so there are species that have sequences that are not homologous. Bits of the genome have been inverted (turned around and reinserted), causing big differences in sequence in previously similar sequences. Further, pieces of the DNA have been moved from one chromosome to another, so DNA sequences previously in the same place are now in another place, leading to a difference in total sequence.

All this leads to a substantially greater DNA divergence between humans and chimps than the 98% figure.  These extra genomic differences were sussed out by Yoo et al. in a Nature paper  from April of last year that you can read by clicking below (or find the pdf here).They did a much improved job in sequencing six of our ape relatives: the chimp (Pan troglodytes), bonobo (Pan paniscus), Western gorilla (Gorilla gorilla), Bornean orangutan (Pongo pygmaeus), Sumatran orangutan (Pongo abelii), and the siamang (Symphalangus syndactylus), an endangered species of gibbon from SE Asia.

First, the authors give a revised set of divergence times based on DNA differences between living species.  The human vs. chimp/bonobo species, for example, split from their common ancestor about 5.5-6.3 million years ago (mya), roughly in line with previous estimates. The divergence between humans and other African apes (gorillas) occurred between 10.6 and 10.9 mya, and that between humans and orangutans about 18.2-19.6 mya.

There is a ton of genomic information in the paper, including a lessening of the similarity between humans and chimps, but also specific information about what genes and regulatory bits of DNA differ among species. These differences suggest some some intriguing future research. I’ll mention just a couple, but will refer you instead to a long tweet below which shows why the human-chimp differences have increased. It’s an excellent tweet that you can read pretty quickly, though it doesn’t detail all the many differences that the researchers describe in the Nature paper, which is exhausting for those outside the field. There are also genes whose sequences changed very rapidly, suggesting that they were acted on by natural selection.

There are a gazillion sequence and structural differences revealed among the species, including 229 bits of ape DNA (all species) that have evolved rapidly and are thus candidates for natural selection. The paper also reveals parts of the DNA that have evolved especially rapidly in the human lineage since we split from chimps/bonobos. These regions are called HAQERS, and could be candidates for the Holy Grail of such work: seeing “what makes us human”. But that question is a bit misguided.

Nevertheless, the authors found one gene, ADCYAP1, that “is differentially regulated in speech circuits.” The implication is that the changes may have something to do with why humans are the only ape with syntactic spoken language, but that gene does a lot of other stuff, too, so I don’t take that implication seriously. The FOXP2 gene, which evolved rapidly in the modern human genome relative to other species, has mutations that impede people’s ability to speak, and I well remember when it was touted as “the language gene” that enabled humans to speak. But further research showed that the accelerated human evolution of the gene was an artifact, and that the normal function of the gene is manyfold, so nobody these days takes FOXP2 seriously as the “speech gene”. All claims should be regarded as caveat emptor.

There are also several genes that are not only unique to humans, but are “associated with human evolution of the frontal cortex”, suggesting these account for our big brains. The photo below comes from the tweet shown next, and its caption comes from that tweet. (The average chimp brain is about 400 g in mass—less than a third the mass of the human brain, which weighs in at 1300-1400 g in adults.)  Again, caveat emptor with regard to the two specified genes.

Figure 3. Radiograph illustrating cranial expansion in the human lineage, which is associated with increased neocortical growth – Chimpanzee skull (left), Modern Human skull (right).

Other genes that differ strongly among ape species involve those producing immunoglobulin, major histocompatibility products (MCH) and T-cell receptors, but especially immunoglobulin genes—involved in production of antibodies. Why have these evolved so rapidly within apes? Your guess is as good as mine, but suggests that reaction to antigens was an important element of ape evolution.

Here is the authors’ summary, and most of the paper will be of interest only to geneticists familiar with the argot (not necessarily me):

The complete sequencing of the ape genomes analysed in this study significantly refines previous analyses and provides a valuable resource for all future evolutionary comparisons. These include an improved and more nuanced understanding of species divergence, human-specific ancestral alleles, incomplete lineage sorting, gene annotation, repeat content, divergent regulatory DNA and complex genic regions as well as species-specific epigenetic differences involving methylation. These preliminary analyses revealed hundreds of new candidate genes and regions to account for phenotypic differences among the apes. For example, we observed an excess of HAQERS corresponding to bivalent promoters thought to contain gene-regulatory elements that exhibit precise spatiotemporal activity patterns in the context of development and environmental response99. Bivalent chromatin-state enrichments have not yet been observed in fast-evolving regions from other great apes, which may reflect limited cross-species transferability of epigenomic annotations from humans. The finding of a HAQER-enriched gene, ADCYAP1, that is differentially regulated in speech circuits and methylated in the layer 5 projection neurons that make the more specialized direct projections to brainstem motor neurons in humans shows the promise of T2T genomes to identify hard to sequence regions important for complex traits. Perhaps most notably, we provide an evolutionary framework for understanding the about 10–15% of highly divergent, previously inaccessible regions of ape genomes. In this regard, we highlight a few noteworthy findings.

The importance of the paper for now seems to be the presentation of the sequences and their differences rather than explaining the differences or their significance in ape adaptations—especially in humans—for studying adaptive hypotheses involves a lot of work for each single region that differs among species or evolved quickly. Nevertheless, useful questions have been raised—like why genes involved in the immune response changed so rapidly—that will be subject to future work.

I am not sure who runs the Origins Unveiled site dealing with evolutionary anthropology, but based on the clarity of the tweet below from that site (click on screenshot to see the tweet in situ), it deserves more followers. It’s only about a year old, which may explain the follower issue.

This tweet from September of this year explains why the 98% similarity between humans and chimps drops to 84.7% when you take translocations, inversion, duplications, insertions, and other genomic rearrangements into account. And these rearrangements are not necessarily trivial, for duplications can lead to divergent gene families, and insertions can act to regulate genes in a new way.

Again, click below and read; it’s short and lucid:

I’ve shown one figure from the tweet above: the brain differences. Below is another figure showing how the 99% similarity between humans and chimps has traditionally been calculated, requiring alignment of nearly identical but perhaps slightly different bits of DNA. All captions come from the tweet. This figure shows how they line up chimp and human sequences (you see the gross similarity), but also that here there’s been a single nucleotide substitution in one of the two lineages, rendering this sequence 92.3% similar. (This is a made-up sequence for purposes of illustration.)  When you did that with the whole genome comparison based on earlier data, you got about a 2% difference. The problem, as I said, is that we didn’t have great chimp (or any ape) sequences and there are parts that you simply couldn’t line up this way. And those parts, when compared among species, increase the genetic difference between us and our closest relatives.

Figure 1 — Simplified Mock Alignment Illustrating Nucleotide Sequence Similarity Between Chimpanzee and Human Genomes. Out of 13 positions, one substitution (single-nucleotide variant, circled in red) results in ~92.3% DNA similarity. This example demonstrates the methodology behind the misleading 98–99% human-chimpanzee DNA similarity figures.

Below is another figure showing how various rearrangements, insertions, deletions, and translocations reduce similarity, but I’ll show only four of the six parts of the figure, giving the captions for a-d. You can see how these changes make humans and chimps less genetically similar than previously thought (again, captions come from the tweet; click to enlarge).  These are also “mock alignments” meant for purposes of illustration, but they do show the kind of thing seen in the Yoo et al. paper:

Figure 2 — Simplified Mock Alignments Illustrating Structural Variation Between Chimpanzee and Human Genomes. Note: Structural variants are not taken into account when calculating the 98–99% Chimpanzee-Human DNA similarity figures.
( a) Insertions and deletions contributing to sequence divergence. Out of 34 positions, 3 indels (insertions circled in orange; deletions in yellow) result in ~91.2% DNA similarity. Note: These indels are relative, as without a suitable outgroup (i.e. gorilla), an insertion in one genome appears as a deletion in the other.
(b) Duplication contributing to sequence divergence. Out of 34 positions, a duplication of 12 bases (duplicated segment encircled in blue; original in purple) results in ~64.7% DNA similarity.
(c) Inversion contributing to sequence divergence. Out of 34 positions, an inversion of 11 bases (encircled in green) results in ~67.6% DNA similarity. Note: Although bases may match within the inverted region, they do not contribute to sequence similarity due to misalignment. Without a suitable outgroup (i.e. gorilla), it is unknown whether the inversion occurred on the chimpanzee or human genome.
(d) Translocation contributing to sequence divergence. Out of 34 positions, a translocation of 20 bases (encircled in brown) results in ~41.2% DNA similarity. Note: A translocation is a DNA segment that has been “copy and pasted” or “cut and pasted” from another part of the genome.

So, when you hear that we’re nearly genetically identical to our closest relatives, just say, “Wait a tick. Not all that identical.” We have about 15% difference in sequence, which is not trivial.

UPDATE: I’m aware now that creationists and IDers have been using this 85% to cast doubt on human evolution, our place in the ape family tree, and whether evolutionists are honest.  This is bogus: the 85% vs. 98% depends on two different methods of calculating similarity. Which ever method you choose (alignment vs. total genomic similarity), the same family tree of the great apes appears, with chimps/bonobos our closest ancestors, then gorillas a bit more distance, and then orangutans, and then other apes.  The point of this post is not to cast doubt on human or ape evolution, but to show different ways of calculating genetic similarity.

Readers’ wildlife photos

December 1, 2025 • 8:15 am

Today we have the first part of a series of photos taken at Down House, where Darwin lived most of his life. The photographer is Neil K. Dawe, who lives on Vancouver Island, British Columbia. Neil’s captions and IDs are indented, and you can enlarge his photos by clicking on them.

Down House, Kent, UK

On our UK trip this past June, we stopped at a special place, Down House, where we spent some time wandering through the home and grounds of Charles Darwin. The house has been carefully preserved and we spent some time on the upper floor, essentially an exhibition of his life. There we saw a number of Darwin artifacts such as some of the equipment and reference books he took with him on the Beagle voyage, some of his notebooks, as well as manuscript pages from On the Origin of Species.

Darwin purchased the house on 22 July 1842 for £2,200 and moved in that September. He described it as “… a good, very ugly house with 18 acres, situated on a chalk flat, 560 feet above sea. There are peeps of far distant country and the scenery is moderately pretty: its chief merit is its extreme rurality. I think I was never in a more perfectly quiet country”:

The downstairs includes a number of rooms that are laid out much as Darwin and Emma, his wife, had left them, including Darwin’s study, where he wrote On the Origin of Species. We walked through the study, which has been restored to the original 1870s arrangement with original furniture and many of Darwin’s possessions. Since photographs are not allowed in the home I have included the following image of his study by Anthonyeatworld, via Wikimedia Commons, licensed under CC BY-SA 3.0, Cropped from the original:

Later, we wandered through the estate gardens to visit the vegetable garden (on the right of the photo) and Darwin’s greenhouse and cloches where he conducted many of his experiments. After completing construction of the heated greenhouse, Darwin requested plants from Kew Gardens and upon their arrival he notes in a letter to J.D. Hooker, “I am fairly astounded at their number! why my hot-house is almost full!. . . I have not yet even looked out their names; but I can see several things which I wished for, but which I did not like to ask for.”:

The greenhouse, where Darwin carried out many of his experiments, was fully stocked during our visit:

A Pitcher Plant (likely Nepenthes spp.) in the greenhouse; Nepenthes was included in a list of nursery plants Darwin planned to purchase:

Another greenhouse plant, an orchid, likely from the genus Lycaste:

We then wended our way over to the Sandwalk. Darwin leased 1.5 acres in 1846 from Sir John Lubbock, planted it with hazel, birch, privet, and dogwood, and created the gravel path. Francis Darwin recalled that “The Sand-walk was our play-ground as children, and here we continually saw my father as he walked round.” Huxley also spoke of “… the famous Sandwalk, where Darwin used to take his allotted exercise after each spell of work, freshening his mind and shaping his thought for the task in hand.” Darwin used stones to count laps, kicking one aside each time he passed, to avoid interrupting his thoughts as he walked his “thinking path.”:

Here I’m walking along the Sandwalk in the footsteps of Charles Darwin, birding as I go.  From Darwin’s notes: “Hedge-row in sand-walk planted by self across a field (years ago when I held field which had from time immemorial been ploughed & 3 or 4 years before the Hedge was planted, had been left as pasture — soil plants, chiefly Hard or clayed & very poor.— . . . plants, have now sprung up in hedge — preserves how the seeds having been brought by birds, for all are esculent & the protection afforded by spinose thorns — a sort of common land—” Photo: Renate Sutherland.

Part 2 to follow.

Nature screws up again: touts need for severe revision of evolutionary theory while harboring a conflict of interest

November 9, 2025 • 10:00 am

Nature has shown some bad behaviors lately, and now you can add onto them two more: an ignorance of evolutionary biology and a lack of fact-checking. Both of these are instantiated in a recent book review, which, as we see so often, describes modern evolutionary biology as woefully incomplete.  The review, moreover, fails to mention all the critics of this “need for speed.” Finally, the review (of a book touting the deficiency of evolutionary theory), was written by a collaborator of several authors of the book, showing a severe conflict of interest. It’s no surprise that the authors’ colleague gave their book a glowing review.

A letter written by some well known evolutionary biologists pointing out these two deficiencies was promptly rejected by Nature.

I’ll give a critique of the book review first, and then show the letter sent to Nature that was rejected. Finally, I’ll give one of the signers’ responses to the rejection: Brian Charlesworth. I won’t give the names of the other signers of the letter (there were three), as Brian gave me permission to reproduce the letter but I haven’t asked the others.

First, the review. The book is Evolution Evolving: The Developmental Origins of Adaptation and Biodiversity, with authors Kevin Lala [formerly “Laland”], Tobias Uller, Natalie Feiner, Marcus Feldman and Scott Gilbert, published last winter by Princeton University Press, which apparently didn’t get the book vetted by competent evolutionists. The Nature review by Eva Jablonka, Israeli evolutionist and epigenetics maven, came out in January, so I’m a bit late to the party. Still, this shows that there remains a vocal minority of biologists who can’t resist showing us the many ways that evolutionary biology is wrong or incomplete, yet they’re singing the same old tune, one that’s been rebutted many times before.

Click below to read the fulsome review of the book; one that doesn’t even mention the many issues with the “new view of evolution” that have been pointed out for years.

Before I point out a few misguided statements, I urge you to read my take on a Nature paper called “Does evolutionary biology need a rethink?“, in which one group of “revisionists, with Laland (“Lala” above) being the first author, answers, “Yes, urgently”, while another group, with Greg Wray the first author, answers “No, all is well.”  As you’ll see from reading my piece, I side with the second group. Note that that exchange is already eleven years old, yet the promoters of the “rethink” view are advancing exactly the same arguments they made back then. These arguments are misguided because they are either flat wrong (e.g., their criticism of the neo-Darwinian view that mutations are “random”), or misleading (e.g., their view that development drives evolution, with development changing first and only then permitting adaptive genetic change). In her review above, Jablonka also throws in epigenetics, her speciality, which, while important in some respects, cannot form the basis of permanent adaptive evolution because environmentally-induced changes in DNA (“epigenetic” changes) persist at most for only two generations before the epigenetic marks are wiped away during gamete formation.

But I’m getting ahead of myself.

First, for the topic of “development leading evolution,” “nongenetic forms of evolution” (learning, culture, etc.), and epigenetics, all touted in Jablonka’s article, see my post above, this one, and my several discussions of the flaws of touting epigenetics as a critical and neglected factor in adaptive evolution.  I won’t repeat my arguments, but I will point out a couple of howlers in Jablonka’s review.  Her quotes are indented below.

First, on development as the guiding factor of evolution:

Under the extended evolutionary synthesis, the questions that are fundamental to the field change. Instead of just asking what genetic mutations might give one organism an advantage over its peers, the authors argue, evolutionary biologists should also focus on the developmental mechanisms and structures that underlie fitness differences.

It’s time to admit that genes are not the blueprint for life.

A developmental focus, they say, could help in understanding phenomena that are mysterious under the modern synthesis. For example, selective breeding for ‘tameness’, whether in sheep, pigs, horses, dogs or foxes, leads to the evolution of a common series of traits that are not necessarily adaptive — including smaller brains and teeth, curly tails, white patches and flat muzzles. This link, across different animal groups, bred in different ways and at different times, baffled Darwin and others for more than a century.

. . . All these features involve the same embryonic cell type (the neural crest) and their development is thus driven by similar sets of genes.

Well, as Dawkins pointed out years ago, genes are not the “blueprint for life,” but the “recipe for life,” as one needs environmental inputs to convert the DNA into an organism. As for development guiding evolution, what Jablonka and her pals apparently mean that existing developmental pathways constrain evolution: mutations can only show their effect within and already-evolved system of gene interactions. The pleiotropic effect of “tameness” mutations on several species is easily explained because you’re selecting at the same time for the side effects of tameness genes, which happen to affect morphology and color. That’s not new, and certainly doesn’t mandate a rethink of evolution.  As Brian wrote me:

“As has always been acknowledged by anyone with half a brain, the phenotypic effects of mutations are constrained by the existing developmental system. As Haldane put it, selection on humans could produce a race with the intellect of Shakespeare and the physique of Carnera, but for a race of angels we’d have to wait for the necessary mutations, both for the wings and the moral qualities.” 

But then Jablonka as well as Lala et al. (and other miscreants like Denis Noble) use this observation to claim that NEW TRAITS AND PRESUMABLY THE MUTATIONS UNDERLYING THEM ARE NOT RANDOM. From Jablonka:

The modern synthesis dictates that genetic mutations arise at random, which makes it hard to understand why these traits would consistently evolve in all these tamed animals. But seen through a developmental lens, things are clearer. . . . Thus, new traits do not arise at random. Some are more likely than others, and suites of traits often arise together. Understanding such ‘developmental biases’ can enable researchers to better understand how traits originate, what directions future evolution might take and how rapidly evolution might proceed.

They simply do not understand what evolutionists mean when they say features (and mutations) arise “at random” in evolution. The meaning is that mutations and the traits they produce occur irrespective of whether they are good or bad for the individual’s reproduction. Of course some changes are more likely than others, and mutations often have pleiotropic (“side”) effects on other traits. This means that what is subject to selection is the net effect of a mutation on the replication rate of the mutated gene.

What are examples of the “better understanding” that comes from considering development? The ones given by Jablonka, presumably from Lala et al., are not impressive. Here’s an example called “inheritance beyond genes”:

For example, certain whales learn from their mothers how to corral schools of fish into air bubbles. Desert woodrats (Neotoma lepida) eat their mothers’ faeces, which contain gut microorganisms that allow the woodrats to digest plants rich in highly toxic creosote. And molecules called epigenetic marks, which are associated with DNA and modify gene activity, are passed down through generations too. Epigenetic marks that form when mice in the laboratory are trained to link a particular smell with an electric shock, for example, have been passed down to their grandchildren — the young mice are scared of the same smell, even though they have never received the shock.

Two quick points: have the authors ever heard of “learning”? Or that learning might be primed by genes, as our learning of languages primes us to produce comprehensible syntax, but which language we speak depends on our environment? Is imitation of adaptive parental behavior (itself either genetically primed or learned) something new? Nope.  And as for epigenesis, I have heard of the mouse study, but no epigenetic trait produced by the environment can persist for more than a handful of generations, as epigenetic modifications of DNA are wiped out during gamete formation. This form of “Lamarckian” inheritance won’t work.

Here’s one more:

Furthermore, some organisms construct environments to benefit the development of subsequent generations. Dung beetles, for instance, make balls of cow dung, into which they add their own faeces as food, and lay a single egg. The nutrients and microbes in these balls influence how the larvae develop, and in turn the sizes and shapes of the beetles and how they evolve.

Is it a revolutionary insight to discover that parents do things that benefit the fitness of their offspring? Human mothers feed their babies, and sometimes what they feed them could affect their own future evolution. Big whoop!

This all shows that the insights that supposedly mandate a new theory of evolution aren’t new at all, but are comfortably part of the already-existing Modern Synthesis of evolutionary theory.  But these authors, it seems, want to make their mark by advancing the same old tired arguments that have long been refuted.

Along with several other authors, Brian Charlesworth noted that Jablonka seems resistant to even mentioning the many objections to the “new” theory of evolution. Brian and others sent the letter below to Nature for consideration for publication. The references given in the submitted letter are included, and I’ve put in the links. Doug Futuyma’s paper is especially thorough and on the mark, and here’s his point, given in the last sentence of the abstract: “Evolutionary theory will continue to be extended, but there is no sign that it requires emendation.”

The letter:

We are writing to express our concern about the review in Nature by Eva Jablonka of the recent book by Kevin Lala et al. (Evolution Evolving)(16th January 2025 pages 539-541). The book expounds the “Extended Evolutionary Synthesis” or “EES” which is claimed by its proponents to repair problems with the science of evolutionary biology. Prof. Jablonka was a co-author with two of the book’s authors of an article promoting these claims 1, which would seem to be a conflict of interest for its reviewer. The article that accompanied that publication and refuted such claims 2, is not mentioned by Jablonka, nor are other critiques of the EES, e.g., 3. These papers make clear that several of Jablonka’s assertions are wrong, including the claim that evolutionary biologists believe that mutations “arise at random” with respect to their effects on traits, and that constraints imposed by development on evolutionary changes have been ignored by them. The review gives a false impression of the current state of the flourishing field of evolutionary biology, which owes little to the EES. It is regrettable that Nature should give a platform for such disinformation.

1          Laland, K. et al. Does evolutionary theory need a rethink? Yes, urgently. Nature 514, 161-164 (2014). https://doi.org/10.1038/514161a

2          Wray, G. A. et al. Does evolutionary theory need a rethink? No, all is well. Nature 514, 161-164 (2014). https://doi.org/10.1038/514161a

3          Futuyma, D. J. Evolutionary biology today and the call for an extended synthesis. Interface Focus 7, 20160145. http://dx.doi.org/10.1098/rsfs.2016.0145 (2017). [JAC: This is a Royal Society journal]

What transpired is that Brian says he heard nothing from Nature for a long time. He wrote back to the editor asking what happened to the joint letter. The editor explained that an automatic email response had been sent saying that if the authors didn’t hear anything within three weeks, then the letter was rejected. Brian says he didn’t see that response and admits it could have been binned without him reading it.  The editor also explained why the letter above was rejected, but I can’t reproduce that email without permission. However, you can get a sense of what the editor said from Brian’s final response here:

Dear EDITOR’S NAME REDACTED

Thank your for response. I and my co-authors do not consider it to besatisfactory, for the following reasons.

First, no automated response was received by me; our email was simply ignored.

Second, you say that “the comment piece cited in the review did include both pro and con arguments and authors from both camps”. I assume that you are referring to the reference to Laland et al. 2015, which is the only citation given by Jablonka. This was a polemical piece, arguing for the EES [“Extended Evolutionary Synthesis”] with a few dismissive references to works by mainstream evolutionary biologists.

Third, if asking someone to review a book by their close collaborators is not a conflict of interest, it’s hard to see what would constitute one.

Fourth, you say that “it didn’t make a fresh point that would be of broad interest to readers”. The point of our letter was to make it clear that Jablonka and other advocates of the EES consistently ignore the counterarguments made by ourselves and others in the evolutionary biology and genetics community. Indeed, her review contains the same tired old mistatements about randomness of mutations and developmental constraints that she and her clique keep on making. lt’s hardly our fault that these are not novel. The title of the review “A new vision for evolution is long overdue” gives the completely misleading impression that there are serious problems with our field. This is a view that is held only by a small, but extremely vocal, fringe group, most of whom (including Jablonka) have made no significant original research contributions to the field. No other field of science seems to get this kind of treatment from Nature.

Fifth, you say that “in the end the main goal of our book reviews is to set out issues in a readable way for readers across all disciplines, and we consider that Jablonka did a reasonable job here”. This seems to assign lesser importance to scientific accuracy. Indeed, you have just published a letter about the Jablonka review by a Chinese scientist trying to revive Darwin’s long discredited theory of pangenesis. He states that the theory was published in the last edition of the Origin of Species in 1859 (in fact, the last edition was published in 1872 and contains no reference to pangenesis, which was described in Darwin’s Variation in Animals and Plants under Domestication in 1868. Seemingly, the most basic fact checking is not done by Nature).

In view of these concerns about the treatment of the field of evolutionary biology by Nature, which are shared by my cosignatories (who are all regarded as leading figures in the field, and members of various national academies), I am cc-ing this email to your chief editor.

Yours sincerely,
Brian Charlesworth

Sadly the readers of Nature who are not evolutionary biologists will now think that Lala et al.’s book has indeed shown the need for a “new vision of evolution.” Given the history of the arguments made by the authors, and Jablonka’s summary of the book in her review, there is no such need. Nature blew it by rejecting the letter, which makes essential points (especially Jablonka’s failure to say that the “new vision” is deeply controversial), and also by getting a pal of the book’s authors to review it. What kind of review did they expect?