Brian Charlesworth on the errors of a new paper supposedly showing that a fundamental assumption of neo-Darwinian evolution is wrong

May 9, 2022 • 8:00 am

Intro by Jerry: One of the pillars of neo-Darwinian evolution is the assumption, supported by a great deal of evidence, that mutation is “random.” This does not mean that mutations occur with equal frequency everywhere in the genome (they don’t), that different genes have the same mutation rate (they don’t), or that even within a gene some mutations don’t occur more often than others (they do). Rather, the statement that “mutation is random” means that the likelihood of a mutation occurring does not depend on whether in a given situation it would be advantageous or deleterious.

The idea that mutations are “nonrandom”—usually meaning that adaptive mutations are more likely to occur in some situations (e.g., a change in environment)—has been bruited about for years, mainly because if this was a fairly common phenomenon, it would create a substantial rethinking of the neo-Darwinian theory of evolution. But there is no way we know of that the frequency of an error in the DNA sequence, which is what a mutation is, can be elevated in the adaptive direction when the environment changes. (We know that environmental changes can raise the overall mutation rate, but this is not an adaptive phenomenon because the vast majority of mutations are harmful.) Because of this lack of evidence for “adaptive mutation,” and the absence of a mechanism whereby it could occur, evolutionists continue to accept that mutations are “random” in the sense I defined.

Recently, a paper appeared that seemed to show that at least one mutation in human hemoglobin—the one causing sickle-cell anemia when present in two copies—could occur more frequently in areas where the mutation is adaptive: malaria-ridden areas of Africa. The sickle-cell mutation, as Brian Charlesworth shows below, is adaptive, but only when present in one copy, when, together in a “heterozygote” with one copy of the “normal” hemoglobin beta chain, it confers substantial protection against malaria. The heterozygote has higher survival and reproductive fitness than either the homozygote for the ‘normal’ allele, which is more prone to fatal malaria, and the sickle-cell homozygote, which has the disease sickle-cell anemia and is prone to die before adulthood. The mechanics of population genetics show that if a heterozygote with one copy of each of two alleles has higher reproductive ability (read “survivorship” here) than either of the two homozygotes, it will be maintained in the population at a stable equilibrium frequency, regardless of how bad off the homozygotes are. The sufferings of those with sickle-cell anemia can be seen as the price paid because of the higher malaria resistance of heterozygotes carrying only one copy of the gene. It also shows that evolution doesn’t create the optimum situation: that would be a single mutation that causes malaria resistance when present in either one or two copies.

This, by the way, explains why African-Americans are more prone to sickle-cell anemia than people from other populations, for they still carry the “HbS” mutation prevalent in their ancestors who were brought to America as slaves. The frequency of the HbS mutation in the U.S., however, is now falling, and for two reasons: we don’t have malaria in the U.S., which is necessary to keep the gene at an equilibrium frequency, and because African-Americans have intermarried with whites, who don’t carry copies of HbS. Eventually, prenatal testing and genetic counseling will be able to eliminate sickle-cell anemia, and the HbS allele, completely.

At any rate, the paper, by Melamed et al. (reference below), appeared to show that the mutation rate from the “normal” DNA sequence to the HbS “sickle-cell” sequence was higher in Africans than in Europeans. This was quickly picked up by the popular press as an example of “adaptive mutation” and as a refutation of modern evolutionary theory. (The “Darwin Was Wrong” trope still sells newspapers, especially in America!) Many readers wrote me and asked me about this paper, which I hadn’t yet read, but I told them that a better analysis was in the works.

I pointed this out to my friend, colleague, and ex-chairman (at Chicago) Brian Charlesworth, one of the world’s premier evolutionary geneticists. He quickly spotted the error in the Melamed et al. paper that refuted its conclusion of “adaptive mutation,” but was too busy to refute it on paper. After I kept hectoring him to write something up since the “Darwin was wrong” trope was associated with this paper in many articles in the popular press, he finally deigned to write a short and sweet refutation. Rather than submit it as a rebuttal to the journal (he said he has two refutations of other papers in press, and doesn’t want to get a reputation as a debunker), Brian allowed me to publish the rebuttal here. I’ve put it between the lines below.

Note that the error in Melamed et al. stems from a flaw in the assumptions: that all the new mutations analyzed were independent.

No evidence for an unusually high mutation rate to an adaptive variant

Brian Charlesworth
Institute of Evolutionary Biology
School of Biological Sciences
The University of Edinburgh
Edinburgh, UK

The hemoglobin S variant (HbS) causes the near-lethal sickle cell disease when homozygous (present on both the maternal and paternal chromosomes) and confers protection against malaria when heterozygous (present on either the maternal or paternal chromosome). The HbS variant exists at substantial frequencies in several populations in Africa, as well as in Arabia and India. It is the classic example of heterozygote advantage, whereby a mutation that increases the fitness of its heterozygous carriers cannot replace its alternative because of the loss of fitness to homozygotes. (Note that 2022 is the 100^th anniversary of R.A. Fisher’s discovery of how this process works). The HbS mutation is a single change from adenine to thymine at the sixth amino acid position in the beta globin gene, resulting a change in the amino-acid in the corresponding protein for valine to glutamic acid (it was the first mutation to be identified as causing a change in the sequence of a protein). Studies of the DNA sequences of chromosomes carrying the HbS mutation show that there are five major classes of sequences associated with it, but recent analyses show that the mutation probably arose only once, followed by recombination events that placed it onto different genetic backgrounds. This provides a classic example of what is known as a “partial selective sweep”, in which a new mutation with a selective advantage arises on a single genetic background, so that variants present on this background spread through the population in association with it.

Melamed et al. (2021) claim to have evidence that challenges the standard neo-Darwinian view that natural selection acts on mutations that arise “randomly”, i.e., without reference to their effects on the survival or fertility of their carriers (indeed, most mutations with noticeable effects reduce the fitness of their carriers). The evidence for Melamed et al.’s claim comes from an experiment in which the authors applied a novel technique for identifying new mutations in millions of sperm cells. With regard to the detection of HbS mutations, they characterized sperm from 7 African and 4 European men. They observed 9 instances of the HbS mutation in the sperm of Africans and none in the Europeans. They pointed out that HbS is at a selective advantage in Africans but not in Europeans, and suggested that the seemingly higher mutation rate is the result of a hypothetical process proposed by Adia Livnat, a co-author of the paper, whereby “adaptations and mutation-specific rates jointly evolve”. This claim has been disseminated in the media as evidence against the neo-Darwinian view of selection on random mutations [JAC: see below for some of these media references]– here it is claimed that mutations that are selectively advantageous in a particular environment arise more frequently than in environments where they lack an advantage.

However, there is no statistical support for the claim that there is a higher mutation rate to HbS in African men. While the authors looked at very large number of sperm, these came from only 11 individuals. Five of the nine HbS mutations occurred in a single individual, and 2 other individuals contributed 2 mutations each. The events within individuals cannot be treated as independent of each other, because there is a large population of dividing cells that are precursors of the mature sperm. If a mutation occurs in a cell that gives rise to several sperm after a number of divisions, there will be several copies of the mutation in the sperm pool. This is the cause of the well-established fact that the frequencies of mutations in human sperm increase with the man’s age. If we treat each individual as a single observation, we have 3 cases of HbS mutations among 7 Africans and 0 among 4 Europeans. Fisher’s exact test shows that the difference between Africans and Europeans has a probability of about 11% of arising by chance in the absence of any true difference.

There are other reasons for doubting this claim. First, it is exceedingly hard to see how there could be any biological process that could cause the HbS mutation to have a higher mutation rate in order to allow Africans to evolve malaria resistance, which is thought to have become a significant selective factor at most around 20,000 years ago. Mutations arise as errors in the replication of DNA molecules or as the result of damage to non-replicating molecules. There is no known mechanism whereby an organism could devise a process that would allow it to produce one specific class of mutation at a higher-than-average frequency just when that mutation is at an advantage. Further, the genetic evidence referred to above suggests that the HbS variant prevalent in human populations traces its ancestry back to a single ancestral mutation (Shriner and Rotimi, 2018; Laval et al., 2019) , so that there is no reason to believe that a high mutation rate has enabled multiple copies of the mutation to spread.

References

D. Melamed et al. 2022. De novo mutation rates at the single-mutation resolution in a human HBB gene region associated with adaptation and genetic disease. Genome Research 32:1-11. Free pdf here.

D. Shriner and C. N. Rotimi. 2018. Whole-genome-sequence-based haplotypes reveal single origin of the sickle allele during the Holocene wet phase. Am. J. Hum. Genet. 102:547-556.

G. Laval et al. 2019. Recent adaptive acquisition by African rainforest hunter-gatherers of the late Pleistocene sickle-cell mutation suggests past differences in malaria exposure. Am. J. Hum. Genet. 104:553-561.

Among the many popular articles that cite Melamed et al. as a rebuttal of modern evolutionary theory, see here, here, here, here, here, ad infinitum:

Two examples (click on screenshot)s:

And here’s Brian:

Once again, Darwin gets dragged into the muck by the Woke

January 8, 2022 • 11:00 am

Do you want uplifting news or depressing news? I have both. In the interests of having your day improve later, I’ll proffer the depressing news first. That news involves further attempts to drag Darwin down into the mud.

Dan Dennett called Darwin’s theory of evolution by natural selection a “dangerous idea” because it was like a corrosive acid that ate through and destroyed all ideas of design and a designer as explanations of nature and the way we think about it. Howard University biologist Rui Diogo, however, has a different take. Darwin’s views are “dangerous” because, apparently, they are sexist and racist. And, he adds, this tarnishes his theories and his legacy.

Now I’ve explained in detail, as have others, that yes, Darwin was a man of his time and emitted views that would be considered racist today, though he was ambiguous about even that, as you can see from reading The Voyage of the Beagle (this is part of my Antarctica talk on Darwin and the Fuegians). But there is no doubt that Darwin was far more of an abolitionist than most Brits of his time: his family (the Wedgewoods) had been opposed to slavery since the late 18th century, and Darwin never wavered on his dislike of slavery and support of abolitionism.

So we already know that Darwin wasn’t perfect by modern lights, but he was a damn sight better than most of his peers. I always ask people who like Diogo who tar Darwin with the label of “racist” or “misogynist” if they would have held fully modern and progressive views in the mid 19th century. I doubt it.

Yet the Pecksniffs insist on bringing up Darwin’s racism over and over again, as if we and the public haven’t heard enough about it. And it’s not just brought up to fill in a historical gap about the man’s views—for we already know that—but to cast aspersions on Darwin’s legacy in biology.

Case in point: the topic of the upcoming lecture noted below. Speaker Rui Diogo‘s talk is billed as “an unflinching look at how the racism and sexism of the Victorian era undermined Darwin’s scientific work and legacy.” (My bold.) There will be no flinching by Diogo, but there shouldn’t be by anyone.

First, what he’ll say is already well known by evolutionary biologists, historians of science, and any of the public who care to look up Darwin’s views.

More important, Diogo is dead wrong in asserting that Darwin’s biased views “undermine his scientific work and legacy.” Perhaps in Diogo’s eyes, but not in the eyes of most others. Are we supposed to think less of the theory of evolution, or of natural selection, or of Darwin himself, because he held views more liberal than those of his peers, but not up to snuff in the eyes of a Progressive Democrat? The goal of Diogo, it seems, is to tarnish the luster of Darwin. He won’t succeed because, in the main, Darwin got his science right.

But nobody’s perfect, and I highly doubt that if Diogo was an upper-class Englishman in the Victorian era, he’d be waving signs saying “Black Lives Matter.”

If you want to pay $30 to hear this nonsense, be my guest. But remember that this is sponsored by the Smithsonian Institution. Click on the screenshot if you want to be fleeced.

UPDATE: I’ve found that Dr. Diogo seems to be dining out on Darwin. To see a related lecture from last fall, click on the screenshot:

I can’t be arsed to rebut the following summary of this lecture, as probably written by Diogo. Let me just say that yes, there were precursors of Darwin’s ideas before The Origin, including even natural selection by Patrick Mathew. But his greatness was cobbling together a magnificent edifice that has, in the main, stood the test of time. The bolding is mine:

Profs and Pints presents: “The Damage Done by Darwin,” a look at how the acclaimed naturalist’s racism and sexism undermined his work and haunts us to this day, with Rui Diogo, associate professor of anatomy at Howard University’s College of Medicine and resource faculty member at George Washington University’s Center for the Advanced Study of Hominid Paleobiology.

[Under current District of Columbia regulations attendees will be required to wear a mask except while eating or drinking. The Bier Baron will be requiring proof of Covid-19 vaccination or a negative Covid-19 test from the previous 72 hours for entry. It also will be requiring ticketed event attendees to purchase a minimum of two items, which can be food or beverages, including soft drinks.]

Charles Darwin has long been put on a pedestal and idolized as an objective, rational thinker who challenged the theist views of this day and changed how we see the world for the better. The truth, however, is a lot more complicated. Many of Darwin’s ideas were less original than widely believed and, in many cases, repackaged the false assumptions and prejudices of his era as the purported product of scientific observation. They helped buttress racist and sexist worldviews in ways that would do tremendous damage even to this day.

Tremendous damage? HOW? We already know that Hitler was not a Darwinian, so where’s all that harm? Answer: Diogo is making it up.

If others misused Darwin’s ideas to perpetrate bigotry, that’s not Darwin’s fault. But wait! There’s more!

Join Rui Diogo, an evolutionary biologist who has extensively reviewed Darwin’s books, diaries, notebooks, and letters, for an unflinching examination of Darwin’s life, thinking, and impact.

Professor Diogo will look at how almost none of the grand ideas attributed to Darwin—including the theory of natural selection—truly originated with him. He’ll discuss how Darwin stated as “fact” inaccurate constructions based on Victorian biases and stereotypes. And he’ll explore how Darwin’s assertions, and their warm reception, were very much a reflection of a broader ideological war that had left England’s wealthy Victorian elite eager to find new justifications for their relative privilege in the face of feared revolution.

Many scientists involved in similar research during Darwin’s time were not nearly as racist or sexist in their thinking. But Darwin was more skilled than most in packaging his ideas in ways that made them accessible and appealing to the general public. As a result, his writings became easy ammunition for generations of colonialists, white supremacists, and others seeking to defend social hierarchies, discrimination, and oppression.

Here is a man who doesn’t understand what Darwin actually accomplished.

h/t: Anthony

Faculty response to Western Washington University’s proposal to cancel the name of T. H. Huxley

August 20, 2021 • 11:30 am

As I reported on August 9, Western Washington University (WWU) is poised to change the name of its well known Huxley College of the Environment, named after “Darwin’s Bulldog” Thomas Henry Huxley and listed as one of the University’s “notable degree programs“. The reason? It’s the usual, detailed in a committee-produced document residing on the website of WWU’s President. One quote:

Even though Thomas Huxley made significant contributions in the field of biology [JAC: none are given], he also had significant contributions to scientific racism. He was a polygenist: someone who is of the belief that all races evolved from different origins instead of coming from one homosapien [sic]. This is not only scientifically disproven, but also a racist mindset, and an argument that one of his “archrivals” at the time called Richard Owen attempted to refute with evidence that we all are the same species that evolved from the same homosapien [sic] thousands of years ago. Huxley won the argument, and it is historian Nicolaas Rupke’s thesis that this argument between Huxley and Owen in which Huxley’s “deeply racist, polygenist viewpoint” won lead to building the scientific racism of the early 20th century.

Huxley’s supposed racism is said to cause “harm” to people, both in furthering racism and making students at Huxley College and WWU uncomfortable—in fact, causing them “harm.” The latter claim is simply ludicrous, while the former misguided.

There’s other bad stuff Huxley’s said to have done or said as well, but all of it, without exception, is either wrong or grossly exaggerated. If you know anything about Huxley, you’ll recognize that painting him as a racist who contributed to the discipline of eugenics which then was implemented in humans is risible. Further, his positive contributions to both science and society were completely neglected in the document, which was produced by people who had no expertise in nineteenth century England or Huxley in particular.

Now, eight academics from the Huxley College, trying to set the record straight, have produced a response to WWU’s proposal (the name of Huxley College is only one of several up for cancellation), and it’s pretty telling. I suggest you read it to see how distorted the original proposal for cancellation was. It made several blatant errors, is rife with false and exaggerated claims, and draws largely on material produced by young-earth creationists who want to attack evolution by cancelling a school named after evolution’s most famous early defender.

You can see the document by clicking on the link below:

A few quotes to give you the tenor of the defense:

Natural Racial and Gender Inequality

Regarding the first claim, that Huxley held views of natural racial and gender inequality, we strongly encourage the Board of Trustees to reread the views of the historians, included in Appendix C. The LRTF’s summary is simply not an accurate reflection of their views, Rupke excepted. The concluding words of Paul White, one of those distinguished historians, presents a more accurate synthesis of those views:

Huxley is described as an abolitionist, he was in fact much more than this. He called for the elimination of all political, legal, and economic prejudices, equal rights and opportunities for people of all races (and sexes). If the staff and students agree to remove Huxley’s name, they should at least do so with a better understanding of his views, and an appreciation for his place in the history of human emancipation and activism.

An extremely troubling aspect of the LRTF report is that it lifts quotes first mined by creationists to confirm the racism and sexism claims against Huxley, while ignoring Huxley’s writings and other evidence that disprove the claims. Additionally, the report relies on earlier writings of Huxley, but totally ignores the evolution of thought that led him to see the unity and equality in all humanity. To be sure, Huxley’s earlier views reflected the same Victorian-era prejudices and bigotry of his scientific and clerical peers. But the report ignores the fact that Huxley escaped these prejudices to adopt views expressive of full racial and gender equality.

I guess if you engage in Wrongthink, but then come to Righthink later, it’s already too late. You’re in perdition forever.

Another false claim of WWU, one that I attacked in my earlier post:

Human Hierarchy and Scientific Racism

As for the second and third claims, that Huxley promoted a hierarchy of humans and scientific racism, the LRTF again relies on the ideas of Lyndon LaRouche operative Paul Glumaz (but without citation) and Rupke to paint Huxley as a polygenist (someone who accepts the idea that the human “races” evolved from different origins) and as holding that there exists a greater difference among “the races of man” than that between “the lowest Man and the highest Ape.”

First, it is a complete fabrication to claim that Huxley was a polygenist. This is simply another gaslighting distortion that was uncritically accepted by the LRTF. The consensus view in the history of science literature is that Huxley opposed the theistic theory of monogenesis – the idea that humans descended from Adam and Eve. This does not make him a polygenist. What he did support was scientific monogenesis, or the “new monogenism” – that H. sapiens is a single species with a monophyletic (one population) origin followed by diversification through migration and geographic isolation. The “poly-” element to Huxley’s thinking explicitly relates to the diversification through migration and geographic isolation, not to human origin.

Huxley’s view is wholly consistent with current scientific consensus and follows current thinking based on DNA evidence. The claim that Huxley’s views were not monogenist demonstrates fundamental misrepresentation of his views, the basic tenets of evolution, and the seeds of disinformation planted by creationists. Huxley in fact wrote that polygenists “have as yet completely failed to adduce satisfactory positive proof of the specific diversity of mankind.”

And, to make a long report short, the WWU cancellation document completely ignores the many positive contributions Huxley made. He was a big reformer of education and spent much of his later life giving lectures on science to working people. But here’s from the new rebuttal document:

. . . the report utterly ignores the demonstrable benefit and good that Huxley did create in his life work. In reality, the whole thrust of Huxley’s career was to make science, and education, more inclusive. Paul White again:

Huxley devoted a great deal of his career to them in the field of education reform. He campaigned tirelessly for universal education, for the introduction of science and other modern subjects to schools and universities, for a true ‘liberal education’ as well as technical education for the working classes. In doing so, he opposed some of the most entrenched ideological and institutional hierarchies in Britain at the time, those of class.

The LRTF report completely overlooks the concrete evidence of positive impact Huxley made on society generally, and in the lives of its marginalized and underrepresented members in particular. Historians recognize Huxley as “the premier advocate of science in the nineteenth century”. He is also recognized as the single most influential person in the democratization of science and science education, for his role in the founding of the journal Nature, as founder and president of many scientific societies, for his work on the Jamaica Committee, and for his work on ten Royal commissions. He is widely recognized for his leadership in the creation of the field of science education, for devising modern K-12 education curriculum for both the privileged and the masses, for bringing college and vocational opportunities to the working class, for fighting for the admission of women to universities, and as history’s greatest popularizer of science for common people. Lastly, Huxley’s life and work contributed significantly to the secularization of society and secular educational institutions like WWU.

Also not acknowledged in the LRTF report is Huxley’s decades-long battle against the idea of scientific racism, and its chief proponent, James Hunt. He also vehemently opposed Hunt and the Anthropological Society for their support of not only the Confederacy, but for the institution of slavery.

I’ll stop here, but, having read the original de-naming proposal and the rebuttal (yes, of course I’m biased), I have to say that the original proposal is not only ignorant, but unscholarly and, at times, illiterate (“homosapien”??). They didn’t even check their sources about things like Huxley’s supposed polygenism (his view was in fact the opposite), and Huxley’s claim that there was a greater evolutionary distance between the “highest and lowest humans” (races) than between the “lowest” humans and the “highest” apes, like chimps and gorillas. That’s not what Huxley said, and the “law”, mentioned only once in the old literature, isn’t even in the consciousness of modern biologists.

One gets the sense that the de-naming proposal was a rush job, confected from dubious sources, ignoring Huxley’s contributions, and designed to give succor to those individuals who claimed that the name of the school caused them “harm” (I’m sorry, but I have trouble working up empathy for that claim). The cancellation of his name may be a done deal, but if it’s not, this new document should change the mind of any rational person. Of course, it’s dangerous to assume that university administrators are rational, as they’re easily swayed by the quotidian breezes of political change.

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The pro-evolution website The Panda’s Thumb has also covered this controversy, defending Huxley in three posts (here, here, and here). They also give two other useful links:

Also, today at 8:50 am PDT, Dr. Wayne Landis and I will be making public comments at the BOT meeting, introducing them to the response document and briefly summarizing it.

You may find documentation for the meeting here. The meeting itself will be audiocast here.

Response by Brian Charlesworth to the latest episode of Darwin-dissing

June 9, 2021 • 9:30 am

My friend, colleague, and former chair Brian Charlesworth, a well known evolutionary geneticist, had some thoughts about Agustín Fuentes’s op-ed critique of Charles Darwin recently published in Science. (See my own posts about Fuentes here, here, and here.) As you’ll see, he feels that Fuentes distorted Darwin’s views; Brian attempts a longer and more objective summary.

Fuentes’s thesis was not just that Darwin himself was, on the subject of human evolution, often sexist, racist, and bigoted, but that his views were injurious, justifying “empire and colonialism” as well as “genocide” to those who adopted the thesis of “survival of the fittest.” As I’ve argued before, Fuentes grossly exaggerates Darwin’s bigotry, for although the man shared some of the prejudices of his time, he was far more liberal than the average English gentleman. (For one thing, Darwin was an ardent abolitionist.) Also, Darwin is not responsible, and in fact rejected, the “social darwinism” that justified oppression and conflict by saying it was “natural”.

Brian’s collection of thoughts on Fuentes’s piece is below. Statements by Darwin himself are indented in normal type, while Fuentes’s statements are indented and italicized. But first, here’s Brian’s explanation of why he put together the notes; I’ve added a photo of Brian to the bottom of this post.

Why did I compile these notes on Agustín Fuentes’ Science editorial on The Descent of Man, where he accused Charles Darwin of justifying genocide on the basis of the ‘survival of the fittest’? I had previously been a co-author of a paper (Bodmer, W.F. et al. 2021 Heredity ; https://doi.org/10.1038/s41437-020-00394-6) that described the views on eugenics and race of the great statistician and geneticist, R.A. Fisher. This prompted a good deal of criticism, including attempts by an anti-racist group at the University of Edinburgh to have the paper suppressed, on the grounds that it was a “defence of the geneticist R.A. Fisher’s abhorrent views on race and eugenics” (https://twitter.com/UoEREN/status/1374408913861308431). This attracted the attention of the UK national press, with the Daily Mail newspaper asserting that Fisher advocated “sterilisation of people from races he considered ‘mentally inferior’ ” (University of Edinburgh in free speech row over article praising scientist who advocated eugenics | Daily Mail Online).

Both this episode and the Fuentes article raise two issues. First, while I strongly support removing social and racial injustices, I feel that it is important that we examine the context of opinions expressed in past times, and arrive at a judgement of how positive achievements can be recognised, even when some beliefs are expressed that are obnoxious to people today. Conducting such an examination should not be viewed as defending views that are today regarded as abhorrent, as happened to the paper about Fisher. Enormous benefits have accrued to humanity from Fisher’s statistical innovations and from Darwin’s biological discoveries. This contrasts with slave traders, slave owners, segregationists and Nazis, who did nothing but harm. Second, we must get the facts right. Darwin never justified genocide (indeed, he had a lifelong hatred of cruelty in any form); Fisher never referred to ‘inferior races’ or advocated their sterilization.

My notes on the Fuentes article represent an attempt to give a clearer picture of what Darwin actually wrote and thought than was conveyed by the article itself.

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Some Notes on A. Fuentes’ Science Editorial about Darwin’s The Descent of Man

(Science 2021, 372: 769 DOI: 10.1126/science.abj4606)

Brian Charlesworth, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh

First, it should be recognized that modern readers of the Descent will find a number of statements and wordings objectionable, notably the use of the terms “lower races” and “savages”. This was, however regrettable, the language commonly used by Victorian writers. It does not shed a flattering light on the prejudices of that age, but it should be recognized that Darwin’s general views on social issues, such as his hatred of slavery and child labour, were among the most enlightened of his time. For example, he was a member of the 1864 committee that urged the prosecution of Governor Eyre of Jamaica for his brutal suppression of protests by the black population.

This aspect of Darwin is barely acknowledged by Fuentes, who remarks that:

“Descent” is often problematic, prejudiced, and injurious. Darwin thought he was relying on data, objectivity, and scientific thinking in describing human evolutionary outcomes. But for much of the book, he was not. “Descent,” like so many of the scientific tomes of Darwin’s day, offers a racist and sexist view of humanity.

This gives a distorted view of the book as a whole. Including Selection in Relation to Sex, there are 954 text pages in the 1874 second edition (John Murray version; the pagination varies among versions), and pp. 319-845 are devoted to animals, not humans. On my reading, the other 45% of the book includes seven passages that express what appear to be racist and sexist views. The most obnoxious of these (p.213) was not written by Darwin himself, but is a lengthy quotation from a Mr Greg concerning competition between Saxons and Celts (the latter being held to be inferior).

[From Fuentes’s piece]:

Darwin portrayed Indigenous peoples of the Americas and Australia as less than Europeans in capacity and behavior. Peoples of the African continent were consistently referred to as cognitively depauperate, less capable, and of a lower rank than other races.

There is only a handful of references to the mental abilities of Africans in the book; contrary to the impression given by Fuentes. Darwin’s statements about mental differences between the races are ambiguous and fluctuating, and many of them are very enlightened compared with remarks by his contemporaries such as T.H. Huxley, Karl Marx and Walt Whitman. For example, on p.276 he says:

“ .. they [races] are found to resemble each other closely in a multitude of points. Many of these are of so unimportant or of so singular a nature that it is extremely improbable that they should have independently acquired by aboriginally distinct species or races. The American aborigines, Negroes and Europeans are as different from each other in mind as any three races that can be named, yet I was incessantly struck while living with the Fuegians on board the “Beagle”, with the many little traits of character, shewing how similar their minds were to ours; and so it was with a full-blooded negro with whom I happened once to be intimate.”

Furthermore, in Darwin’s diary of the voyage of the Beagle (July 3, 1832), he describes the black men of Brazil in complimentary terms:

“I cannot help believing they will ultimately be the rulers. I judge of it from their numbers, from their fine athletic figures … & from clearly seeing their intellects have been much underrated; they are the efficient workmen in all necessary trades.”

It should be remembered that Darwin (and his contemporaries) had no clear grasp of the distinction between genotype and phenotype that is at the core of modern genetics, and he attached considerable significance to the inheritance of acquired characters in the Descent. Therefore, when he referred to race or sex differences in mental traits, it is often unclear whether he thought they were purely cultural in origin, or were innate; but several passages make it clear that Darwin attached considerable importance to cultural factors. When comparing the indigenous inhabitants of New Zealand and Tahiti, he remarked on the effects of education by missionaries on “teaching them the arts of civilization” on the former and the “kind, simple manners” of the latter (Letter to Caroline Darwin, 27 December 1835).

At the end of Chapter 7, Darwin argued forcefully that civilized societies have comparatively recently emerged from barbarian societies and (p.223) noted that:

“The Tahitians when first visited had advanced in many respects beyond the inhabitants of most of the other Polynesian islands. There are no just grounds for the belief that the high culture of the native Peruvians and Mexicans was derived from abroad.”

Fuentes goes on to say:

These assertions are confounding because in “Descent” Darwin offered refutation of natural selection as the process differentiating races, noting that traits used to characterize them appeared nonfunctional relative to capacity for success. As a scientist this should have given him pause, yet he still, baselessly, asserted evolutionary differences between races.

Darwin appealed to sexual selection as a process in differentiating human populations; this is simply a sub-class of natural selection as far as evolutionary mechanisms are concerned.

Fuentes’s statement seems to suggest that he thinks that there are no genetic differences between human populations and that natural selection has nothing to do with them. This is in contradiction with many findings of human population geneticists concerning the action of selection on important traits, such as resistance to malaria, the ability to resist anoxia in high altitude populations, and lactose tolerance in populations that consume milk products. Even without selection, genetic differences between populations in selectively neutral characters can evolve by random genetic drift – subtle differences in the frequencies of large numbers of DNA sequence variants have been revealed even within the population of the British Isles.

Accepting the evidence for genetic differences between human populations carries no implication of believing in racial purity or superiority, or the related pseudo-scientific justifications for discrimination with which we are all too familiar. For quantitatively varying traits, which are subject to both environmental and genetic influences, differences between populations are statistical, in the sense that there is much variability within populations (as Darwin himself noted in relation to human races), which is often greater than any between-population variation. Without complete standardisation of the environment, it is impossible to determine whether observed differences in the mean values of a trait between populations has a genetic basis (this is the basis for the classic “common garden” experiments of plant evolutionary geneticists).

He went beyond simple racial rankings, offering justification of empire and colonialism, and genocide, through “survival of the fittest.”

There is no evidence Darwin use his science to justify “empire and colonialism, and genocide”. It is true that, like most Victorians, he took a favourable view of British colonization of the Americas, Australia and New Zealand, as shown by some of his statements. But his discussion of the extinction of indigenous populations in Chapter 7 of the Descent emphasised the role of disease and demoralisation, and it is unjust to suggest that he thought that such extinctions were to be applauded.

For example, in his Beagle Diary (4^th-7^th of September 1833), he exclaims with horror about the massacres of Indians in Patagonia:

“Who would believe in this age in a Christian, civilised country that such atrocities were committed? … The country will be in the hands of white Gaucho savages instead of copper coloured Indians. The former being little superior in civilisation, as they are inferior in every moral virtue”.

Fuentes also says:

In “Descent,” Darwin identified women as less capable than (White) men, often akin to the “lower races.” He described man as more courageous, energetic, inventive, and intelligent, invoking natural and sexual selection as justification, despite the lack of concrete data and biological assessment. His adamant assertions about the centrality of male agency and the passivity of the female in evolutionary processes, for humans and across the animal world, resonate with both Victorian and contemporary misogyny.

This presumably refers to the following passage on p.858 of the Descent:

“It is generally admitted that with women the powers of intuition, of rapid perception, and perhaps of imitation, are more strongly marked than in man; but some, at least of these, are characteristic of the lower races and therefore of a past and lower state of civilisation.

The chief distinction in the intellectual powers of the two sexes is shown by man’s attaining to a higher eminence, in whatever he takes up, than can woman – whether requiring deep thought, reason or imagination, or merely the use of the senses and hands.”

This was followed by (pp.859-860):

“These latter faculties [various mental traits] … will have been developed in man, partly through sexual selection… and partly through natural selection… Thus man has ultimately become superior to woman. It is, indeed, fortunate that the law of equal transmission of characters to both sexes prevails with mammals; otherwise it is probable that man would have become as superior in mental endowment to woman, as the peacock is in ornamental plumage to the peahen.”

This certainly shows that Darwin believed in the mental inferiority of women, and that this had, at least in part, an innate rather than cultural basis. This was the prevalent view at his time, which persisted until very recently (Fuentes’ institution, Princeton University, did not admit women until 1969, and my old Cambridge college only allowed the entry of female students in 1983).

However, Darwin strongly emphasized the importance of female choice in the evolution of sexual dimorphism in animals, so that Fuentes’ characterization of his views of the role of females in evolution is inaccurate. Darwin even extended it to humans (pp.914-915):

“Preference on the part of the women, steadily acting in any one direction, would ultimately affect the character of the tribe; for the women would generally choose not merely the handsomest, according to their standard of taste, but those who were at the same time best able to defend and support them. Such well-endowed pairs would commonly rear a larger number of offspring than the less favoured.”

Darwin’s theory of sexual selection was not well received, partly because of the emphasis on female choice, and (apart from R. A. Fisher’s advocacy in 1930), it did not start to receive serious attention from biologists until the late 1950s. Today, of course, it is recognized as a major factor in evolution, illustrating Darwin’s originality when he was able to free himself from prejudice.

Fuentes alleges that:

Racists, sexists, and white supremacists, some of them academics, use concepts and statements “validated” by their presence in “Descent” as support for erroneous beliefs, and the public accepts much of it uncritically.

I doubt that characters like Governor George Wallace and Sheriff Clark were much influenced by reading The Descent; in any case, most US racists probably do not believe in evolution.

Darwin scholars have discussed in great detail how a variety of ideologues of very different political persuasions have appealed to Darwin’s writings. Social Darwinism is, of course, notorious. On the other hand, Robert Richards, in his 1986 book (p.526), described how August Bebel, the 19^th century leader of the German Social Democrats, thought that “capitalism put artificial restraints on the action of natural selection, so that the idiot son of the factory owner had the advantage over the talented son of the factory worker.” Bebel believed that “the natural forces of progressive evolution would produce a classless society in which property would cease to exist and women would not longer suffer political and sexual subjugation”. Other German thinkers, such as Ernst Haeckel, drew entirely opposite political conclusions; as Richards states (p.533), these contributed to the rise of Nazi ideology. But Richards adds that “The Nazi elite resisted evolutionary theory, despite its scientific charms. After all, could the Aryan race have descended from a tribe of baboons?”.

It seems that, unless you are an out-and-out creationist, you can interpret Darwin to justify almost any a priori belief.

Fuentes concludes by asserting that:

In the end, learning from “Descent” illuminates the highest and most interesting problem for human evolutionary studies today: moving toward an evolutionary science of humans instead of “man.”

First, “man” as used in the title of the Descent is a gender-neutral term referring to “humans”, as was common English language usage until recently.

Second, the last phrase suggests (perhaps unintentionally) that the modern evolutionary biology of humans has hardly moved on since Darwin’s day, and is still burdened with racial and sexist prejudices. This is a misleading caricature; while evolutionary biologists respect Darwin’s towering achievements in founding their field, they recognise that he (inevitably) was wrong about many things, most notably the mechanism of inheritance. There is a damaging confusion here between the views on certain issues of individuals who pioneered a branch of science, and the content of the science as it is currently practised and taught.

More “evolutionary theory overturned” hype, but, as usual, it’s overrated

October 5, 2020 • 12:45 pm

Once again the magazines are hyping Big New Changes in Evolutionary Theory. This time, though, it’s the respected The Economist, which has a policy of not showing the authors’ names. They should have, for some authors should be given an education about their subject, or at least be held accountable for errors. I am surprised that the website has such a long article, though I don’t often read The Economist, so I was unaware that they did long-form science.

Unfortunately, this is not good long-form science because it distorts and exaggerates the evidence for the role of hybridization in speciation.

First, note the subtitle of the new article below (thanks to many readers for sending it to me). “The origin of species is more complex than Darwin envisaged.” That’s not even wrong. Darwin didn’t advance much of a theory of speciation in The Origin, as he had little idea of what a species was. And what he did say about speciation in that book was, as I note on the first page of my and Allen Orr’s book Speciation, “muddled or wrong.” Nobody touts Darwin as an expert on speciation, despite the title of his great book.

The modern theory of speciation began coalescing in the 1930s and 1940s with the works of Theodosius Dobzhansky and Ernst Mayr, supplemented by Ledyard Stebbins, whose big contribution was to show that in plants, a form of hybrid speciation called “allopolyploidy,” was important in forming new species. All of these authors took speciation to mean the origin of reproductive isolating barriers impeding gene exchange between separate species, with the barriers generally arising by selection causing evolutionary divergence between geographically isolated populations. If substantial barriers arose as a byproduct of that evolutionary divergence, then speciation had occurred.

That view hasn’t changed much, although our view of how species arise has been a bit refined. But it surely hasn’t been “upturned,” as the article implies: what we know about speciation still rests on a scaffold erected 80 years ago. Yes, of course Darwin’s view of speciation has been completely revised, but we’ve known that for eight decades. It’s like saying, “How genetics has upturned the theory of inheritance,” with the subtitle, “The way heredity works is more complex than Darwin envisaged.”

And the major framework of Darwinism, the five-fold thesis that organisms evolved, that they did so slowly rather than instantly (and in a replacement rather than an individual transformation way), that there is a branching tree of life that began with one ancestral species, that all species, living or dead, have common ancestors, and that the mechanism for creating adaptations (the “match” between an organism, its way of life, and the environment) is due to natural selection—none of these five propositions are affected by the discovery that, as the article notes, hybridization is more common than we used to think. Yes, hybridization is more common than we used to think. What is not true—or at least is unevidenced and probably untrue—is that hybridization is a major cause of speciation in animals. (It is in plants.) But have a read below; The Economist piece is free:

The article was written to show the increasing prevalence of gene exchange between “species” in nature, and, more important, to emphasize that this gene exchange has been instrumental in creating new species. That is, there is a non-Darwinian form of speciation that involves not bifurcation of family trees, but exchange between branches of family trees, leading to new species. That is, here’s how we get new species, and one can say that it is indeed does not lie within the bifurcating-tree framework of Darwinism as limned above (figure from the Evolution paper below):

There are two ways this can happen. First, species can produce full hybrids and then the hybrid genome, forming a full population of hybrid individuals, can sort itself out into a new species—that is, a new group of populations that are reproductively isolated from the parental species. And this itself can take two forms. The first, allopolyploidy in plants, involves two plant species with different chromosome numbers (or arrangements) hybridizing, and that hybrid then doubles its number of chromosomes, forming an “allopolyploid” population that will be reproductively isolated from the two parental species. (Hybrids with the parents will produce sterile individuals with three sets of chromosomes.) In my book Speciation with Allen Orr, we show that this kind of speciation is pretty common, accounting for up to 4% of speciation events in flowering plants and 7% in ferns.

The second form of full-hybrid speciation is called “homoploid hybrid speciation”, and involves not an increase in chromosome number, but a normal diploid hybrid forming a population of hybrids, which then evolves into a population reproductively isolated from both parents. The Economist claims this is fairly common. But data I show below suggest it isn’t.

Finally, there is a third way that hybridization can contribute to speciation. That is through introgression: the occasional infusion of genes between species that could be used in adaptation and speciation. (To be part of speciation, those infused genes have to contribute to reproductive isolation between the new “part hybrid” species and its ancestors.) Thus we don’t get an entire population of full hybrids evolving into a new species; rather, speciation occurs in a population that’s taken up a handful of genes from another species through occasional hybrids. This introgression has happened between modern Homo sapiens and the Neandertals on the one hand and the Denisovans on the other, but it hasn’t lead to new species. That form of introgression is roughly equivalent to mutation on a larger scale, introducing genetic variation that can be (and was, in the case of Neanderthals) used to adapt to environmental changes.

This form of “introgressive speciation”, too, is much rarer than The Economist says, and for the same reasons why homoploid hybrid speciation is rare: we simply don’t have many examples of parental genes in hybrids actually causing the reproductive isolation themselves, though they may cause new morphologies and traits in hybrids that can speciate by more conventional means. (That is, natural selection operates on hybrid or introgressed populations, producing reproductive isolation as a byproduct of the adaptive change, so that genes in the original parents aren’t the cause of reproductive barriers.)

This paper on birds in Evolution, published in 2014, sets out the criteria for homoploid hybrid speciation. Nearly all the examples cited in The Economist piece were already published by then:

Here are the authors’ criteria for homoploid hybrid speciation, the case most emphasized by The Economist:

. . . we define hybrid speciation as a speciation event in which hybridization is crucial in the establishment of reproductive isolation. Although we agree with previous reviews on the definition, we focus this piece on establishing standards for the genetic and phenotypic evidence required to demonstrate that homoploid hybrid speciation has occurred. To demonstrate that hybrid speciation has occurred given this definition, three criteria must be satisfied: (1) reproductive isolation of hybrid lineages from the parental species, (2) evidence of hybridization in the genome, and (3) evidence that this reproductive isolation is a consequence of hybridization. By contrast, a large number of empirical studies have simply used genetic evidence of hybridization (Criterion 2) as support for hybrid speciation (see below).

In our discussion, we evaluate the strength of evidence for homoploid hybrid speciation in studies published in the last decade against these three criteria. We argue that much of the evidence presented in proposed cases of homoploid hybrid speciation does not provide strong support for the hypothesis of hybrid speciation. In addition, we outline the evidence required to support hybrid speciation and suggest promising directions for future studies.

The criteria, though stringent, seem quite reasonable to apply to claims of hybrid speciation. I won’t go through all the analysis, but just present this graph of how many cases fit each of the authors’ three criteria. Plants are in dark green, fungi in lighter green, and animals in very light green. Note the y axis is number of studies, and it goes up to only fifty. The last column are the cases that fit all three criteria, that is, cases that might well represent homoploid hybrid speciation. Note how low the bar is!

For meeting all the authors’ criteria for homoploid hybrid speciation (last column), we have three cases in plants (all involve the superb work of Loren Rieseberg’s group on sunflowers in the genus Helianthus), none in fungi, and exactly one in animals, the hybrid butterfly species Heliconius heurippa.

The “Big Bird” case of a hybrid species of Galápagos finch that starts out The Economist‘s article isn’t considered, but it, too, is a bit problematic, as it involves a very few finches that show some reproductive isolation but are in a population of very recent origin that hasn’t been examined in about a decade, as I recall. If that small population persists and remains reproductively isolated from the two other finches on the island, we’ll have one more case in animals. That would make a total of five cases of homoploid hybrid speciation among all three groups examined, and that’s a very small number. It’s certainly not enough cases to say that this kind of hybrid speciation has been at all common, much less ubiquitous. Now it may be that there are more cases that we simply don’t know about, but until we find them, we’re not justified in saying that they’re common, much less that “evolutionary theory is upturned.”

A related paper published in 2018 examines claimed cases of hybrid speciation in birds. Click on the screenshot to read it:

Author Jente Ottenburghs examines seven purported cases of hybrid speciation in birds, some of which are mentioned in the Economist piece. He uses two criteria for whether bird speciation is homoploid hybrid speciation, the same type considered by Schumer et al. above. That is, these are cases in which a hybrid population is supposed to have evolved into new species. And, like Schumer et al., he judges the evidence on whether the reproductive isolation comes directly as a result of the hybridization, which is true hybrid speciation, or whether the hybrid population evolves reproductive isolation by more conventional processes, like natural selection acting on new mutations to create evolutionary divergence—with the byproduct of reproductive isolation—in geographically separated populations.

Ottenburghs finds only one convincing case of homoploid hybrid speciation in birds: the “Big Bird” case of incipient speciation in Galápagos finches. He finds just three cases in which species form after hybridization but the reproductive isolation is not the direct consequence of hybridization (Audubon’s Warbler, likely to be renamed by the Woke), the Golden-crowned Manakin, and the Italian Sparrow. So even here, in a group where hybrid speciation is supposed to be common, we have fairly convincing evidence in only four cases.

The upshot. Considering eukaryotes—I’m not dealing with bacterial “species” here, a complicated issue discussed in Speciation—we have at most five cases of true homoploid hybrid speciation, and then a few more cases of speciation after hybridization in which the reproductive isolation evolves by conventional Darwinian means. There is a difference between hybrid speciation and speciation that occurs via neo-Darwinian processes in a population of hybrids.

In other words, we don’t have near enough data to “overturn evolutionary theory”, or to say that new species often don’t form by a branching process. As far as we know, Darwin’s bifurcating tree is still good for nearly all eukaryotes.

Nor do we think that “Darwin’s concept of speciation as a slow and gradual process” is overturned by homoploid hybrid speciation, which, if it evolves via normal processes of selection and drift, could still be very slow. Yes, polyploidy is quick (a new species arises in three generations), and is not something Darwin considered. But allopolyploidy (the hybrid form of polyploid speciation) has been recognized as an important form of speciation in plants since at least 1950, when Ledyard Stebbins published Variation and Evolution in Plants, drawing plants into the Modern Evolutionary Synthesis. Well, that was 70 years ago. Allopolyploidy is important, but it’s old news.

But one thing we know now that we didn’t know before, and I think I’ve emphasized this, is that introgression—genes moving into species from other species—is more common than we used to think. This comes from the molecular innovations that have made such introgressions detectable. But that doesn’t mean that hybrid speciation is more common than we used to think. In fact, it may well be less common than we used to think.

It seems to me that The Economist‘s policy of not naming the authors of its pieces is not a good one for stuff like this, for the author, whoever he or she is, is represented as giving scientific facts and conclusions. If they’re exaggerated or misrepresented, the author should be held accountable.

The intellectual vacuity of New Scientist’s evolution issue: 4. The supposed importance of genetic drift in evolution

September 29, 2020 • 10:45 am

Genetic drift is the random change in frequencies of alleles (forms of a gene, like the A, B, and O alleles of the Landsteiner blood-group gene) due to random assortment of genes during meiosis and the fact that populations are limited in size. It is one of only a handful of evolutionary “forces” that can cause evolution—if you conceive of “evolution,” as many of us do, as “changes in allele frequencies over time” (“allele frequencies” are sometimes called “gene frequencies”). Other forces that can cause evolutionary change are natural selection and meiotic drive.

Genetic drift certainly operates in populations, for it must given that populations are finite and alleles assort randomly when sperm (or pollen) and eggs are formed. The question that evolutionists have been most concerned with is this: “How important is genetic drift in evolution?” We know that, if populations are sufficiently small, for instance, drift can actually counteract natural selection, leading to high frequencies of maladaptive genes. This is what has happened in small human isolates, such as religious communities like the Amish and Dunkers. It’s not clear, though, that this has happened with any appreciable frequency in other species.

Drift was once implicated by Sewall Wright, a famous evolutionist, in his well-known “shifting balance theory of evolution“, which maintained that drift was essential in producing many adaptations in nature. That theory was once influential, but has now fallen out of favor, and I take credit for some of that (see my collaborative critiques here and here).

Related to this are various theories that see genetic drift and its maladaptive effects as crucial in forming new species (e.g., the “founder-flush” theory of speciation). In my book with Allen Orr, Speciation, we analyze these ideas in chapter 11 and conclude that drift has been of minimal importance in speciation compared to natural selection.

Finally, genetic drift was an important part of Steve Gould’s theory of punctuated equilibrium, for it was the force that allowed isolated populations to undergo random phenotypic change, tumbling them from one face of “Galton’s polyhedron” to another. This was one of the explanations for why change in the fossil record was jerky. Well, the fossil record may well be punctuated, but Gould’s theoretical explanation was pretty soundly dismantled by population geneticists, including several of my Chicago colleagues (see this important critique).

While one can cite examples of genetic drift operating in nature, like the expected loss of genetic variation in very small populations, in my view it hasn’t been of much importance in speciation, morphological and physiological evolution, or in facilitating adaptive evolution by pushing populations through “adaptive valleys.” Even the view that it has made species vulnerable to extinction by reducing the pool of genetic variation needed to adapt to environmental change has been exaggerated. I know of no extinctions caused by genetic drift, though I haven’t checked on the cheetah example lately (they were said to be highly inbred because of small populations, but I’m not sure that this is what makes them vulnerable to extinction). In fact, for conservation purposes, I believe the importance of loss of genetic variation through drift has been much less than the importance of reduced population size itself that makes populations vulnerable to extinction because individuals can’t find mates or overgraze their environment, or simply because if you’re a small population, random fluctuations in numbers are more likely to make you go extinct. This is demographic rather than genetically based extinction.

But drift has been important in molecular evolution, causing a turnover of gene variants over long periods of time. If those variants are “neutral”—that is, they are equivalent in their response to natural selection—then they will turn over at a roughly linear rate with time, and the changes can be used as a sort of “molecular clock” to estimate divergence times between species. This kind of molecular divergence has been used to construct family trees of species as well as to estimate the times when species diverged. This is a fairly new usage, for such molecular tools and estimates have been available only since the 1960s.

On to the New Scientist bit about drift in its latest issue, a special on evolution.

The 13-point section about how new findings will expand our understanding of evolution includes section 9 about drift, called “Survival of the luckiest.” It first recounts, accurately, how drift operates, but then exaggerates its importance by mentioning two studies of urban populations of animals, populations that in principle should show more drift than wild populations because populations living in cities are small and fragmented. The section says nothing about any of the things I just told you, which is what evolutionists have really been concerned about with respect to genetic drift.

Here’s the entirety of how New Scientist says drift is revising our view of evolution (the author of this section is Colin Barass):

Biologists have known about genetic drift for a century, but in recent years they realised that it could be especially common in urban settings where roads and buildings tend to isolate organisms into small populations. A 2016 study of the white-footed mouse, Peromyscus leucopus, in New York supported the idea. Jason Munshi-South at Fordham University, New York, and his colleagues discovered that urban populations have lost as much as half of their genetic diversity compared with rural populations.

Last year, Lindsay Miles at the University of Toronto Mississauga, Canada, and her colleagues published a review of evidence from about 160 studies of evolution in urban environments, in organisms ranging from mammals and birds to insects and plants. Almost two-thirds of the studies reported reduced genetic diversity compared with rural counterparts, leading the researchers to conclude that genetic drift must have played a role. “Genetic drift can definitely be a significant driver of evolution,” says Miles.

These findings have big implications, because populations lose their ability to adapt and thrive if they lack genetic diversity for natural selection to work on. Of course, genetic drift isn’t confined to urban settings, but given how much urbanisation is expected to grow, the extra threat it poses to wildlife is concerning. It highlights the need to create green corridors so that animals and plants don’t become isolated into ever-smaller populations.

I don’t think those findings do have “big implications”, because the important of reduced genetic variation in urban environments is unclear, particularly when the genes assayed have no clear connection with natural selection. And the import of losing half of your genetic diversity is also questionable: after all, a single fertilize female contains half of the “heritability” of an entire population. Everything rests on whether evolution by natural selection depends on very low-frequency genetic variants, present only in big populations, and we don’t really know if this is the case. And the above study is in white-footed mice, only one species among millions, and only for populations in urban environments. That’s not to denigrate it, just to point out that its relevance to nonurban nature is unclear and its relevance to evolution is equally unclear.

You can read the Miles et al. study at the link (here), and having read it, I wasn’t impressed, since the authors themselves don’t come to nearly as strong a conclusion as does New Scientist. Here’s from the paper’s conclusions:

Although our review of the literature with quantitative analyses of published urban population genetic data sets demonstrates trends towards increased genetic drift and reduced gene flow, these patterns were not significant and were not universally seen across taxa. In fact, over a third of published studies show no negative effects of urbanization on genetic diversity and differentiation, including studies supporting urban facilitation models at a much higher proportion than previously realized. How populations and species respond to urbanization clearly depends on the natural history of the taxa investigated, the number and location of cities being sampled, and the molecular techniques used to characterize population genetic structure.

In other words, although two-thirds of the studies showed reduced variation or increased inter-population differentiation, these patterns were not significantly different from non-urban populations. And if those differences were not significant, you needn’t start speculating about genetic drift. The authors conclude simply that different species show different genetic patterns when living in urban environments.

Miles’s statement that “genetic drift can definitely be a significant driver of evolution” is ambiguous, because she doesn’t say what she means by “significant” or by “evolution” (is she talking just about patterns of molecular evolution, like genetic diversity, or other types of evolution?)

New Scientist, in other words, fails to make the case that genetic drift has changed our view of how evolution operates, much less that it’s modified the modern synthetic theory of evolution. We already knew that small populations lose genetic variation because of genetic drift, and that’s been standard lore for decades. The real novel claims about drift—that it facilitates adaptive evolution, that it’s an important driver of speciation, and that it explains punctuated patterns in the fossil record—have disappeared because of the absence of both data and theory supporting those claims.

I am weary of going after New Scientist, and this may be my last critique of that issue. But be aware that virtually every one of the other nine points is exaggerated as well. Move along folks—nothing to see here.

The intellectual vacuity of New Scientist’s evolution issue: 3. The supposed importance of epigenetics in evolution

September 28, 2020 • 11:00 am

I’ll continue on with New Scientist‘s 13-section claim that the modern theory of evolution needs a reboot (see previous posts here and here), though I don’t know how much longer I can stand their uninformed palaver written by incurious journalists. Today we’l take up section 4: “There is more to inheritance than just genes”, which emphasizes the importance of epigenetic changes in evolution. The article appeared in this special issue of the ~~rag~~ magazine:

As I’ve written many times before, epigenetic changes are not good candidates for an inherited basis for evolutionary change, mainly because the vast majority of epigenetic modifications of DNA—usually via methylating DNA bases—disappear within one generation, as the DNA effaces the epigenetic markers during sexual reproduction. A few epigenetically produced traits can persist for a few generations, but that’s not a good basis for permanent evolutionary change, and certainly not a general explanation of adaptation. In fact, we know the genetic basis of adaptation in many cases, and it’s nearly 100% due to changes in the DNA sequence, not to epigenetic modification of the DNA sequence. (Lactose tolerance in pastoral human populations is one example.)

To support the claim that epigenetics is important in evolution, author Carrie Arnold mentions the shopworn example of pregnant Dutch women, deprived of food by the Nazis, giving birth to children who became unhealthy adults, with high levels of obesity, diabetes, and so on. Besides this not being an example of adaptive evolutionary change, it’s still not certain that the changes in the kids were produced by epigenetic modification of the DNA. The pregnant mothers were the ones who passed on the traits, and the fetuses could have been affected by the mother’s physiology, not by changes in her DNA. (It’s telling that the children of undernourished fathers alone didn’t show the changes.) There may have been some epigenetic changes, or maternal effects, in that the grandchildren seem to be affected too, but that’s where the train of changes comes to a stop.

Then Arnold mentions an experiment with which I wasn’t familiar, but supposedly demonstrated epigenetic changes that persisted for many generation—25, to be precise:

Subsequent studies in plants and animals suggest that epigenetic inheritance is more common than anyone had expected. What’s more, compared with genetic inheritance, it has some big advantages. Environments can change rapidly and dramatically, but genetic mutations are random, so often require generations to take hold. Epigenetic marks, by contrast, are created in minutes or hours. And because they result from environmental change, they are often adaptive, boosting the survival of subsequent generations.

Take the pea aphid. It is capable of both sexual and asexual reproduction, and comes in two varieties: winged and wingless. When scientists exposed a group of genetically identical pea aphids to ladybirds, the proportion of winged aphids increased from a quarter to a half. This adaptation, which helped them escape the predatory ladybirds, persisted for 25 generations. The aphid DNA didn’t mutate, the only change was epigenetic.

So I “took” the pea aphid, reading the paper that supposedly showed persistent epigenetic variation over 25 generations. Click on the screenshot below to get the paper (from the journal Heredity):

It’s a long and somewhat tedious read, but there are two points to make.

1.) The plastic response to the predator—growing wings (an adaptation that’s genetically encoded)—did not persist for 25 generations on its own. In fact, if you remove the predator, the stimulus for growing wings, the population becomes wingless again within a single generation. So we do not have a case of epigenetic markers persisting on their own for many generations, much less two generations.

2.) There is no evidence that the production of winged forms is caused by epigenetic modification of the DNA, and the authors admit this.

In other words, everything that Arnold says or implies about this experiment is misguided.

The experiment was started with a single clonal population of aphids, that is, parthenogenetically produced individuals from a single female. The population thus lacked genetic variation except for new mutations that could have occurred after the experiment started. One part of the population was the experimental section, exposed to predatory ladybirds. That one produced winged individuals immediately at a proportion of about 50% of the population. This proportion remained stable for 27 generations. Producing wings in the presence of predators is adaptive, of course, as you can flee them, and not producing wings when the predator is absent is also presumably adaptive, as there’s a metabolic and reproductive cost of producing wings you don’t use. Thus the switching between wings and winglessness is an adaptive plasticity, and is presumably coded (not epigenetically!) in the aphids’ DNA.

The control line, lacking ladybirds, stayed at about 25% winged individuals for 25 generations.

At three intervals, the authors took aphids from the experimental line and put them in an environment without predators. If the epigenetic markers persisted in the absence of the predator, and through meiosis, you’d expect these “reversion” lines to still show a higher frequency of winged individuals. They didn’t. They basically reverted to the control level of winglessness within a single generation, presumably because the switch for growing wings (ladybirds) wasn’t there.

So what we see is that to get the adaptive trait, wings, to persist, you need the stimulus to be there constantly. The presence of the predator somehow induces the aphids to grow wings, just as the presence of fish in a pond causes some rotifers to grow fish-repelling spines. And when you take the predator away, the aphids switch back to the wingless form. Here’s a plot showing the frequency of wings in the experimental population (red line), in the control predator-less population, (black line) and the reverted population in which predators were removed (blue line):

(From paper): Proportions of winged adult aphids (mean ± SE) across generations of the experimental evolution with predators (in red), without predators (in black) and in branch lines for which predators were removed after generations 3, 13, and 22 (in blue). “*” or “NS” denote the significance (P < 0.05, or P > 0.05, respectively) of differences between controls (without predator, black dots) and branch lines after predator removal (blue dots). The vertical black dotted line indicates the time of initial predator introduction in the treatment lines

Unlike the Dutch situation, or others that report persistence of environmentally induced changes for a few generations, in this case the induced change, the presence of wings, reverts to control levels within a generation. We do not see the kind of trait persistence here that epigenetics advocates tout as important in making the phenomenon important in evolution.

And indeed, we don’t even know if the switch from winglessness to wings is an epigenetic change, as opposed to some chemical change that occurs in the aphids when they sense the presence of predators that turns on “wing-making genes”. (That’s how it works in rotifers: when a fish eats a rotifer, it releases chemicals into the water that induce the other rotifers to produce spines. That’s not an epigenetic modification of the DNA.) If you think that any environmental change is “epigenetic”, then yes, this one could be, but that’s not the way the cool kids construe “epigenetic” these days. It’s taken to mean “alterations of the DNA structure”, which is what journalist Arnold means by mentioning “epigenetic marks [that] are created in minutes or hours.”

There’s one twist in the experiment as well: in the lines subject to predators, the plasticity of individuals became reduced; that is, they were less likely to respond to changes in predators with changes in wings. The paper’s authors impute this to epigenetics, but it could well be due to selection occurring on mutations that arose in the predator lines. That is, since predation was omnipresent, there was less selection pressure to maintain a “switching system,” and your plasticity could erode. To maintain a switch between wings and winglessness, the lineage has to experience periodic bouts of predation alternated with bouts of no predation. So the loss of plasticity itself also says nothing about whether epigenetic markers were accumulating in the DNA.

And, at the end, the paper’s authors admit that we don’t know whether this switch is due to epigenetic modification of the DNA, as the New Scientists reporter claims. From the Heredity paper:

We can thus tentatively attribute the decline in plasticity observed in lines that were exposed to predators for many generations to the action of some non-genetically transmitted information (i.e. information not encoded in the DNA sequence). The hypothesis that observed phenotypic changes were caused by reversible epigenetic changes is thereby more likely but in order to be confirmed, this hypothesis would require to be backed up by molecular analyses.

I can find nothing in this paper that even suggests that epigenetic changes were happening to the aphids’ DNA, much less any kind of inherited changes that persist for more than one generation. This paper is certainly not an example of what New Scientist says it is.

This is the third buzzwordy phenomenon tendered by New Scientist as an exciting new finding that can modify the Modern Evolutionary Synthesis. And it’s the third one that is wrong. I am growing weary, and will see if I need to persist in debunking further claims in the article. Rest assured, though, that most of them are even weaker than the three I’ve discussed. But what does New Scientist care? They want clicks, not accuracy, and I fear that I’m wasting my time. I’d rather write about the new paper on consciousness in crows.

At least the New Scientist article admits that epigenetics is controversial:

The extent of epigenetic inheritance is contested. Some sceptics point out that, during mammalian reproduction, the creation of sperm and egg cells involves erasing epigenetic markers. Others argue that epigenetic transmission across generations is extremely widespread and useful. In plants, for example, it can account for differences in fruit size, flowering time and many other survival-boosting traits.

Yes, but it’s because the transmission across generations lasts about two or three generations at most that is why epigenetic modification by itself is not a good candidate for the “replicator” that produces adaptive evolution.

Lunchtime!

The intellectual vacuity of New Scientist’s evolution issue: 1. Genetic plasticity

September 26, 2020 • 11:30 am

As I reported the other day, New Scientist has a special issue on evolution (photo below), which apparently consists of their admission that Darwin was right after all, along with a “feature special” described as follows:

Our modern conception of evolution started with Charles Darwin and his idea of natural selection – “survival of the fittest” – to explain why certain individuals thrive while others fail to leave a legacy. Then came genetics to explain the underlying mechanism: changes in organisms caused by random mutations of genes. Now this powerful picture is changing once more, as discoveries in genetics, epigenetics, developmental biology and other fields lend a new complexity and richness to our greatest theory of nature. Find out more in this 12-page feature special.

The article, which you can’t access online—though judicious inquiry will yield you a copy—consists of 13 numbered scientific areas that are supposedly prompting a reboot of modern evolutionary theory. I’m not going to reprise all of them, as I’ve done so already about many of the “buzzwordy” areas, including epigenetics and niche construction, but I will single out, over the next week, several of the areas that are, to my mind, exaggerated or grossly misrepresented. For readers who’ve said that New Scientist isn’t so bad, my response is, “Well, its coverage of evolution, at least, is dreadful if you know things about modern evolutionary biology.”

True, in some of these areas the article pays lip service to the fact that they’re “controversial”, but the impression one gets is that evolutionary biology is teeming not just with new ideas, but with new ideas that are non-Darwinian and promise a dramatic revision of the theory. The problem is that most of these new areas are either mistakenly conceived or don’t constitute much of a change in evolutionary theory. In fact, none of them do more than put a new duckling under the wing of Darwinism, and none of them replace the mother duck.

Today’s target is GENETIC PLASTICITY, the first of the supposedly “new” areas of evolutionary biology. It’s described under the clickbait-y title “Genes Aren’t Destiny.”

My immediate response is that we’ve known about genetic plasticity for over a century. But let’s back up: what is genetic plasticity?

It’s simple: it’s the observation that for many genes, their expression depends on the environments in which the organism that carries them (and hence the genes themselves) develops or experiences. There are a gazillion examples. For some genes, you get a permanent effect depending on the environment obtaining during the organism’s growth. One example, which I and two colleagues used in an experiment on the temperature flies encounter in the wild, is the mutant allele white-blood, which affects eye color. The expression of the mutation is sensitive to temperature during just a narrow window of time when eye color forms in the pupal stage. If the temperature is high, the eye can turn out very light yellow or even white, but if the temperature is lower, the eye is darker, down to dark purple. After this sensitive period, the eye color stays the same for the fly’s life. The color is said to be “plastic with respect to temperature.”

Likewise, if you don’t get enough food as a kid, you’ll be permanently small after puberty. That’s because the genes involved in creating “height” are sensitive to the amount of nutrition the organism gets, making “human height” a plastic trait. There are a gazillion genes that are plastic in related ways; in fact, I know of very few genes whose expression isn’t affected by the environment (perhaps genes for polydactyly in humans and cats are examples of the latter).

Some genes can vary their expression over an organism’s lifetime. Cats get thicker coats in winter and revert to shorter coats in summer: the genes producing hair are reversibly plastic to temperature. Snowshoe hare become white in winter and brown in summer, a reversible case of pigment genes sensitive to temperature.

The fact is that since the advent of Mendlian genetics at the beginning of the 20th century, geneticists have recognized the plasticity of genes and the traits to which they contribute. The terms back then were that genes had “variable expressivity” or “variable penetrance” depending on the environment. (White-blood was described in 1945.) The idea of plasticity is not at all new, and was featured in the founding works of the Modern Evolutionary Synthesis in the 1930s and 1940s. It was an integral part of our modern view of development, which has long recognized that almost no traits are produced as invariant by genes acting independently of the environment, while the expression of most genes and traits involve an interaction between genes and environment.

I give you this primer because New Scientist, in #1 of its litany, pretends this idea and its instantiation in organisms is something new and exciting. In fact, they say, citing the Human Genome Project, that we now realize that this kind of interaction refutes genetic determinism:

The more we learn about genetics, the clearer it becomes that “genetic determinism” – the idea that genes and genes alone fix our destiny – is a myth. A given set of genes has the potential to produce a variety of observable characteristics, known as phenotypes, depending on the environment. An Arctic fox changes its coat colour with the seasons. The presence of predators causes water flea Daphnia longicephala to grow a protective helmet and spines.

The power of flexibility

Even a change in social environment can prompt a shift. In the European paper wasp (Polistes dominula), for example, when the queen dies, the oldest worker transforms herself into a new queen. But she isn’t the only one to respond. Seirian Sumner at University College London and her colleagues found that the death of a colony’s queen results in temporary changes in the expression of genes in all workers, as though they are jostling genetically for succession. This flexibility is key to the survival of the colony and the species, says Sumner.

The power of genetic plasticity can be seen in the humble house finch. In the past 50 years, it has colonised the eastern half of North America, moving into habitats ranging from pine forests near the Canadian border to swampland in the Gulf of Mexico. The finch’s underlying developmental plasticity provided the raw material from which novel features evolved, including a range of new colourings and other physical and behavioural traits, says David Pfennig at the University of North Carolina at Chapel Hill. “Stop thinking about this as being like genes or environment, because it’s a combination of the two,” he says.

That’s all she wrote (the author of this section is Carrie Arnold).

Let us note that some plasticity, like hair growth in mammals during winter and coat color in snowshoe hares, has evolved: the changeability of the genes in new environments is an adaptive phenomenon (creating more warmth with longer hair and better camouflage in winter). Plasticity is not always a given and inherent characteristic of genes and traits, but in many cases has evolved as organisms have experienced different environments during their species’ evolutionary history, making lability an advantage over fixity.

Further, one can construe “genetic determinism” in two ways, which the article conflates. First, one can see it the proportion of variation in one trait in one population of organisms that’s caused by the variation among the genetic endowment of individuals. The proportion of variation among individuals in a population due to variation in their genes is called the heritability of that trait, and ranges from 0% to 100%. In humans, for example, the heritability of height in many populations is about 80%, meaning that about 80% of the variation in human tallness that we see in a given population is due to variation in genes. This does not mean that height itself cannot be affected by the environment, for it clearly can (I used the example of nutrition above). But under the existing conditions in a population, one can construe the heritability as an index of genetic determinism in a given population under existing environments.

But one can also construe genetic determinism as the degree to which the expression of a trait or gene in an individual is affected by the environment. If this is what the article means, and I think it does, yes, plasticity does show that genes are not the be-all and end-all of a trait.

The important thing, though, is what I said above: THIS IS NOT NEW AT ALL!. It is simply either ignorant or mendacious of New Scientist to pretend that genetic plasticity is both a recent discovery and one that has revised neo-Darwinism. Genetic plasticity was recognized well before neo-Darwinism was formulated in the 1930s as a fusion of genetics, natural history, and evolution, because genetic plasticity was known since the very early days of genetics—almost since Mendel’s work was rediscovered in 1900.

So, if you are masochistic enough to read the entire New Scientist article, you can just move along when you get to point 1; nothing to see here. It’s almost as if the authors touted the claim that the idea of natural selection (which really wasn’t widely accepted until the 1920s) is a new and exciting addition to Darwinism.

New Scientist: Darwin wasn’t wrong after all

September 24, 2020 • 1:45 pm

The new issue of New Scientist is interesting given the rag’s history of dissing the neo-Darwinian theory of evolution, including this cover in 2009, which I wrote about at the time.

Now the “wrong” bit wasn’t meant to dismiss Darwin’s entire theory, but the claim did attack an important part of that theory: Darwin’s idea that there is a branching tree of life that, in principle, can be reconstructed. The idea that life started once, and then ramified to produce all living and extinct species, so that any pair of species, living or dead, had a common ancestor, was one of Darwin’s major ideas. New Scientist asserted that this was wrong.

As I wrote at the time:

What is so wrong with the tree of life? Well, an article by Graham Lawton asserts that horizontal gene transfer (the movement of bits of DNA between species by “infection”), a phenomenon often seen in bacteria and some protists, and occasionally in complex metazoa, invalidates the whole idea of a tree with bifurcating branches. This, of course, is nonsense. Such gene transfer may fuzz out or even obscure genealogies in some prokaryotes, but nobody thinks it’s going to efface the genealogy of most other groups. Can we expect to find that we’re really more closely related to gibbons than to chimpanzees, a truth that has been obscured by massive horizontal transfer from eating bush meat? Don’t expect huge changes in the genealogy of life that we’ve already assembled from molecular data.

Several of us were really miffed at this inflammatory cover, which of course played into the hands of creationists, and wrote a letter to the editor of New Scientist (here’s the shorter version; I can send the longer one to anyone who wants it):

Now the journal has revised its view a bit. In its latest issue, which highlights evolution, New Scientist proudly proclaims that “DARWIN WAS RIGHT” (it’s an intro on the inside).

And here’s their new take, which fortuitously has the same title as our letter to the editor:

Darwin was right

New Scientist

September 23, 2020

THE theory of evolution is one of the greatest accomplishments of the human intellect. Some might argue that it is the greatest, although quantum theory or relativity would have their supporters too. But in the biological sciences, it stands unrivalled. It is no less than the grand unified theory of life.

It is also a theory in the truest sense of the word: an interlocking and consistent system of empirical observations and testable hypotheses that has never failed scrutiny. Nothing has even been discovered that falsifies any part of it, despite strenuous efforts by detractors. It all stacks up.

Yet we should resist the temptation to think that evolution is carved in tablets of stone. The radical but irresistible ideas put forward by Charles Darwin and Alfred Russel Wallace in 1859 remain the core of the theory, yet it has constantly accommodated new knowledge. This happened most conspicuously about a century ago, when the new science of genetics was melded with natural selection to create what became known as the “modern synthesis”.

Today, we are arguably in the midst of another upgrade. Over the past 30 years, discoveries in developmental biology, epigenetics and elsewhere have needed to be brought under the wing of evolution. As our special report on page 38 shows, they largely have been. Only hindsight will be able to judge whether what emerges is Evolution 3.0, or merely Modern Synthesis 1.1. If nothing else, the flurry of activity is proof that evolution – and hence biological science – is a vibrant, living-and-breathing entity still in its prime.

Evolution has also achieved something that is arguably more important: it has seen off its culture warrior detractors. A decade ago, it was on the front line of the war on science, under attack from creationism and its pseudoscientific alter ego, intelligent design. Those voices have now largely fallen silent, worn down by the patient drumbeat of reason.

Sadly, that remains an isolated victory in the wider anti-science culture war. But it shows that victories aren’t impossible. Evolution won because it is true. Eventually, truth will out.

Well, this is a bit mendacious given their new assertion that “nothing has even been discovered that falsified any part of [Darwin’s theory]” contradicts their 2009 claim that “Darwin was wrong about the tree of life”. In fact, the branching tree of life and its converse—looking backwards to realize that all species have common ancestors—is one of the crowning achievements of Darwin’s theory.

But the good bit is their true claim that creationism and Intelligent Design are pretty much defunct. That will really tick off the IDers. But it’s true! Creationism died as a scientific proposition long ago, and its gussied up cousin, ID, has now devolved into a series of attacks on evolutionists. ID has produced no research program, which it promised long ago was “right around the corner”, and it hasn’t nudged evolutionary theory one micron out of school curricula. Both creationism and ID have been recognized by the courts as religious views, not scientific theories. Sometimes I feel sorry for clowns like Michael Egnor and David Klinghoffer, doomed to bawl up rainspouts (to borrow from Mencken) until they die.

There are many parts of New Scientist‘s supposed “upgrade” of evolution, and I’ll deal with them tomorrow. Of course that theory has changed a lot since 1859: we had no fossil record to speak of then, and knew nothing about genetics. But the journal touts many of the buzzwordy “upgrades” that have proved to be mere tack-ons to the Modern Synthetic theory of evolution accepted in the last few decades. The ones for which we have evidence are indeed nestled under the wing of evolution (e.g. epigenetics and horizontal gene transfer, the latter of which can be seen as a dramatic form of mutation, but one that doesn’t efface the tree of life), and so are part of Modern Synthesis 1.1, not Evolution 3.0. Some of other touted “upgrades” (e.g.. genetic assimilation of acquired traits, the claim that species don’t exist) are either unimportant, ambiguous or false. The Modern Synthesis needs to accommodate new facts, but the “upgrades” don’t mandate a revision nearly as drastic as when genetics married Darwinism to give birth to the Modern Synthesis in the 1930s and 1940s.

We’ll deal with the some of these upgrades tomorrow—if I have the stomach.

h/t: Matthew

Science again corrupted by ideology: Slate distorts evolutionary biology to make it seem capitalistic and anti-socialistic

January 25, 2020 • 11:00 am

UPDATE: I left this comment after the Slate piece, but it appears to have been removed. I’m not sure why, as there are far more vitriolic comments in the thread.

Jerry Coyne

The claim that the idea of cooperation is novel and paradigm-shifting in evolutionary biology is palpably ridiculous. All of the examples given by the author are not only known, as well as many other examples of mutualism that long preceded Margulis (lichens, termites, cleaner fish and “cleanees”), but fit firmly within the neo-Darwinian paradigm. There’s nothing new here except the author’s claim that the idea of cooperation is novel. To anybody who’s studied evolutionary biology, this is nonsense. Further, the author apparently hasn’t read Prum, who actually tried to RESURRECT Darwin’s idea of sexual selection.

I have written a long critique of this piece at my website http://www.whyevolutionistrue.com. It’s the latest piece, and since I may not be allowed to post links, just go to my site and read it. The upshot: this piece evinces either ignorance or deliberate obfuscation, and is also misleading in that it tries to distort the history and nature of evolutionary biology in the service of an ideology (apparently socialism).

______________________

Once again we have a collision between ideology and science, but in this case the perceived conclusions of science are in fact wrong, so the called-for revision of evolutionary biology in light of woke ideology isn’t needed. In a new article in Slate (see below), John Favini argues that evolutionary biologists are completely wedded to the paradigm of competition between individuals and between species, and further argues that the idea of individuals or species being cooperative is both reviled, new, and non-Darwinian. If you’re at all familiar with the history of reciprocal altruism, kin selection, and mutualism between species, you’ll know that these ideas—which all involve the evolution of cooperation—are both over half a century old and well ingrained in modern evolutionary theory.

But Favini is either unfamiliar with this literature, which is inexcusable for a graduate student in anthropology who claims a knowledge of biology, or hides it, which is duplicitous. I won’t make a judgment except that this article, which seems more attuned to the Discovery Institute (or even Salon), doesn’t belong in Slate, which is supposed to be a decent site. (Hitchens used to write for it.)

Favini is identified at the site as “a Ph.D. candidate in anthropology at the University of Virginia and a freelance writer. He is interested in climate change, environmental politics, and science as a cultural domain.”

From this you can derive one speculation and one conclusion. The speculation is that Favini is a cultural rather than a physical anthropologist; the former tend to be social justice warriors who often downplay scientific facts in favor of their ideology (they often, for example, completely dismiss the idea of “race”, though it has a qualified reality that’s meaningful). Second, the “science as a cultural domain” bit is worrying, and in fact is what gave rise to the Slate article (click on screenshot below to see it).

Favini situates Darwin at the outset as a white, elite, Englishman subject to the social forces of his time, and predisposed to think about competition because his theory of natural selection originated after reading Malthus on competition. From this, throughout the article, he concludes that all of Darwinism, then and now, is marinated in the idea of competition.

. . . like all humans, Darwin brought culture with him wherever he traveled. His descriptions of the workings of nature bear resemblance to prevailing thinking on human society within elite, English circles at the time. This is not a mere coincidence, and tracing his influences is worthwhile. It was, after all, the heyday of classical liberalism, dominated by thinkers like Adam Smith, David Hume, and Thomas Malthus, who valorized an unregulated market. They were debating minor points within a consensus on the virtues of competition. In an especially humble (and revealing) moment, Darwin characterized the principles underlying his thinking as naught but “the doctrine of Malthus, applied with manifold force to the whole animal and vegetable kingdoms.”

. . . More than just a cliché, though, the supposed naturalness of competition has played a central role in substantiating the laissez-faire variety of capitalism the majority of the American political spectrum has championed for the past four or so decades. Indeed, any non-market-based solution to social issues usually falls prey to claims of utopianism, of ignoring the fundamental selfishness of the human species. . . . To put it simply, we have let Darwinism set the horizon of possibility for human behavior. Competition has become a supposed basic feature of all life, something immutable, universal, natural.

Regardless of the idea of “social Darwinism” (which Darwin never held and which has been completely abandoned by intellectuals), the facts of competition between genes (i.e., natural selection), competition between individuals (which produces natural selection), and competition between members of different species (which also produces natural selection as well as interesting aspects of ecology) are real and important. In fact, without competition between the different forms of genes for representation in later generations, we wouldn’t have natural selection at all!

And to the extent that natural selection is responsible for most interesting features of life, including biodiversity itself, it is “natural and universal.” But “natural” doesn’t mean that we have to put up with it, for we derail natural selection all the time by using doctors, dentists, and optometrists, and by using contraception. Further, we’ve tamed competition between individuals with laws against aggression, rape, and so on. Finally, we’re beginning to tame the competition between species by removing invasive species from places they don’t belong and by giving up the foolish idea that we humans should dominate all of nature.

Why is Favini attacking competition at such great length? We get a clue early in the article, as well as later. Early on, he says this:

Yet new research from across various fields of study is throwing the putative scientific basis of this consensus into doubt. Mind you, there have always been people, scientists and otherwise, who conceived of life outside a Darwinian paradigm—the idea of evolutionary biology is and has been a conversation among a mostly white and male global elite. Yet, even within centers of institutional power, like universities in North America, competition’s position as the central force driving evolution has been seriously challenged recently. In fact, criticisms have been mounting at least since biologist Lynn Margulis began publishing in the late ’60s.

You guessed it. It’s those damn white males, again, Jake! They are the ones with the power to push an unwarranted consensus about competition in the “elite universities.” According to Favini, it took a female, Lynn Margulis, to dethrone competition as the centerpiece of evolutionary biology. Well, that’s not quite true, because Darwinian speculations about cooperation, and the recognition that evolution can promote it both within and between species, has been an accepted part of evolution well before Margulis found that a form of “cooperation” was responsible for the advent of the eukaryotic cell. Later on, we’ll hear Favini touting the “heterodox voices” of indigenous Americans as helping dethrone the idea of competition, a woke concept that, sadly, isn’t true, either.

Favini then bangs on at length about all the supposedly non-Darwinian instances of cooperation that he says, have “fractured Western biology’s consensus on Darwin”. This is, to be gauche, pure bullshit. Most of these phenomena have been known for decades, and none of those pose any kind of challenge for Darwinism. They include the merging of two prokaryotes into a cell containing mitochondria, and, in plants, a cell containing chloroplasts. This “endosymbiosis” idea was a wonderful and true hypothesis pushed (but not originated) by Lynn Margulis. And it can be seen as an example of cooperation, in which the “big” cell benefits from having energy-generating organelles, while the organelles (which, like the cell itself, underwent evolution to promote the interaction) gain protection and sustenance.

Margulis’s theory was initially met with some resistance, but was quickly accepted after microscopic and especially DNA evidence showed that she was right. But the important thing in our discussion is that this is just one example of the kind of symbiosis that was accepted long before Margulis. Well known symbioses include those between leafcutter ants and fungi, between the termites and the protists and bacteria that help them digest cellulose, between the algae and fungi that constitute lichens, between cleaner fish and the “cleanees,” between clownfish and the sea anemones they inhabit, and the many species that have symbiotic bacteria or algae, like the bacteria that inhabit light organs and produce light in deep-sea fish (see photo at bottom).

It’s important to recognize that these examples of interspecific symbiosis (“mutualisms,” in which both partners benefit), are perfectly consistent with neo-Darwinism, and have never been seen as a challenge to the theory. Each species benefits from associating with the other, and natural selection will act and has acted to tighten the mutualisms. More recent findings of a mutualistic “microbiome” in ourselves and other species are also something that slots perfectly into a Darwinian paradigm, just as does another form of symbiosis: parasitism.

I’ll add here that cooperation within groups, beginning with kin selection that forges bonds between relatives (and explaining the wonderfully cooperative castes within a social-insect colony), and extending to “reciprocal altruism”, in which small bands of animals undergo individual selection to treat their groupmates better, has also never been problematic for Darwinism. With the recognition by Hamilton, Trivers, and others that genes in you are also genes in your relatives, and that genes for scratching the backs of others who scratch yours can also be advantageous, the multifarious forms of cooperation in nature have developed into a wonderful story and a true story, but also, contra Favini, an old story.

Favini, however, pretends that all this work on cooperation has upended evolutionary biology, fracturing our consensus on Darwinism. Given that all the examples he adduces haven’t tarnished evolutionary theory one bit, he’s just reaching wildly to pretend that he’s found something new. He even cites the renegade “Third Way” group of evolutionists who, to my mind, don’t pose any serious alternative to Darwinism:

Put simply, life is beginning to look ever more complex and ever more collaborative. All this has fractured Western biology’s consensus on Darwin. In response to all these new insights, some biologists instinctively defend Darwin, an ingrained impulse from years of championing his work against creationists. Others, like Margulis herself, feel Darwin had something to offer, at least in understanding the animal world, but argue his theories were simplified and elevated to a doctrine in the generations after his passing. Others are chartering research projects that depart from established Darwinian thinking in fundamental ways—like ornithologist Richard Prum, who recently authored a book on the ways beauty, rather than any utilitarian measure of fitness, shapes evolution. Indeed, alongside the research I have explored here, works by scientists like Carl Woese on horizontal gene transfer and new insights from epigenetics have pushed some to advocate for an as-yet-unseen “Third Way,” a theory for life that is neither creationism nor Neo-Darwinian evolution.

Note that Favini gives Darwin only a bit of credit here, saying that “Margulis [felt] Darwin had something to offer.” DUHHH! And as far as Prum’s book on sexual selection for “beauty” goes, well, as you may recall, in that book Prum revives Darwin’s own theory of sexual selection! Did Favini even read the book? While Prum grossly exaggerates the ubiquity of and evidence for the “runaway” model of sexual selection, make no mistake about it: Prum’s theory is thoroughly Darwinian, incorporating Favini’s despised “utilitarian measures of fitness.” (Just look at the theoretical models of runaway sexual selection.)

I’ll add, to complete the record on Darwin, that he did not ignore cooperation. In The Descent of Man, for instance, he speculates on the origin of human altruism, although he floats a theory of group selection to explain it. He also ponders the evolution of cooperation in social insects, and, in the chapter on “Instinct” in The Origin, suggests that sterile castes can be produced by “family selection,” which many have taken to be one of the first inklings of kin selection among relatives.

It’s at the end of the piece that Favini’s mask slips as he plunges into wokeness, touting the insights of indigenous Americans (which haven’t influenced evolutionary theory), and then dissing capitalism, which he sees as the outcome of Darwinism rather than of economic and social forces.

First, the indigenous people:

This lack of agreement isn’t such a bad thing. Leaving the Darwinian consensus behind means a more capacious, diverse, and ultimately more rigorous science. The recent dissensus has opened up more room for important, heterodox voices like Robin Wall Kimmerer, a botanist and member of the Citizen Potawatomi Nation. Kimmerer speaks of plants as highly intelligent beings and teachers, a sharp departure from the reductionist, utilitarian approach to plant and animal life that passed as scientific rigor within the Darwinian framework. Much of the recent research I have highlighted might count as what Kim TallBear, a scholar and enrolled member of the Sisseton-Wahpeton Oyate, calls “settler epiphanies”—belated “discoveries” by settlers of Indigenous knowledge that was either ignored or outright suppressed by colonial land appropriation and attempted genocide.

Certainly ethnobotany and the knowledge of indigenous people included in that field, have been extremely valuable. A huge proportion of our drugs, for example, come from plants, some based on how they were used by locals. But indigenous peoples haven’t changed the scientific “way of knowing” with their “spiritual way of knowing” (something that Kimmerer seems to tout), nor have they made Darwinism swerve even a millimeter from its path. (Note Favini’s denigration of evolutionary biology as “reductionist and utilitarian”. It is of course neither.)

Finally, Favini lapses into socialism. But whatever its merits, socialism cannot and should not be justified by citing the evolution of cooperation, or by arguing that an unjustified view of evolutionary biology has severely impeded its acceptance by propping the notion that capitalism’s competitition is “natural” Social Darwinism might have been mildly influential at the time of Herbert Spencer, but that view has long since fallen by the wayside.

Overall, then, what we get in Favini’s piece is pure politics, with some Darwinism thrown in to demonize and blame for competition:

Far too many environmentalists assume that people, driven by innate self-interest, are bound to harm ecology, that we will inevitably clear-cut, extract, consume, so long as it gives us an advantage over the next guy. This leaves us deeply disempowered, with few solutions to climate change outside limiting humanity’s impact through some kind of population control. When competitive self-interest is revealed to be a mutable behavior, the causes of climate change come into greater clarity: not human nature, but an economic system that demands competition, that distributes resources such that a tiny elite can live tremendously carbon-intensive lifestyles while the rest of us struggle for a pittance. Leaving competition behind, we can also imagine richer solutions: climate policies that problematize the tremendous wealth of the few, that build economies concerned with collective well-being and sustainability.

. . . Science can play a critical role in liberating our imagination from competition’s grip. It can show us all the symbioses that make life possible. Such a science can remind us that we can act and be otherwise—that the shortsighted self-interest that motivates, for instance, continued fossil fuel extraction is endemic to capitalism, not to our species, much less to life itself. We can find ways to live collaboratively with the bewildering array of life that roots and scurries across our planet, but only if we reckon with competition’s hold on our thinking—for if we see life as merely a competitive struggle to survive, we will make it one.

I’ve pondered why Favini has so badly misrepresented the history and content of evolutionary biology, and the only conclusion I can reach is that he’s a woke cultural anthropologist who is willing to distort the nature and history of science in the interest of promoting a socialist program. But he’s dead wrong in claiming that evolution is completely obsessed with competition (except between genes when you talk about natural selection), and equally wrong about the evolution of cooperation having been completely neglected until Lynn Margulis came along.

Since Favini is young, I won’t be too hard on him, except to advise him to drop this particular hobbyhorse, as it will only hurt what reputation he has. Or, rather, what reputation he has among evolutionists, as cultural anthropology is largely a miasma of nescience.

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