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 (4th-7th 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 19th 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.

Brian Charlesworth

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.

A mutualism: a female anglerfish, Linophryne polypogon, with her light organ fueled by bacteria. Photo by Peter David in Wired. See this source for more information about the mutualism.

 

Bret Weinstein unfairly disses evolutionary biology (and New Atheism)

September 19, 2019 • 12:30 pm

While Bret Weinstein is a stalwart champion of free speech and progressivism because of his brave behavior at Evergreen State, his views on evolution often seem to me to be pretty wonky. And not just biology: look at these tweets he exchanged with Sam Harris:

Non-Darwinian? New Atheism, which is simply the revival of Old Atheism in popular format, along with a healthy dose of science, is not “non-Darwinian” at all!

Here’s the Q&A session of a discussion between Alister McGrath, a philosopher of science and theologian, and Weinstein hosted by Justin Brierley, a podcaster and religionist. (The link to the main discussion is below.) Sadly, it was apparently sponsored by both The Templeton Religious trust and Christian Radio.

The part that concerned me most was Weinstein’s claim at the outset that evolutionary theory hasn’t moved much since 1976, when Dawkins’s book The Selfish Gene was published.  (This is the first question on the video.)  Weinstein argues that there hasn’t been a theoretical breakthrough since then, and we have only empirical studies. When Bret discussed this with Richard Dawkins, Richard said that was probably because previous generations had gotten the Big Stuff pretty much right.

In response, Bret says no, Dawkins is wrong because, as he says,

“What I know from my own work is that that’s not true because there are a great many questions that we can’t yet answer—big questions, like about the nature of sexual selection, what we call “lekking”, about speciation. These big questions have simply moved into another phase where we’ve stopped asking them and embarrassing themselves because we can’t answer the question. Why, for example, are there more species more densely packed as one moves from the poles to the Equator.   That’s a question we should be able to answer. . . .Why can’t we answer it? Because we’ve lost the thread of the conversation, not because we’ve answered all the questions. In some sense progress seems to have stopped; why it’s stopped we can argue about, but that we should do something to jump-start it is almost beyond question.”

Well, no. Speciation, sexual selection, and the latitudinal diversity gradient are active areas of research, and I should know about speciation because that was my own area of work. Allen Orr and I wrote a book about it in 2004, and much of the progress that occurred in speciation, documented in the book, took place after 1976. And yes, we do understand speciation a lot better now than we did 45 years ago.

The diversity gradient remains an active area of research, and the various theories about its existence (as with theories of speciation) are well known and being tested.

Finally, there is a ton of work on sexual selection going on as you read this. Here, too, there are lots of theories about how it works (see this paper for a compendium), but they’re hard to test in the wild, and so our knowledge accumulates slowly. But none of these areas need jump-starting: the theoretical frameworks are in place, and what remains is the empirical slogging and testing that Weinstein seems to deem unproductive.

What Weinstein is saying here is equivalent to saying, in 1900, that Darwin’s theory of evolution by natural selection is insufficient because there hasn’t been a Big New Theory since 1859 proposing how life evolved, and there’s just a bunch of empirical studies needed to confirm it. But Darwin got it pretty much right at the outset. (No, not completely right, of course, but his theses of evolutionary change, gradualism rather than saltation, common ancestry, splitting of lineages, and natural selection as a cause of “designoid” features of organisms are still accepted as true.)

In short, I’d take Bret’s (and his brother Eric’s) claims that evolutionary biology is in the doldrums, and that some newer paradigm is needed, with a grain of salt.

Here you go:

Here’s a link to the 70-minute main part (part I) of the discussion, called “Religion: Useful fiction or ultimate truth?” I haven’t yet listened to it, but reader publius ovidus has, and comments: “Part 1 has [Weinstein] comparing scientists’ faith with religious faith. He says scientists operate on faith because they have to assume they are real and the materials they are working on are real.”  If that’s what Bret said, it conflates “faith” as “confidence in replicated observations” (scientific “faith”) with religious “faith”: belief in propositions and events that aren’t supported by strong evidence (see my Slate piece, “No faith in science.“)

At any rate, I’d be delighted if any readers would listen to part I and put any comments below.

h/t: Nilou, publius ovidus

Rich Lenski answers ID creationist Michael Behe, dismantles “Behe’s First Rule of Adaptive Evolution”

February 17, 2019 • 10:00 am

Rich Lenski, a well known biologist at Michigan State University and head of the team which has conducted an equally well known long-term evolution experiment in E. coli (they have a generation every twenty minutes or so, and the experiment has run for 30 years), is the subject of a long attack in Michael Behe’s new Intelligent-Design (ID) book, Darwin Devolves.  Apparently Behe argued that Lenski’s work didn’t show real progressive evolution of a meaningful sort, but simply showed that bacteria could adapt to lab conditions by “breaking genes”: deactivating genes through missense or nonsense mutations. As Lenski and coauthors Nathan Lents and Joshua Swamidass showed in a short but damning review of Behe’s book in Science, Behe’s claim about Lenski’s experiment was wrong:

In the grand scheme of evolution, mutations serve only to break structures and degrade functions, Behe argues. He allows that mutation and natural selection can explain species- and genus-level diversification, but only through the degradation of genes. Something else, he insists, is required for meaningful innovation. Here, Behe invokes a “purposeful design” by an “intelligent agent.”

There are indeed many examples of loss-of-function mutations that are advantageous, but Behe is selective in his examples. He dedicates the better part of chapter 7 to discussing a 65,000-generation Escherichia coli experiment, emphasizing the many mutations that arose that degraded function—an expected mode of adaptation to a simple laboratory environment, by the way—while dismissing improved functions and deriding one new one as a “sideshow” (1). (Full disclosure: The findings in question were published by coauthor Richard Lenski.)

As I’ve written before, Behe’s thesis here is meant to show that, without the help of the “Intelligent Designer” (aka God), real progressive evolution is self-limiting, for all it does it create adaptations based on broken or deactivated genes. The accumulation of broken genes eventually makes further evolution impossible: once you have a genome full of broken genes, further progress is limited and so God has to step in to make those mutations that can’t occur naturally. (I’m always amused at the religious IDers diminution of God’s role from de novo creator of all organisms to that of a mutagen: a Divine Carcinogen.)

Behe’s thesis is expressed in his “First Rule of Adaptive Evolution”, which Lenski analyzes (and dismantles) in a post on his website (see link below).

I didn’t know that Lenski even had a website, but there you go. It’s called Telliamed Revisited, and his latest post (click below) is the first of three essays in which he’ll analyze Behe’s book. This is useful, as the three-authored Science critique was only 650 words long—not sufficient to analyze the scientific theses of a 352-page book. Lents has already expanded the criticism of Behe’s book on The Human Evolution Blog and on the AIPT site., but since Lenski and his microbial experiment were the targets of special criticism by Behe, it’s especially appropriate that Lenski himself respond.

First, Lenski summarizes Behe’s “First Rule” (my emphasis below):

Behe’s latest book is centered around what he calls “The First Rule of Adaptive Evolution: Break or blunt any gene whose loss would increase the number of offspring.” As he wrote in an immediate, dismissive response to our review: “The rule summarizes the fact that the overwhelming tendency of random mutation is to degrade genes, and that very often is helpful. Thus natural selection itself acts as a powerful de-volutionary force, increasing helpful broken and degraded genes in the population.

Then Lenski makes a simple point which appears to show that Behe is being intellectually dishonest. (He’s already been intellectually dishonest by implying that nearly all adaptive mutations are known to degrade or break genes, as we have many counterexamples.) Here’s what he says, referring to the sentence I’ve put in bold above (the bold below is Lenski’s):

Behe’s next sentence then asserts the power of the “de-evolutionary” process of gene degradation. This is an unjustifiable extrapolation, yet it is central to Behe’s latest book. (It’s not the sort of error I would expect from anyone who is deeply engaged in an earnest effort to understand evolutionary science and present it to the public.) Yes, natural selection sometimes increases the frequency of broken and degraded genes in populations. But when it comes to the power of natural selection, what is most frequent versus most important can be very different things. What is most important in evolution, and in many other contexts, depends on timescales and the cumulative magnitude of effects. As a familiar example, some rhinoviruses are the most frequent source of viral infections in our lives (hence the expression “common cold”), but infections by HIV or Ebola, while less common, are far more consequential.

. . . In the same vein, even if many more mutations destroy functions than produce new functions, the latter category has been far more consequential in the history of life. That is because a new function may enable a lineage to colonize a new habitat or realm, setting off what evolutionary biologists call an “adaptive radiation” that massively increases not only the numbers of organisms but, over time, the diversity of species and even higher taxa.

. . . Summing up, Behe is right that mutations that break or blunt a gene can be adaptive. And he’s right that, when such mutations are adaptive, they are easy to come by. But Behe is wrong when he implies these facts present a problem for evolutionary biology, because his thesis confuses frequencies over the short run with lasting impacts over the long haul of evolution.

This isn’t rocket science. If Behe’s thesis is that broken genes present a big problem for continuing adaptive evolution, then one has to accept the thesis that nearly all broken or degraded genes are those genes involved in adaptation. And yes, some inactivated genes are involved in adaptations. But we also know of many adaptations based on non-broken genes, including those with changed functions as well as duplicated genes, cobbled-together genes, horizontally transferred genes, and so on. If, as I’ve said, only 50% of all adaptations involve these sorts of genes as opposed to “broken” genes, the natural selection will not lead to the stalling of evolution so important to Behe. Further, if a higher proportion of “changed function/new function mutations” are involved in major adaptations that are associated with the rise of new taxa, then the broken or blunted genes become even less important.

As Lenski notes, the frequency of mutations that degrade rather than change the function of genes does not tell us the frequency of degraded genes that are involved in adaptation, and the frequency of degraded genes that are involved in adaptation does not tell us the frequency of degraded genes involved in adaptations that are associated with new biological diversity. Behe surely realizes this, as he’s not stupid, but chooses not to make that point. Lenski had to make it for him.

Lenski is being quite kind when he says “it’s not the sort of error I would expect from anyone who is deeply engaged in an earnest effort to understand evolutionary science and present it to the public.” I would go farther and say “this is the sort of error that I would expect from a neo-creationist who’s trying to distort the empirical data in order to delude the public into thinking that there are severe problems with modern evolutionary theory.”

Behe is notoriously thin-skinned, and will undoubtedly go after Lenski at the intelligent-design Evolution News site, which, understandably, does not allow any comments. Behe’s ID buddies will also pitch in and help him out, as they’ve already been doing, for they want this book to sell well and create the widespread scientific acceptance of ID that the Wedge Document said would occur by 2018. LOL on that!

ID has not been widely accepted in science: it’s been scorned, laughed at, and deemed by the courts as religion and not science. If it were scientifically accepted, you’d get a better panoply of people endorsing the book than these four people who constitute the entirety of the editorial reviews on the Amazon page of Darwin Devolves:

Axe and Minnich are both associated with the ID-creationist Discovery Institute, and so are already in bed with Intelligent Design. Carlson is a member of the Christian Faculty Forum, has testified publicly about his deep faith, and thus shows that virtually all proponents of ID are religious. He’s also a Fellow of the Id-ish International Society for Complexity, Information, and Design; other fellows include William Lane Craig, Alvin Plantinga, and the whole Discovery Institute crew (Nelson, Behe, Dembski, and so on). Leisola is also an ID advocate and has written a book about his transformation from advocate of naturalism to worshiper of the Great Designer.  Leisola’s  Finnish Wikipedia page notes (translated by Google):

Leisola is a creationist . He believes that the world is only a few thousand years old and sees the flood of water as a historic global flood. [18]

Leisola has delivered several books in Finnish, whose authors adopt a pseudo-scientific [19] concept of ” intelligent design ” and make claims against the scientific theory of evolution . In 1981, he delivered AE Wilder-Smith’s Natural Sciences Not Known for Evolution (WSOY, 144 p.). Leisola founded the Datakirjatpublishing company in 2000 because Finnish publishers refused to publish his translation of the book ” Evolution – critical analysis ” by Siegfried Scherer and Reinhard Junker . [20] Dictionaries published The first edition of the Evolutionary-Critical Analysis book in 2000. [21]  The dictionaries have since published other pseudo-scientific and evolutionary works:

  • William A. Dembski, 2002, Intelligent Plan Idea , Data Books, 256 s.

  • Marwin Lubenow, 2005, Myth of Monkeys – Controversy over Timing of Fossils , Data Books, 380s .

 

These are hardly the brand of endorsements you want if you’re trying to divorce ID from creationism and make it part of mainstream science.

The Discovery Institute’s “Scientific Dissent from Darwinism” not so scientific

February 11, 2019 • 11:15 am

The Discovery Institute (DI) likes to make its case for Intelligent Design simply by getting people to sign a petition, the “Scientific Dissent from Darwinism“, which reads thusly:

Signatories of the Scientific Dissent From Darwinism must either hold a Ph.D. in a scientific field such as biology, chemistry, mathematics, engineering, computer science, or one of the other natural sciences; or they must hold an M.D. and serve as a professor of medicine. Signatories must also agree with the following statement:

“We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged.”

You can see the signatories here; according to The College Fix article below, and a blurb by the Discovery Institute, they now number 1,043. The fact that the signers exceeded 1000 is cause for great celebration in Seattle.

Although there’s not, as far as I know, a list of scientists who accept “Darwinism” (I’d call it “modern evolutionary theory”), it would of course be much longer.  But scientific truth isn’t determined by lists of names, even of people who hold Ph.Ds (see below for their “qualifications”). It’s determined by the published work of scientists and whether it’s accepted by the scientific community. And using that criterion, ID has failed miserably.

It’s sad that The College Fix, a right-wing website that often has decent though slanted articles on the shenanigans of woke students at universities, has chosen the anti-evolution hill to die on. Of course the author of this article (click on screenshot) goes to Liberty University, where you have to sign on to creationism as a student and teacher.

The Right apparently hasn’t realized yet that they don’t gain intellectual credibility by espousing creationism or attacking established truths in evolutionary biology.

At any rate, The Sensuous Curmudgeon isn’t impressed. In a post about the list a week ago, they note this about “Project Steve“, which is the National Center for Science Education’s lighthearted but real list of scientists named Steve who have a Ph.D. and support evolution. The NCSE of course doesn’t use lists to support the truth of evolution; this is just a list to mock the Discovery Institute’s list.  Here’s what the 1400 Steves signed:

Evolution is a vital, well-supported, unifying principle of the biological sciences, and the scientific evidence is overwhelmingly in favor of the idea that all living things share a common ancestry. Although there are legitimate debates about the patterns and processes of evolution, there is no serious scientific doubt that evolution occurred or that natural selection is a major mechanism in its occurrence. It is scientifically inappropriate and pedagogically irresponsible for creationist pseudoscience, including but not limited to “intelligent design,” to be introduced into the science curricula of our nation’s public schools.

And the Sensuous Curmudgeon’s comment on the DI’s crowing about the 1000+ signers of their anti-Darwin list:

The Discoveroids have a new post about it at their creationist blog: Skepticism About Darwinian Evolution Grows as 1,000+ Scientists Share Their Doubts. Here are some excerpts, with bold font added by us for emphasis, and occasional Curmudgeonly interjections that look [like this]:

Over 1,000 doctoral scientists from around the world have signed a statement publicly expressing their skepticism about the contemporary theory of Darwinian evolution. [Gasp!] The statement, located online at dissentfromdarwin.org, reads: “We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged.”

We always contrast that with “Project Steve,” a splendid enterprise of our friends at the National Center for Science Education (NCSE). It has its own page at their website, and it’s their response to the Discoveroids’ list. The last time we wrote about it was over two years ago: ‘Project Steve’ Now Has 1,400 Steves. They say: “About 1% of the United States population possesses such a first name, so each signatory represents about 100 potential signatories.”

. . . We don’t know how many Steves are on NCSE’s list now, but only ten Steves are statistically equal to all the 1,000 signatures on the Discoveroids’ list. If the Discoveroids limited their list to only “Steves,” they’d have about 10 names. Also, The Discoveroids are far less selective than NCSE in choosing their signatories. The Discoveroids’ list includes a significant number of MDs, dentists, engineers, meteorologists, industrial hygiene specialists, nutritionists, philosophers, political “scientists,” sociologists, and such. On the other hand, everyone on NCSE’s list of Steves has a PhD, and a majority of them are in a biological field.

The Curmudgeon concludes:

So where are we? Well, the Discoveroids finally got their list up to 1,000 names, so that’s something. It’s difficult to come up with a figure for the actual number of scientists in the world, because that term (like the Discoveroids’ list) can include social scientists, political scientists, etc. For the US alone, the American Association for the Advancement of Science has over 120,000 members, so the Discoveroids still have a lot of work to do.

But you’re probably asking yourself, “Well, who are those Ph.D.s who signed the DI’s statement?” Fortunately, DonExodus2 examined the list 11 years ago when there were about 100 signers, and you won’t be impressed by those who put their name to the document. (The videomaker contacted most of the people who signed the document.) Have a listen:

It’s pathetic that the DI spends its time getting signatures on the petition when it should be getting empirical evidence for its theory. After all, in 1998 the Wedge Document said that its 20-year goal was to see ID as the dominant paradigm in science. It’s 2019 now, and that hasn’t happened. And so the Discoveroids engage in ludicrous activities like this.